Paste or Type Multiple Values: You can enter data by pasting a series of numbers representing trait values into this area.
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2c0ba586..c4b510d4 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -156,12 +156,6 @@ def index_page():
import_collections = params['import_collections']
if import_collections == "true":
g.user_session.import_traits_to_user(params['anon_id'])
- #if USE_GN_SERVER:
- # # The menu is generated using GN_SERVER
- # return render_template("index_page.html", gn_server_url = GN_SERVER_URL, version=GN_VERSION)
- #else:
-
- # Old style static menu (OBSOLETE)
return render_template("index_page_orig.html", version=GN_VERSION)
@@ -343,14 +337,10 @@ def intro():
@app.route("/tutorials")
def tutorials():
- #doc = Docs("links", request.args)
- #return render_template("docs.html", **doc.__dict__)
return render_template("tutorials.html")
@app.route("/credits")
def credits():
- #doc = Docs("links", request.args)
- #return render_template("docs.html", **doc.__dict__)
return render_template("credits.html")
@app.route("/update_text", methods=('POST',))
@@ -368,12 +358,9 @@ def submit_trait_form():
@app.route("/create_temp_trait", methods=('POST',))
def create_temp_trait():
logger.info(request.url)
-
- #template_vars = submit_trait.SubmitTrait(request.form)
-
doc = Docs("links")
return render_template("links.html", **doc.__dict__)
- #return render_template("show_trait.html", **template_vars.__dict__)
+
@app.route('/export_trait_excel', methods=('POST',))
def export_trait_excel():
@@ -487,21 +474,17 @@ def export_perm_data():
mimetype='text/csv',
headers={"Content-Disposition":"attachment;filename=" + file_name + ".csv"})
+
@app.route("/show_temp_trait", methods=('POST',))
def show_temp_trait_page():
logger.info(request.url)
template_vars = show_trait.ShowTrait(request.form)
- #logger.info("js_data before dump:", template_vars.js_data)
template_vars.js_data = json.dumps(template_vars.js_data,
default=json_default_handler,
indent=" ")
- # Sorting the keys messes up the ordered dictionary, so don't do that
- #sort_keys=True)
-
- #logger.info("js_data after dump:", template_vars.js_data)
- #logger.info("show_trait template_vars:", pf(template_vars.__dict__))
return render_template("show_trait.html", **template_vars.__dict__)
+
@app.route("/show_trait")
def show_trait_page():
logger.info(request.url)
--
cgit v1.2.3
From 1b0566d7c9779b979d20c350f66d5628fb55eba6 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Fri, 23 Apr 2021 23:22:46 +0300
Subject: debugging for fetching probe data
---
wqflask/base/data_set.py | 51 ++++++++++++++++++++--
wqflask/wqflask/correlation/correlation_gn3_api.py | 2 +-
wqflask/wqflask/views.py | 3 ++
3 files changed, 51 insertions(+), 5 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 178234fe..468c4da0 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -115,7 +115,8 @@ Publish or ProbeSet. E.g.
except:
pass
- self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
+ self.redis_instance.set(
+ "dataset_structure", json.dumps(self.datasets))
def set_dataset_key(self, t, name):
"""If name is not in the object's dataset dictionary, set it, and update
@@ -154,10 +155,12 @@ Publish or ProbeSet. E.g.
if t in ['pheno', 'other_pheno']:
group_name = name.replace("Publish", "")
- results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone()
+ results = g.db.execute(
+ sql_query_mapping[t].format(group_name)).fetchone()
if results:
self.datasets[name] = dataset_name_mapping[t]
- self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
+ self.redis_instance.set(
+ "dataset_structure", json.dumps(self.datasets))
return True
return None
@@ -169,7 +172,8 @@ Publish or ProbeSet. E.g.
# This has side-effects, with the end result being a truth-y value
if(self.set_dataset_key(t, name)):
break
- return self.datasets.get(name, None) # Return None if name has not been set
+ # Return None if name has not been set
+ return self.datasets.get(name, None)
# Do the intensive work at startup one time only
@@ -651,6 +655,43 @@ class DataSet(object):
"Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
+ def fetch_probe_trait_data(self, sample_list=None):
+ if sample_list:
+ self.samplelist = sample_list
+ else:
+ self.samplelist = self.group.samplelist
+
+ if self.group.parlist != None and self.group.f1list != None:
+ if (self.group.parlist + self.group.f1list) in self.samplelist:
+ self.samplelist += self.group.parlist + self.group.f1list
+
+ query = """
+ SELECT Strain.Name, Strain.Id FROM Strain, Species
+ WHERE Strain.Name IN {}
+ and Strain.SpeciesId=Species.Id
+ and Species.name = '{}'
+ """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
+ logger.sql(query)
+ results = dict(g.db.execute(query).fetchall())
+ sample_ids = [results[item] for item in self.samplelist]
+
+ query = """SELECT * from ProbeSetData WHERE Id in ( SELECT ProbeSetXRef.DataId FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and ProbeSetFreeze.Name = 'HC_M2_0606_P' and ProbeSet.Id = ProbeSetXRef.ProbeSetId order by ProbeSet.Id ) and StrainId in ({})""".format(
+ ",".join(str(sample_id) for sample_id in sample_ids))
+
+ results = g.db.execute(query).fetchall()
+
+ # with conn:
+ # cursor = conn.cursor()
+ # cursor.execute(query)
+ # results = cursor.fetchall()
+ trait_data = {}
+ for trait_id, StrainId, value in results:
+ if trait_id in trait_data:
+ trait_data[trait_id].append(value)
+ else:
+ trait_data[trait_id] = [value]
+ self.trait_data = trait_data
+
def get_trait_data(self, sample_list=None):
if sample_list:
self.samplelist = sample_list
@@ -670,6 +711,7 @@ class DataSet(object):
logger.sql(query)
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
+ print("the number of sample ids are", len(sample_ids))
# MySQL limits the number of tables that can be used in a join to 61,
# so we break the sample ids into smaller chunks
@@ -720,6 +762,7 @@ class DataSet(object):
trait_sample_data.append(results)
trait_count = len(trait_sample_data[0])
+ print("the trait count is >>>", trait_count)
self.trait_data = collections.defaultdict(list)
# put all of the separate data together into a dictionary where the keys are
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index e7394647..51bf5fb5 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -78,7 +78,7 @@ def compute_correlation(start_vars, method="pearson"):
# }
sample_data = process_samples(
start_vars, this_dataset.group.samplelist)
- target_dataset.get_trait_data(list(sample_data.keys()))
+ target_dataset.fetch_probe_trait_data(list(sample_data.keys()))
this_trait = retrieve_sample_data(this_trait, this_dataset)
print("Creating dataset and trait took", time.time()-initial_time)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 072db466..2c239425 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -881,7 +881,10 @@ def network_graph_page():
def corr_compute_page():
logger.info("In corr_compute, request.form is:", pf(request.form))
logger.info(request.url)
+ import time
+ initial_time = time.time()
correlation_results = compute_correlation(request.form)
+ print(">>>>Time taken by this endpoint",time.time()-initial_time)
return render_template("demo_correlation_page.html",correlation_results=correlation_results[1:20])
@app.route("/corr_matrix", methods=('POST',))
--
cgit v1.2.3
From 067d27460965aaf1ceaa863a315a0c7dbc47ae02 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 26 Apr 2021 17:05:06 +0300
Subject: fix:remove debug statements and commented code
---
wqflask/base/mrna_assay_tissue_data.py | 25 ---------
wqflask/wqflask/correlation/correlation_gn3_api.py | 60 +++-------------------
2 files changed, 8 insertions(+), 77 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 0220d73b..5a64afb2 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -52,33 +52,9 @@ class MrnaAssayTissueData(object):
# lower_symbols[gene_symbol.lower()] = True
if gene_symbol != None:
lower_symbols[gene_symbol.lower()] = True
-
- import time
- # initial_time = time.time()
- # conn,cursor = database_connector()
- # cursor.execute(query)
- # for result in cursor.fetchall():
- # symbol = result[0]
- # self.data[symbol].gene_id = result[1]
- # self.data[symbol].data_id = result[2]
- # self.data[symbol].chr = result[3]
- # self.data[symbol].mb = result[4]
- # self.data[symbol].description = result[5]
- # self.data[symbol].probe_target_description = result[6]
-
-
- # print("my loop takes>>>>",time.time()-initial_time)
- # conn.close()
- # r
-
- # takes 5 seconds
- initial_time = time.time()
results = list(g.db.execute(query).fetchall())
for result in results:
symbol = result[0]
- # if symbol is not None
- # exists = lower_symbols.get(symbol.lower())
- # if symbol.lower() in lower_symbols:
if symbol is not None and lower_symbols.get(symbol.lower()):
symbol = symbol.lower()
@@ -89,7 +65,6 @@ class MrnaAssayTissueData(object):
self.data[symbol].mb = result.Mb
self.data[symbol].description = result.description
self.data[symbol].probe_target_description = result.Probe_Target_Description
- print("time taken in the loop is",time.time()-initial_time)
###########################################################################
#Input: cursor, symbolList (list), dataIdDict(Dict)
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index c945f699..3c21a850 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -63,9 +63,6 @@ def sample_for_trait_lists(corr_results, target_dataset, this_trait, this_datase
"trait_sample_data": sample_data,
"trait_id": start_vars["trait_id"]
}
- # trait_lists = dict([(list(corr_result)[0],True) for corr_result in corr_results])
- # target_dataset.trait_data =list(filter(lambda dict_obj: dict_obj.keys()[
- # 0] in corr_results_traits, target_dataset_data))
results = map_shared_keys_to_values(
target_dataset.samplelist, target_dataset.trait_data)
correlation_results = compute_all_sample_correlation(corr_method="pearson",
@@ -77,33 +74,15 @@ def sample_for_trait_lists(corr_results, target_dataset, this_trait, this_datase
def tissue_for_trait_lists(corr_results, this_dataset, target_dataset, this_trait):
- # # print(corr_results[0])--
- # [{"awsdsd_at": {'corr_coeffient': 0.49714692782257336, 'p_value': 1.872077762359228e-05, 'num_overlap': 67}}]
-
- print("creating trait_lists")
- # corr_results = corr_results[0::]
trait_lists = dict([(list(corr_result)[0], True)
for corr_result in corr_results])
- print("finished creating trait_list")
-
traits_symbol_dict = this_dataset.retrieve_genes("Symbol")
- print("Retrieved symbol dict")
- print("creating dict here>>>>>>>>>")
- import time
- init_time = time.time()
traits_symbol_dict = dict({trait_name: symbol for (
trait_name, symbol) in traits_symbol_dict.items() if trait_lists.get(trait_name)})
- print("time taken to create this max dict is>>>>", time.time()-init_time)
- print("finished creatinf the dict")
- print("Fetching tissue datas")
primary_tissue_data, target_tissue_data = get_tissue_correlation_input(
this_trait, traits_symbol_dict)
- print("finihsed>>>>>>>>>>>>>>>>>>")
- print("Calling experimental_compute_all_tissue_correlation")
corr_results = experimental_compute_all_tissue_correlation(
primary_tissue_dict=primary_tissue_data, target_tissues_data=target_tissue_data, corr_method="pearson")
- # print('finished calling this tissue reuslts',corr_results)
-
return corr_results
@@ -123,22 +102,14 @@ def compute_correlation(start_vars, method="pearson"):
corr_input_data = {}
if corr_type == "sample":
- import time
- initial_time = time.time()
- # corr_input_data = {
- # "target_dataset": target_dataset.trait_data,
- # "target_samplelist": target_dataset.samplelist,
- # "trait_data": {
- # "trait_sample_data": sample_data,
- # "trait_id": start_vars["trait_id"]
- # }
- # }
+
sample_data = process_samples(
start_vars, this_dataset.group.samplelist)
+ initial_time = time.time()
target_dataset.get_trait_data(list(sample_data.keys()))
this_trait = retrieve_sample_data(this_trait, this_dataset)
+ print("Creating target dataset and trait took", time.time()-initial_time)
- print("Creating dataset and trait took", time.time()-initial_time)
this_trait_data = {
"trait_sample_data": sample_data,
@@ -151,15 +122,9 @@ def compute_correlation(start_vars, method="pearson"):
this_trait=this_trait_data,
target_dataset=results)
- print("computedd>>>>>>>>>>>>>")
-
print("doing sample correlation took", time.time()-initial_time)
-
- other_results_time = time.time()
- other_results = tissue_for_trait_lists(
- correlation_results, this_dataset, target_dataset, this_trait)
- print(">>>time taken for this is", time.time()-other_results_time)
-
+ # other_results = tissue_for_trait_lists(
+ # correlation_results, this_dataset, target_dataset, this_trait)
# requests_url = f"{GN3_CORRELATION_API}/sample_x/{method}"
return correlation_results
@@ -177,17 +142,9 @@ def compute_correlation(start_vars, method="pearson"):
target_tissues_data=corr_input_data[
"target_tissues_dict"],
corr_method=method)
- print("correlation y took", time.time()-initial_time)
- # initial_time = time.time()
- # correlation_results = compute_all_tissue_correlation(primary_tissue_dict=corr_input_data["primary_tissue"],
- # target_tissues_data=corr_input_data["target_tissues_dict"],
- # corr_method=method)
- # print("time taken for compute tissue is", time.time()-initial_time)
-
- # requests_url = f"{GN3_CORRELATION_API}/tissue_corr/{method}"
-
- sample_results = sample_for_trait_lists(
- correlation_results, target_dataset, this_trait, this_dataset, start_vars)
+ print("computing tissue took >>>>", time.time()-initial_time)
+ # sample_results = sample_for_trait_lists(
+ # correlation_results, target_dataset, this_trait, this_dataset, start_vars)
return correlation_results
elif corr_type == "lit":
@@ -203,7 +160,6 @@ def compute_correlation(start_vars, method="pearson"):
species=species, gene_id=this_trait_geneid)
return lit_corr_results
- print("the time taken is", time.time()-initial_time)
# requests_url = f"{GN3_CORRELATION_API}/lit_corr/{species}/{this_trait_geneid}"
# corr_input_data = geneid_dict
# corr_results = requests.post(requests_url, json=corr_input_data)
--
cgit v1.2.3
From 65a2c8c1f455c5fad48fbac1a3e75310d49ed844 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 28 Apr 2021 19:45:37 +0000
Subject: Added something to jsonable in trait.py to account for temp traits
(this is necessary for them to show up correctly when selecting traits from
collections in pop-up windows, like when selecting cofactors for mapping)
---
wqflask/base/trait.py | 4 ++++
1 file changed, 4 insertions(+)
(limited to 'wqflask/base')
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index df96d46e..b4b4452a 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -337,6 +337,10 @@ def jsonable(trait):
dataset_name=dataset.shortname,
location=trait.location_repr
)
+ elif dataset.name == "Temp":
+ return dict(name=trait.name,
+ dataset="Temp",
+ dataset_name="Temp")
else:
return dict()
--
cgit v1.2.3
From 10da4248b29b92e18c61323640acea59dd7244dc Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 20:31:26 +0300
Subject: base: data_set: Rewrite data_set using @dataclass
@dataclasses should be used to hold only data. Since dataset only
encapsulates data, re-writing it using a dataclass makes it more
readable and easier to follow.
---
wqflask/base/data_set.py | 86 +++++++++++++++++++++++++++---------------------
1 file changed, 48 insertions(+), 38 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index cc5a428c..e3a85ff6 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -17,7 +17,10 @@
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
# This module is used by GeneNetwork project (www.genenetwork.org)
-
+from dataclasses import dataclass
+from dataclasses import field
+from dataclasses import InitVar
+from typing import Optional, Dict
from db.call import fetchall, fetchone, fetch1
from utility.logger import getLogger
from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
@@ -74,11 +77,10 @@ def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_n
return dataset_class(dataset_name, get_samplelist)
+@dataclass
class DatasetType:
-
- def __init__(self, redis_instance):
- """Create a dictionary of samples where the value is set to Geno,
-Publish or ProbeSet. E.g.
+ """Create a dictionary of samples where the value is set to Geno,
+ Publish or ProbeSet. E.g.
{'AD-cases-controls-MyersGeno': 'Geno',
'AD-cases-controls-MyersPublish': 'Publish',
@@ -89,21 +91,28 @@ Publish or ProbeSet. E.g.
'All Phenotypes': 'Publish',
'B139_K_1206_M': 'ProbeSet',
'B139_K_1206_R': 'ProbeSet' ...
-
+ }
"""
+ redis_instance: InitVar[Redis]
+ datasets: Optional[Dict] = field(init=False, default_factory=dict)
+ data: Optional[Dict] = field(init=False)
+
+ def __post_init__(self, redis_instance):
self.redis_instance = redis_instance
- self.datasets = {}
- data = self.redis_instance.get("dataset_structure")
+ data = redis_instance.get("dataset_structure")
if data:
self.datasets = json.loads(data)
- else: # ZS: I don't think this should ever run unless Redis is emptied
+ else:
+ # ZS: I don't think this should ever run unless Redis is
+ # emptied
try:
data = json.loads(requests.get(
- GN2_BASE_URL + "/api/v_pre1/gen_dropdown", timeout=5).content)
- for species in data['datasets']:
- for group in data['datasets'][species]:
- for dataset_type in data['datasets'][species][group]:
- for dataset in data['datasets'][species][group][dataset_type]:
+ GN2_BASE_URL + "/api/v_pre1/gen_dropdown",
+ timeout=5).content)
+ for _species in data['datasets']:
+ for group in data['datasets'][_species]:
+ for dataset_type in data['datasets'][_species][group]:
+ for dataset in data['datasets'][_species][group][dataset_type]:
short_dataset_name = dataset[1]
if dataset_type == "Phenotypes":
new_type = "Publish"
@@ -112,15 +121,15 @@ Publish or ProbeSet. E.g.
else:
new_type = "ProbeSet"
self.datasets[short_dataset_name] = new_type
- except:
+ except Exception: # Do nothing
pass
-
- self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
+ self.redis_instance.set("dataset_structure",
+ json.dumps(self.datasets))
+ self.data = data
def set_dataset_key(self, t, name):
- """If name is not in the object's dataset dictionary, set it, and update
- dataset_structure in Redis
-
+ """If name is not in the object's dataset dictionary, set it, and
+ update dataset_structure in Redis
args:
t: Type of dataset structure which can be: 'mrna_expr', 'pheno',
'other_pheno', 'geno'
@@ -128,19 +137,20 @@ Publish or ProbeSet. E.g.
"""
sql_query_mapping = {
- 'mrna_expr': ("""SELECT ProbeSetFreeze.Id FROM """ +
- """ProbeSetFreeze WHERE ProbeSetFreeze.Name = "{}" """),
- 'pheno': ("""SELECT InfoFiles.GN_AccesionId """ +
- """FROM InfoFiles, PublishFreeze, InbredSet """ +
- """WHERE InbredSet.Name = '{}' AND """ +
- """PublishFreeze.InbredSetId = InbredSet.Id AND """ +
- """InfoFiles.InfoPageName = PublishFreeze.Name"""),
- 'other_pheno': ("""SELECT PublishFreeze.Name """ +
- """FROM PublishFreeze, InbredSet """ +
- """WHERE InbredSet.Name = '{}' AND """ +
- """PublishFreeze.InbredSetId = InbredSet.Id"""),
- 'geno': ("""SELECT GenoFreeze.Id FROM GenoFreeze WHERE """ +
- """GenoFreeze.Name = "{}" """)
+ 'mrna_expr': ("SELECT ProbeSetFreeze.Id FROM "
+ "ProbeSetFreeze WHERE "
+ "ProbeSetFreeze.Name = \"%s\" "),
+ 'pheno': ("SELECT InfoFiles.GN_AccesionId "
+ "FROM InfoFiles, PublishFreeze, InbredSet "
+ "WHERE InbredSet.Name = '%s' AND "
+ "PublishFreeze.InbredSetId = InbredSet.Id AND "
+ "InfoFiles.InfoPageName = PublishFreeze.Name"),
+ 'other_pheno': ("SELECT PublishFreeze.Name "
+ "FROM PublishFreeze, InbredSet "
+ "WHERE InbredSet.Name = '%s' AND "
+ "PublishFreeze.InbredSetId = InbredSet.Id"),
+ 'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE "
+ "GenoFreeze.Name = \"%s\" ")
}
dataset_name_mapping = {
@@ -154,22 +164,22 @@ Publish or ProbeSet. E.g.
if t in ['pheno', 'other_pheno']:
group_name = name.replace("Publish", "")
- results = g.db.execute(sql_query_mapping[t].format(group_name)).fetchone()
+ results = g.db.execute(sql_query_mapping[t] % group_name).fetchone()
if results:
self.datasets[name] = dataset_name_mapping[t]
self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
return True
-
return None
def __call__(self, name):
-
if name not in self.datasets:
for t in ["mrna_expr", "pheno", "other_pheno", "geno"]:
- # This has side-effects, with the end result being a truth-y value
+ # This has side-effects, with the end result being a
+ # truth-y value
if(self.set_dataset_key(t, name)):
break
- return self.datasets.get(name, None) # Return None if name has not been set
+ # Return None if name has not been set
+ return self.datasets.get(name, None)
# Do the intensive work at startup one time only
--
cgit v1.2.3
From 61972109b36c752264b89ae98bcb40cc3657fa1d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 20:52:11 +0300
Subject: base: data_set: Remove unused method
* wqflask/base/data_set.py (riset): Delete class method.
---
wqflask/base/data_set.py | 5 -----
1 file changed, 5 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index e3a85ff6..5bd3e40c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -575,11 +575,6 @@ class DataSet(object):
"""Gets overridden later, at least for Temp...used by trait's get_given_name"""
return None
- # Delete this eventually
- @property
- def riset():
- Weve_Renamed_This_As_Group
-
def get_accession_id(self):
if self.type == "Publish":
results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
--
cgit v1.2.3
From c10f4670c103f8d3d65aaedb7f297b539b08c2f8 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 20:52:45 +0300
Subject: base: data_set: Apply pep-8
---
wqflask/base/data_set.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5bd3e40c..2ab3204d 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -62,7 +62,8 @@ logger = getLogger(__name__)
DS_NAME_MAP = {}
-def create_dataset(dataset_name, dataset_type=None, get_samplelist=True, group_name=None):
+def create_dataset(dataset_name, dataset_type=None,
+ get_samplelist=True, group_name=None):
if dataset_name == "Temp":
dataset_type = "Temp"
--
cgit v1.2.3
From dd0116f7cc3bed84777d625b6a22d716a3ba4fe2 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 20:53:56 +0300
Subject: base: data_set: Remove unused method
* wqflask/base/data_set.py (Dataset.get_accession_id): Delete it.
---
wqflask/base/data_set.py | 4 ----
1 file changed, 4 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 2ab3204d..1ae138d2 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -572,10 +572,6 @@ class DataSet(object):
self.group.get_samplelist()
self.species = species.TheSpecies(self)
- def get_desc(self):
- """Gets overridden later, at least for Temp...used by trait's get_given_name"""
- return None
-
def get_accession_id(self):
if self.type == "Publish":
results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
--
cgit v1.2.3
From 67703a57db19c9a1ebcc6991087479979cbbca18 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 21:33:11 +0300
Subject: base: trait: Remove unused function
* wqflask/base/trait.py (jsonable_table_row): Delete it.
---
wqflask/base/trait.py | 68 ---------------------------------------------------
1 file changed, 68 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index df96d46e..a9223a32 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -341,74 +341,6 @@ def jsonable(trait):
return dict()
-def jsonable_table_row(trait, dataset_name, index):
- """Return a list suitable for json and intended to be displayed in a table
-
- Actual turning into json doesn't happen here though"""
-
- dataset = create_dataset(dataset_name)
-
- if dataset.type == "ProbeSet":
- if trait.mean == "":
- mean = "N/A"
- else:
- mean = "%.3f" % round(float(trait.mean), 2)
- if trait.additive == "":
- additive = "N/A"
- else:
- additive = "%.3f" % round(float(trait.additive), 2)
- return [''+str(trait.name)+' ',
- trait.symbol,
- trait.description_display,
- trait.location_repr,
- mean,
- trait.LRS_score_repr,
- trait.LRS_location_repr,
- additive]
- elif dataset.type == "Publish":
- if trait.additive == "":
- additive = "N/A"
- else:
- additive = "%.2f" % round(float(trait.additive), 2)
- if trait.pubmed_id:
- return [''+str(trait.name)+' ',
- trait.description_display,
- trait.authors,
- '' + trait.pubmed_text + '',
- trait.LRS_score_repr,
- trait.LRS_location_repr,
- additive]
- else:
- return [' '+str(trait.name)+' ',
- trait.description_display,
- trait.authors,
- trait.pubmed_text,
- trait.LRS_score_repr,
- trait.LRS_location_repr,
- additive]
- elif dataset.type == "Geno":
- return [''+str(trait.name)+' ',
- trait.location_repr]
- else:
- return dict()
-
-
def retrieve_trait_info(trait, dataset, get_qtl_info=False):
assert dataset, "Dataset doesn't exist"
--
cgit v1.2.3
From 23e8e222e8016ea8335d4850070f884ab9b043fe Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 29 Apr 2021 21:45:51 +0300
Subject: Run `sed -i 's/(object)//g'`
See: https://is.gd/pL7IJF
Ran:
find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g'
---
webtests/browser_run.py | 2 +-
wqflask/base/data_set.py | 6 +++---
wqflask/base/mrna_assay_tissue_data.py | 2 +-
wqflask/base/species.py | 6 +++---
wqflask/base/trait.py | 2 +-
wqflask/maintenance/convert_geno_to_bimbam.py | 4 ++--
.../maintenance/generate_kinship_from_bimbam.py | 2 +-
wqflask/maintenance/geno_to_json.py | 4 ++--
wqflask/maintenance/print_benchmark.py | 2 +-
wqflask/utility/__init__.py | 4 ++--
wqflask/utility/benchmark.py | 2 +-
wqflask/utility/gen_geno_ob.py | 6 +++---
wqflask/utility/genofile_parser.py | 4 ++--
wqflask/utility/temp_data.py | 2 +-
.../comparison_bar_chart/comparison_bar_chart.py | 2 +-
wqflask/wqflask/correlation/corr_scatter_plot.py | 2 +-
wqflask/wqflask/correlation/show_corr_results.py | 2 +-
.../wqflask/correlation_matrix/show_corr_matrix.py | 2 +-
wqflask/wqflask/ctl/ctl_analysis.py | 2 +-
wqflask/wqflask/db_info.py | 2 +-
wqflask/wqflask/do_search.py | 2 +-
wqflask/wqflask/docs.py | 2 +-
wqflask/wqflask/external_tools/send_to_bnw.py | 2 +-
.../wqflask/external_tools/send_to_geneweaver.py | 2 +-
.../wqflask/external_tools/send_to_webgestalt.py | 2 +-
wqflask/wqflask/gsearch.py | 2 +-
wqflask/wqflask/heatmap/heatmap.py | 2 +-
.../marker_regression/display_mapping_results.py | 2 +-
wqflask/wqflask/marker_regression/run_mapping.py | 2 +-
wqflask/wqflask/network_graph/network_graph.py | 2 +-
wqflask/wqflask/news.py | 2 +-
wqflask/wqflask/search_results.py | 2 +-
wqflask/wqflask/server_side.py | 2 +-
wqflask/wqflask/show_trait/SampleList.py | 2 +-
wqflask/wqflask/show_trait/show_trait.py | 6 +++---
wqflask/wqflask/snp_browser/snp_browser.py | 2 +-
wqflask/wqflask/update_search_results.py | 2 +-
wqflask/wqflask/user_manager.py | 22 +++++++++++-----------
wqflask/wqflask/user_session.py | 2 +-
wqflask/wqflask/wgcna/wgcna_analysis.py | 2 +-
40 files changed, 62 insertions(+), 62 deletions(-)
(limited to 'wqflask/base')
diff --git a/webtests/browser_run.py b/webtests/browser_run.py
index 7ee540b7..6cf46de5 100644
--- a/webtests/browser_run.py
+++ b/webtests/browser_run.py
@@ -9,7 +9,7 @@ from selenium import webdriver
from selenium.common.exceptions import NoSuchElementException, ElementNotVisibleException
from selenium.webdriver.common.keys import Keys
-class Test(object):
+class Test:
def __init__(self):
#self.browser = webdriver.Chrome('/home/gn2/gn2/webtests/chromedriver')
self.browser = webdriver.Firefox()
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1ae138d2..3183363b 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -220,7 +220,7 @@ def create_datasets_list():
return datasets
-class Markers(object):
+class Markers:
"""Todo: Build in cacheing so it saves us reading the same file more than once"""
def __init__(self, name):
@@ -316,7 +316,7 @@ class HumanMarkers(Markers):
super(HumanMarkers, self).add_pvalues(p_values)
-class DatasetGroup(object):
+class DatasetGroup:
"""
Each group has multiple datasets; each species has multiple groups.
@@ -540,7 +540,7 @@ def datasets(group_name, this_group=None):
return dataset_menu
-class DataSet(object):
+class DataSet:
"""
DataSet class defines a dataset in webqtl, can be either Microarray,
Published phenotype, genotype, or user input dataset(temp)
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index f1929518..1f8224af 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -11,7 +11,7 @@ from utility.db_tools import escape
from utility.logger import getLogger
logger = getLogger(__name__ )
-class MrnaAssayTissueData(object):
+class MrnaAssayTissueData:
def __init__(self, gene_symbols=None):
self.gene_symbols = gene_symbols
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 2771d116..eae3325a 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -6,7 +6,7 @@ from flask import Flask, g
from utility.logger import getLogger
logger = getLogger(__name__ )
-class TheSpecies(object):
+class TheSpecies:
def __init__(self, dataset=None, species_name=None):
if species_name != None:
self.name = species_name
@@ -15,7 +15,7 @@ class TheSpecies(object):
self.dataset = dataset
self.chromosomes = Chromosomes(dataset=self.dataset)
-class IndChromosome(object):
+class IndChromosome:
def __init__(self, name, length):
self.name = name
self.length = length
@@ -25,7 +25,7 @@ class IndChromosome(object):
"""Chromosome length in megabases"""
return self.length / 1000000
-class Chromosomes(object):
+class Chromosomes:
def __init__(self, dataset=None, species=None):
self.chromosomes = collections.OrderedDict()
if species != None:
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index a9223a32..968b6d4b 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -51,7 +51,7 @@ def create_trait(**kw):
return None
-class GeneralTrait(object):
+class GeneralTrait:
"""
Trait class defines a trait in webqtl, can be either Microarray,
Published phenotype, genotype, or user input trait
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index d49742f2..0853b3ac 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -22,7 +22,7 @@ from pprint import pformat as pf
class EmptyConfigurations(Exception): pass
-class Marker(object):
+class Marker:
def __init__(self):
self.name = None
self.chr = None
@@ -30,7 +30,7 @@ class Marker(object):
self.Mb = None
self.genotypes = []
-class ConvertGenoFile(object):
+class ConvertGenoFile:
def __init__(self, input_file, output_files):
self.input_file = input_file
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 60257b28..3e4d1741 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -13,7 +13,7 @@ sys.path.append("..")
import os
import glob
-class GenerateKinshipMatrices(object):
+class GenerateKinshipMatrices:
def __init__(self, group_name, geno_file, pheno_file):
self.group_name = group_name
self.geno_file = geno_file
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 7e7fd241..f5f7e0e7 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -29,7 +29,7 @@ class EmptyConfigurations(Exception): pass
-class Marker(object):
+class Marker:
def __init__(self):
self.name = None
self.chr = None
@@ -37,7 +37,7 @@ class Marker(object):
self.Mb = None
self.genotypes = []
-class ConvertGenoFile(object):
+class ConvertGenoFile:
def __init__(self, input_file, output_file):
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
index b24ce4f1..a1046c86 100644
--- a/wqflask/maintenance/print_benchmark.py
+++ b/wqflask/maintenance/print_benchmark.py
@@ -5,7 +5,7 @@ import time
from pprint import pformat as pf
-class TheCounter(object):
+class TheCounter:
Counters = {}
def __init__(self):
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index 204ff59a..df926884 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -2,7 +2,7 @@ from pprint import pformat as pf
# Todo: Move these out of __init__
-class Bunch(object):
+class Bunch:
"""Like a dictionary but using object notation"""
def __init__(self, **kw):
self.__dict__ = kw
@@ -11,7 +11,7 @@ class Bunch(object):
return pf(self.__dict__)
-class Struct(object):
+class Struct:
'''The recursive class for building and representing objects with.
From http://stackoverflow.com/a/6573827/1175849
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index ea5a0ab6..91ea91e8 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -6,7 +6,7 @@ from utility.tools import LOG_BENCH
from utility.logger import getLogger
logger = getLogger(__name__ )
-class Bench(object):
+class Bench:
entries = collections.OrderedDict()
def __init__(self, name=None, write_output=LOG_BENCH):
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 81085ffe..0a381c9b 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,7 +1,7 @@
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class genotype(object):
+class genotype:
"""
Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
"""
@@ -119,7 +119,7 @@ class genotype(object):
self.chromosomes.append(chr_ob)
-class Chr(object):
+class Chr:
def __init__(self, name, geno_ob):
self.name = name
self.loci = []
@@ -140,7 +140,7 @@ class Chr(object):
def add_marker(self, marker_row):
self.loci.append(Locus(self.geno_ob, marker_row))
-class Locus(object):
+class Locus:
def __init__(self, geno_ob, marker_row = None):
self.chr = None
self.name = None
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 0b736176..f8e96d19 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -12,7 +12,7 @@ import simplejson as json
from pprint import pformat as pf
-class Marker(object):
+class Marker:
def __init__(self):
self.name = None
self.chr = None
@@ -21,7 +21,7 @@ class Marker(object):
self.genotypes = []
-class ConvertGenoFile(object):
+class ConvertGenoFile:
def __init__(self, input_file):
self.mb_exists = False
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 4144ae00..b2cbd458 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -2,7 +2,7 @@ from redis import Redis
import simplejson as json
-class TempData(object):
+class TempData:
def __init__(self, temp_uuid):
self.temp_uuid = temp_uuid
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 92de6073..5855ccf0 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -31,7 +31,7 @@ from MySQLdb import escape_string as escape
from flask import Flask, g
-class ComparisonBarChart(object):
+class ComparisonBarChart:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index c87776bb..d5dc26f5 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -11,7 +11,7 @@ import numpy as np
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class CorrScatterPlot(object):
+class CorrScatterPlot:
"""Page that displays a correlation scatterplot with a line fitted to it"""
def __init__(self, params):
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index fb4dc4f4..cb341e79 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -58,7 +58,7 @@ TISSUE_METHODS = [METHOD_TISSUE_PEARSON, METHOD_TISSUE_RANK]
TISSUE_MOUSE_DB = 1
-class CorrelationResults(object):
+class CorrelationResults:
def __init__(self, start_vars):
# get trait list from db (database name)
# calculate correlation with Base vector and targets
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index f77761d8..d0b4a156 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -41,7 +41,7 @@ Redis = get_redis_conn()
THIRTY_DAYS = 60 * 60 * 24 * 30
-class CorrelationMatrix(object):
+class CorrelationMatrix:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 72b4f3a3..1556e370 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -39,7 +39,7 @@ r_write_table = ro.r["write.table"] # Map the write.table function
r_data_frame = ro.r["data.frame"] # Map the write.table function
r_as_numeric = ro.r["as.numeric"] # Map the write.table function
-class CTL(object):
+class CTL:
def __init__(self):
logger.info("Initialization of CTL")
#log = r_file("/tmp/genenetwork_ctl.log", open = "wt")
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index f420b472..25e624ef 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -10,7 +10,7 @@ from utility.logger import getLogger
logger = getLogger(__name__)
-class InfoPage(object):
+class InfoPage:
def __init__(self, start_vars):
self.info = None
self.gn_accession_id = None
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 00636563..364a3eed 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -17,7 +17,7 @@ from utility.logger import getLogger
logger = getLogger(__name__)
-class DoSearch(object):
+class DoSearch:
"""Parent class containing parameters/functions used for all searches"""
# Used to translate search phrases into classes
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 23fc3cad..207767c4 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -5,7 +5,7 @@ from flask import g
from utility.logger import getLogger
logger = getLogger(__name__)
-class Docs(object):
+class Docs:
def __init__(self, entry, start_vars={}):
sql = """
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index efa17f05..c5c79e98 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -24,7 +24,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class SendToBNW(object):
+class SendToBNW:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 4c958a88..47e4c53a 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -29,7 +29,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class SendToGeneWeaver(object):
+class SendToGeneWeaver:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index 2f068792..e1e5e655 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -29,7 +29,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class SendToWebGestalt(object):
+class SendToWebGestalt:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 907f1180..9bf23d57 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -18,7 +18,7 @@ from utility.type_checking import is_float, is_int, is_str, get_float, get_int,
from utility.logger import getLogger
logger = getLogger(__name__)
-class GSearch(object):
+class GSearch:
def __init__(self, kw):
assert('type' in kw)
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index cca5a4fc..20e3559a 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -14,7 +14,7 @@ Redis = Redis()
logger = getLogger(__name__ )
-class Heatmap(object):
+class Heatmap:
def __init__(self, start_vars, temp_uuid):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 6a5fe2f6..4074f098 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -152,7 +152,7 @@ class HtmlGenWrapper:
return map_
-class DisplayMappingResults(object):
+class DisplayMappingResults:
"""Inteval Mapping Plot Page"""
cMGraphInterval = 5
GRAPH_MIN_WIDTH = 900
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 8f051c14..7dd0bcb6 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -45,7 +45,7 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
import utility.logger
logger = utility.logger.getLogger(__name__ )
-class RunMapping(object):
+class RunMapping:
def __init__(self, start_vars, temp_uuid):
helper_functions.get_species_dataset_trait(self, start_vars)
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 1d5316a2..f5ee5303 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -28,7 +28,7 @@ from utility import corr_result_helpers
from utility.tools import GN2_BRANCH_URL
-class NetworkGraph(object):
+class NetworkGraph:
def __init__(self, start_vars):
trait_db_list = [trait.strip()
diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py
index 0675ec4b..861a93f2 100644
--- a/wqflask/wqflask/news.py
+++ b/wqflask/wqflask/news.py
@@ -1,6 +1,6 @@
from flask import g
-class News(object):
+class News:
def __init__(self):
sql = """
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index f23c0582..36500a8d 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -24,7 +24,7 @@ from utility.type_checking import is_str
from utility.logger import getLogger
logger = getLogger(__name__ )
-class SearchResultPage(object):
+class SearchResultPage:
#maxReturn = 3000
def __init__(self, kw):
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 5f764767..48761fa0 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -2,7 +2,7 @@
-class ServerSideTable(object):
+class ServerSideTable:
"""
This class is used to do server-side processing
on the DataTables table such as paginating, sorting,
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 857e4456..f955f632 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -8,7 +8,7 @@ from pprint import pformat as pf
from utility import Plot
from utility import Bunch
-class SampleList(object):
+class SampleList:
def __init__(self,
dataset,
sample_names,
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index e5e94c7e..f9c5fbe6 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -35,8 +35,7 @@ logger = getLogger(__name__)
##############################################
-class ShowTrait(object):
-
+class ShowTrait:
def __init__(self, kw):
if 'trait_id' in kw and kw['dataset'] != "Temp":
self.temp_trait = False
@@ -54,7 +53,8 @@ class ShowTrait(object):
self.dataset = data_set.create_dataset(
dataset_name="Temp", dataset_type="Temp", group_name=self.temp_group)
- # Put values in Redis so they can be looked up later if added to a collection
+ # Put values in Redis so they can be looked up later if
+ # added to a collection
Redis.set(self.trait_id, kw['trait_paste'], ex=ONE_YEAR)
self.trait_vals = kw['trait_paste'].split()
self.this_trait = create_trait(dataset=self.dataset,
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index a52399a2..8658abf8 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -9,7 +9,7 @@ logger = getLogger(__name__)
from base import species
from base import webqtlConfig
-class SnpBrowser(object):
+class SnpBrowser:
def __init__(self, start_vars):
self.strain_lists = get_browser_sample_lists()
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 672f95b1..22a46ef2 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -10,7 +10,7 @@ from utility.benchmark import Bench
from utility.logger import getLogger
logger = getLogger(__name__)
-class GSearch(object):
+class GSearch:
def __init__(self, kw):
self.type = kw['type']
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 7b25b68e..fcec3b67 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -58,7 +58,7 @@ def timestamp():
return datetime.datetime.utcnow().isoformat()
-class AnonUser(object):
+class AnonUser:
"""Anonymous user handling"""
cookie_name = 'anon_user_v1'
@@ -158,7 +158,7 @@ def create_signed_cookie():
logger.debug("uuid_signed:", uuid_signed)
return the_uuid, uuid_signed
-class UserSession(object):
+class UserSession:
"""Logged in user handling"""
cookie_name = 'session_id_v1'
@@ -353,12 +353,12 @@ def set_cookie(response):
response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie)
return response
-class UsersManager(object):
+class UsersManager:
def __init__(self):
self.users = model.User.query.all()
logger.debug("Users are:", self.users)
-class UserManager(object):
+class UserManager:
def __init__(self, kw):
self.user_id = kw['user_id']
logger.debug("In UserManager locals are:", pf(locals()))
@@ -377,7 +377,7 @@ class UserManager(object):
#logger.debug(" ---> self.datasets:", self.datasets)
-class RegisterUser(object):
+class RegisterUser:
def __init__(self, kw):
self.thank_you_mode = False
self.errors = []
@@ -454,7 +454,7 @@ def set_password(password, user):
)
-class VerificationEmail(object):
+class VerificationEmail:
template_name = "email/verification.txt"
key_prefix = "verification_code"
subject = "GeneNetwork email verification"
@@ -511,7 +511,7 @@ class ForgotPasswordEmail(VerificationEmail):
send_email(toaddr, msg.as_string())
-class Password(object):
+class Password:
def __init__(self, unencrypted_password, salt, iterations, keylength, hashfunc):
hashfunc = getattr(hashlib, hashfunc)
logger.debug("hashfunc is:", hashfunc)
@@ -589,7 +589,7 @@ def password_reset_step2():
return response
-class DecodeUser(object):
+class DecodeUser:
def __init__(self, code_prefix):
verify_url_hmac(request.url)
@@ -695,7 +695,7 @@ def get_github_user_details(access_token):
result = requests.get(GITHUB_API_URL, params={"access_token":access_token})
return result.json()
-class LoginUser(object):
+class LoginUser:
remember_time = 60 * 60 * 24 * 30 # One month in seconds
def __init__(self):
@@ -1039,12 +1039,12 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
server.quit()
logger.info("Successfully sent email to "+toaddr)
-class GroupsManager(object):
+class GroupsManager:
def __init__(self, kw):
self.datasets = create_datasets_list()
-class RolesManager(object):
+class RolesManager:
def __init__(self):
self.roles = model.Role.query.all()
logger.debug("Roles are:", self.roles)
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index c5a577df..cc0ac744 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -63,7 +63,7 @@ def manage_user():
return render_template("admin/manage_user.html", user_details = user_details)
-class UserSession(object):
+class UserSession:
"""Logged in user handling"""
user_cookie_name = 'session_id_v2'
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 6bf75216..21516b30 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -42,7 +42,7 @@ r_png = ro.r["png"] # Map the png function for plotting
r_dev_off = ro.r["dev.off"] # Map the dev.off function
-class WGCNA(object):
+class WGCNA:
def __init__(self):
# To log output from stdout/stderr to a file add `r_sink(log)`
print("Initialization of WGCNA")
--
cgit v1.2.3
From c7e661b8ff9f70955418fbc4527378904beb0cf4 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 30 Apr 2021 12:16:51 +0300
Subject: autopep8: Fix E20-E27
Run:
python -m autopep8 --in-place --recrusive ./ --select\
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\
E242,E251,E252,E26,E265,E266,E27 -p 3
---
wqflask/base/data_set.py | 18 +-
wqflask/base/mrna_assay_tissue_data.py | 16 +-
wqflask/base/species.py | 2 +-
wqflask/base/webqtlConfig.py | 40 +-
wqflask/db/call.py | 6 +-
wqflask/db/gn_server.py | 2 +-
wqflask/db/webqtlDatabaseFunction.py | 10 +-
wqflask/maintenance/convert_dryad_to_bimbam.py | 6 +-
wqflask/maintenance/convert_geno_to_bimbam.py | 10 +-
wqflask/maintenance/gen_select_dataset.py | 16 +-
.../maintenance/generate_kinship_from_bimbam.py | 4 +-
wqflask/maintenance/geno_to_json.py | 26 +-
wqflask/maintenance/quantile_normalize.py | 30 +-
wqflask/maintenance/set_resource_defaults.py | 26 +-
wqflask/tests/unit/wqflask/api/test_correlation.py | 4 +-
.../marker_regression/test_gemma_mapping.py | 14 +-
.../marker_regression/test_qtlreaper_mapping.py | 24 +-
.../wqflask/marker_regression/test_rqtl_mapping.py | 28 +-
wqflask/tests/wqflask/show_trait/testSampleList.py | 6 +-
wqflask/utility/Plot.py | 180 ++--
wqflask/utility/TDCell.py | 6 +-
wqflask/utility/THCell.py | 8 +-
wqflask/utility/__init__.py | 2 +-
wqflask/utility/benchmark.py | 4 +-
wqflask/utility/chunks.py | 2 +-
wqflask/utility/corestats.py | 6 +-
wqflask/utility/elasticsearch_tools.py | 8 +-
wqflask/utility/external.py | 2 +-
wqflask/utility/gen_geno_ob.py | 18 +-
wqflask/utility/helper_functions.py | 2 +-
wqflask/utility/logger.py | 34 +-
wqflask/utility/pillow_utils.py | 2 +-
wqflask/utility/startup_config.py | 10 +-
wqflask/utility/svg.py | 624 +++++------
wqflask/utility/temp_data.py | 2 +-
wqflask/utility/tools.py | 112 +-
wqflask/utility/type_checking.py | 6 +-
wqflask/utility/webqtlUtil.py | 60 +-
wqflask/wqflask/__init__.py | 8 +-
wqflask/wqflask/api/correlation.py | 44 +-
wqflask/wqflask/api/gen_menu.py | 4 +-
wqflask/wqflask/api/mapping.py | 12 +-
wqflask/wqflask/api/router.py | 196 ++--
wqflask/wqflask/collect.py | 20 +-
.../comparison_bar_chart/comparison_bar_chart.py | 12 +-
wqflask/wqflask/correlation/corr_scatter_plot.py | 76 +-
.../wqflask/correlation/correlation_functions.py | 34 +-
wqflask/wqflask/correlation/show_corr_results.py | 38 +-
.../wqflask/correlation_matrix/show_corr_matrix.py | 52 +-
wqflask/wqflask/ctl/ctl_analysis.py | 88 +-
wqflask/wqflask/database.py | 2 +-
wqflask/wqflask/do_search.py | 80 +-
wqflask/wqflask/export_traits.py | 2 +-
wqflask/wqflask/external_tools/send_to_bnw.py | 6 +-
.../wqflask/external_tools/send_to_geneweaver.py | 6 +-
.../wqflask/external_tools/send_to_webgestalt.py | 26 +-
wqflask/wqflask/group_manager.py | 22 +-
wqflask/wqflask/gsearch.py | 2 +-
wqflask/wqflask/heatmap/heatmap.py | 6 +-
wqflask/wqflask/interval_analyst/GeneUtil.py | 24 +-
.../marker_regression/display_mapping_results.py | 1114 ++++++++++----------
wqflask/wqflask/marker_regression/gemma_mapping.py | 2 +-
wqflask/wqflask/marker_regression/plink_mapping.py | 34 +-
.../wqflask/marker_regression/qtlreaper_mapping.py | 70 +-
wqflask/wqflask/marker_regression/rqtl_mapping.py | 82 +-
wqflask/wqflask/marker_regression/run_mapping.py | 134 +--
wqflask/wqflask/model.py | 8 +-
wqflask/wqflask/parser.py | 4 +-
wqflask/wqflask/resource_manager.py | 10 +-
wqflask/wqflask/search_results.py | 16 +-
wqflask/wqflask/show_trait/SampleList.py | 14 +-
wqflask/wqflask/show_trait/show_trait.py | 18 +-
wqflask/wqflask/snp_browser/snp_browser.py | 42 +-
wqflask/wqflask/submit_bnw.py | 2 +-
wqflask/wqflask/update_search_results.py | 6 +-
wqflask/wqflask/user_login.py | 88 +-
wqflask/wqflask/user_manager.py | 143 ++-
wqflask/wqflask/user_session.py | 38 +-
wqflask/wqflask/views.py | 6 +-
wqflask/wsgi.py | 2 +-
80 files changed, 1975 insertions(+), 1994 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 3183363b..55ab45f5 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -150,7 +150,7 @@ class DatasetType:
"FROM PublishFreeze, InbredSet "
"WHERE InbredSet.Name = '%s' AND "
"PublishFreeze.InbredSetId = InbredSet.Id"),
- 'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE "
+ 'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE "
"GenoFreeze.Name = \"%s\" ")
}
@@ -215,7 +215,7 @@ def create_datasets_list():
if USE_REDIS:
r.set(key, pickle.dumps(datasets, pickle.HIGHEST_PROTOCOL))
- r.expire(key, 60*60)
+ r.expire(key, 60 * 60)
return datasets
@@ -239,7 +239,7 @@ class Markers:
for line in bimbam_fh:
marker = {}
marker['name'] = line.split(delimiter)[0].rstrip()
- marker['Mb'] = float(line.split(delimiter)[1].rstrip())/1000000
+ marker['Mb'] = float(line.split(delimiter)[1].rstrip()) / 1000000
marker['chr'] = line.split(delimiter)[2].rstrip()
markers.append(marker)
@@ -369,8 +369,8 @@ class DatasetGroup:
def get_markers(self):
def check_plink_gemma():
if flat_file_exists("mapping"):
- MAPPING_PATH = flat_files("mapping")+"/"
- if os.path.isfile(MAPPING_PATH+self.name+".bed"):
+ MAPPING_PATH = flat_files("mapping") + "/"
+ if os.path.isfile(MAPPING_PATH + self.name + ".bed"):
return True
return False
@@ -416,7 +416,7 @@ class DatasetGroup:
else:
logger.debug("Cache not hit")
- genotype_fn = locate_ignore_error(self.name+".geno", 'genotype')
+ genotype_fn = locate_ignore_error(self.name + ".geno", 'genotype')
if genotype_fn:
self.samplelist = get_group_samplelists.get_samplelist(
"geno", genotype_fn)
@@ -425,7 +425,7 @@ class DatasetGroup:
if USE_REDIS:
r.set(key, json.dumps(self.samplelist))
- r.expire(key, 60*5)
+ r.expire(key, 60 * 5)
def all_samples_ordered(self):
result = []
@@ -531,7 +531,7 @@ def datasets(group_name, this_group=None):
if USE_REDIS:
r.set(key, pickle.dumps(dataset_menu, pickle.HIGHEST_PROTOCOL))
- r.expire(key, 60*5)
+ r.expire(key, 60 * 5)
if this_group != None:
this_group._datasets = dataset_menu
@@ -622,7 +622,7 @@ class DataSet:
WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
AND ProbeFreeze.TissueId = Tissue.Id
AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
- """ % (query_args), "/dataset/"+self.name+".json",
+ """ % (query_args), "/dataset/" + self.name + ".json",
lambda r: (r["id"], r["name"], r["full_name"],
r["short_name"], r["data_scale"], r["tissue"])
)
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 1f8224af..f3264b3d 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -9,7 +9,7 @@ from utility.db_tools import escape
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
class MrnaAssayTissueData:
@@ -20,7 +20,7 @@ class MrnaAssayTissueData:
self.data = collections.defaultdict(Bunch)
- query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
+ query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
from (
select Symbol, max(Mean) as maxmean
from TissueProbeSetXRef
@@ -31,14 +31,14 @@ class MrnaAssayTissueData:
# Due to the limit size of TissueProbeSetFreezeId table in DB,
# performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
if len(gene_symbols) == 0:
- query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
+ query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
'''
else:
in_clause = db_tools.create_in_clause(gene_symbols)
- #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
+ # ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
query += ''' Symbol in {} group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
@@ -64,11 +64,11 @@ class MrnaAssayTissueData:
self.data[symbol].probe_target_description = result.Probe_Target_Description
###########################################################################
- #Input: cursor, symbolList (list), dataIdDict(Dict)
- #output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
+ # Input: cursor, symbolList (list), dataIdDict(Dict)
+ # output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
# key is symbol, value is one list of expression values of one probeSet;
- #function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
- #Attention! All keys are lower case!
+ # function: get one dictionary whose key is gene symbol and value is tissue expression data (list type).
+ # Attention! All keys are lower case!
###########################################################################
def get_symbol_values_pairs(self):
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index eae3325a..cf764d72 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -4,7 +4,7 @@ from flask import Flask, g
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
class TheSpecies:
def __init__(self, dataset=None, species_name=None):
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index bb8704a5..872b52eb 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -1,4 +1,4 @@
-#########################################'
+# '
# Environment Variables - public
#
# Note: much of this needs to handled by the settings/environment
@@ -10,35 +10,35 @@
from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, flat_files, TEMPDIR
-#Debug Level
-#1 for debug, mod python will reload import each time
+# Debug Level
+# 1 for debug, mod python will reload import each time
DEBUG = 1
-#USER privilege
-USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
+# USER privilege
+USERDICT = {'guest': 1, 'user': 2, 'admin': 3, 'root':4}
-#Set privileges
+# Set privileges
SUPER_PRIVILEGES = {'data': 'edit', 'metadata': 'edit', 'admin': 'edit-admins'}
DEFAULT_PRIVILEGES = {'data': 'view', 'metadata': 'view', 'admin': 'not-admin'}
-#minimum number of informative strains
+# minimum number of informative strains
KMININFORMATIVE = 5
-#Daily download limit from one IP
+# Daily download limit from one IP
DAILYMAXIMUM = 1000
-#maximum LRS value
+# maximum LRS value
MAXLRS = 460.0
-#MINIMUM Database public value
+# MINIMUM Database public value
PUBLICTHRESH = 0
-#EXTERNAL LINK ADDRESSES
+# EXTERNAL LINK ADDRESSES
PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-GENOMEBROWSER_URL="https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s"
+GENOMEBROWSER_URL = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s"
NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=%s"
GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
@@ -56,7 +56,7 @@ GEMMA_URL = "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s"
ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=%s"
EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s"
WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s"
-ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
+ENSEMBLETRANSCRIPT_URL = "http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s'
PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s"
OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s"
@@ -71,13 +71,13 @@ RRID_RAT_URL = "https://rgd.mcw.edu/rgdweb/report/strain/main.html?id=%s"
# want to reach this base dir
assert_writable_dir(TEMPDIR)
-TMPDIR = mk_dir(TEMPDIR+'/gn2/')
+TMPDIR = mk_dir(TEMPDIR + '/gn2/')
assert_writable_dir(TMPDIR)
-CACHEDIR = mk_dir(TMPDIR+'/cache/')
+CACHEDIR = mk_dir(TMPDIR + '/cache/')
# We can no longer write into the git tree:
-GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'generated/')
-GENERATED_TEXT_DIR = mk_dir(TMPDIR+'generated_text/')
+GENERATED_IMAGE_DIR = mk_dir(TMPDIR + 'generated/')
+GENERATED_TEXT_DIR = mk_dir(TMPDIR + 'generated_text/')
# Make sure we have permissions to access these
assert_writable_dir(CACHEDIR)
@@ -85,12 +85,12 @@ assert_writable_dir(GENERATED_IMAGE_DIR)
assert_writable_dir(GENERATED_TEXT_DIR)
# Flat file directories
-GENODIR = flat_files('genotype')+'/'
+GENODIR = flat_files('genotype') + '/'
assert_dir(GENODIR)
# assert_dir(GENODIR+'bimbam') # for gemma
# JSON genotypes are OBSOLETE
-JSON_GENODIR = flat_files('genotype/json')+'/'
+JSON_GENODIR = flat_files('genotype/json') + '/'
if not valid_path(JSON_GENODIR):
# fall back on old location (move the dir, FIXME)
JSON_GENODIR = flat_files('json')
@@ -98,4 +98,4 @@ if not valid_path(JSON_GENODIR):
# Are we using the following...?
PORTADDR = "http://50.16.251.170"
INFOPAGEHREF = '/dbdoc/%s.html'
-CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
+CGIDIR = '/webqtl/' # XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 0971d2a2..555878ad 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -12,7 +12,7 @@ from utility.tools import USE_GN_SERVER, LOG_SQL, GN_SERVER_URL
from utility.benchmark import Bench
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
# from inspect import stack
@@ -64,9 +64,9 @@ def gn_server(path):
with Bench("GN_SERVER", LOG_SQL):
res = ()
try:
- res = urllib.request.urlopen(GN_SERVER_URL+path)
+ res = urllib.request.urlopen(GN_SERVER_URL + path)
except:
- res = urllib2.urlopen(GN_SERVER_URL+path)
+ res = urllib2.urlopen(GN_SERVER_URL + path)
rest = res.read()
res2 = json.loads(rest)
logger.debug(res2)
diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py
index da224112..6c7383d0 100644
--- a/wqflask/db/gn_server.py
+++ b/wqflask/db/gn_server.py
@@ -3,7 +3,7 @@
from db.call import gn_server
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
def menu_main():
return gn_server("/int/menu/main.json")
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 2805febd..18ade405 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -24,24 +24,24 @@ from db.call import fetch1
from utility.tools import USE_GN_SERVER
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
###########################################################################
-#output: cursor instance
-#function: connect to database and return cursor instance
+# output: cursor instance
+# function: connect to database and return cursor instance
###########################################################################
def retrieve_species(group):
"""Get the species of a group (e.g. returns string "mouse" on "BXD"
"""
- result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/"+group+".json", lambda r: (r["species"],))[0]
+ result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/" + group + ".json", lambda r: (r["species"],))[0]
logger.debug("retrieve_species result:", result)
return result
def retrieve_species_id(group):
- result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0]
+ result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0]
logger.debug("retrieve_species_id result:", result)
return result
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index 12ce35e9..8eab66e8 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -41,7 +41,7 @@ def read_dryad_file(filename):
return geno_rows
- #for i, marker in enumerate(marker_list):
+ # for i, marker in enumerate(marker_list):
# this_row = []
# this_row.append(marker)
# this_row.append("X")
@@ -53,7 +53,7 @@ def read_dryad_file(filename):
# print("row: " + str(i))
# geno_rows.append(this_row)
#
- #return geno_rows
+ # return geno_rows
def write_bimbam_files(geno_rows):
with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh:
@@ -64,6 +64,6 @@ def convert_dryad_to_bimbam(filename):
geno_file_rows = read_dryad_file(filename)
write_bimbam_files(geno_file_rows)
-if __name__=="__main__":
+if __name__ == "__main__":
input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
convert_dryad_to_bimbam(input_filename)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 0853b3ac..dc01cbb3 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -103,9 +103,9 @@ class ConvertGenoFile:
with open(self.output_files[2], "w") as snp_fh:
for marker in self.markers:
if self.mb_exists:
- snp_fh.write(marker['name'] +", " + str(int(float(marker['Mb'])*1000000)) + ", " + marker['chr'] + "\n")
+ snp_fh.write(marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n")
else:
- snp_fh.write(marker['name'] +", " + str(int(float(marker['cM'])*1000000)) + ", " + marker['chr'] + "\n")
+ snp_fh.write(marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n")
def get_sample_list(self, row_contents):
self.sample_list = []
@@ -178,12 +178,12 @@ class ConvertGenoFile:
print(" Row is:", convertob.latest_row_value)
break
-if __name__=="__main__":
+if __name__ == "__main__":
Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam"""
#Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
#Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
#convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
- #convertob.convert()
+ # convertob.convert()
ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
- #ConvertGenoFiles(Geno_Directory)
+ # ConvertGenoFiles(Geno_Directory)
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 544e2fd1..f480d63f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -61,10 +61,10 @@ def parse_db_uri():
parsed_uri = urllib.parse.urlparse(SQL_URI)
db_conn_info = dict(
- db = parsed_uri.path[1:],
- host = parsed_uri.hostname,
- user = parsed_uri.username,
- passwd = parsed_uri.password)
+ db=parsed_uri.path[1:],
+ host=parsed_uri.hostname,
+ user=parsed_uri.username,
+ passwd=parsed_uri.password)
print(db_conn_info)
return db_conn_info
@@ -120,7 +120,7 @@ def get_types(groups):
if not phenotypes_exist(group_name) and not genotypes_exist(group_name):
types[species].pop(group_name, None)
groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
- else: #ZS: This whole else statement might be unnecessary, need to check
+ else: # ZS: This whole else statement might be unnecessary, need to check
types_list = build_types(species, group_name)
if len(types_list) > 0:
types[species][group_name] = types_list
@@ -133,7 +133,7 @@ def get_types(groups):
def phenotypes_exist(group_name):
#print("group_name:", group_name)
Cursor.execute("""select Name from PublishFreeze
- where PublishFreeze.Name = '%s'""" % (group_name+"Publish"))
+ where PublishFreeze.Name = '%s'""" % (group_name + "Publish"))
results = Cursor.fetchone()
#print("RESULTS:", results)
@@ -146,7 +146,7 @@ def phenotypes_exist(group_name):
def genotypes_exist(group_name):
#print("group_name:", group_name)
Cursor.execute("""select Name from GenoFreeze
- where GenoFreeze.Name = '%s'""" % (group_name+"Geno"))
+ where GenoFreeze.Name = '%s'""" % (group_name + "Geno"))
results = Cursor.fetchone()
#print("RESULTS:", results)
@@ -246,7 +246,7 @@ def build_datasets(species, group, type_name):
dataset_text = "%s Genotypes" % group
datasets.append((dataset_id, dataset_value, dataset_text))
- else: # for mRNA expression/ProbeSet
+ else: # for mRNA expression/ProbeSet
Cursor.execute("""select ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName from
ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue, Species where
Species.Name = '%s' and Species.Id = InbredSet.SpeciesId and
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 3e4d1741..664e9e48 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -52,9 +52,9 @@ class GenerateKinshipMatrices:
break
-if __name__=="__main__":
+if __name__ == "__main__":
Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/"""
Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
- #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
+ # ./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index f5f7e0e7..fa0dcebd 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -66,16 +66,16 @@ class ConvertGenoFile:
self.configurations = {}
#self.skipped_cols = 3
- #if self.input_file.endswith(".geno.gz"):
+ # if self.input_file.endswith(".geno.gz"):
# print("self.input_file: ", self.input_file)
# self.input_fh = gzip.open(self.input_file)
- #else:
+ # else:
self.input_fh = open(self.input_file)
with open(self.output_file, "w") as self.output_fh:
- #if self.file_type == "geno":
+ # if self.file_type == "geno":
self.process_csv()
- #elif self.file_type == "snps":
+ # elif self.file_type == "snps":
# self.process_snps_file()
@@ -105,7 +105,7 @@ class ConvertGenoFile:
this_marker.genotypes.append("NA")
#print("this_marker is:", pf(this_marker.__dict__))
- #if this_marker.chr == "14":
+ # if this_marker.chr == "14":
self.markers.append(this_marker.__dict__)
with open(self.output_file, 'w') as fh:
@@ -115,16 +115,16 @@ class ConvertGenoFile:
#self.latest_col_pos = item_count + self.skipped_cols
#self.latest_col_value = item
- #if item_count != 0:
+ # if item_count != 0:
# self.output_fh.write(" ")
- #self.output_fh.write(self.configurations[item.upper()])
+ # self.output_fh.write(self.configurations[item.upper()])
- #self.output_fh.write("\n")
+ # self.output_fh.write("\n")
def process_rows(self):
for self.latest_row_pos, row in enumerate(self.input_fh):
- #if self.input_file.endswith(".geno.gz"):
+ # if self.input_file.endswith(".geno.gz"):
# print("row: ", row)
self.latest_row_value = row
# Take care of headers
@@ -176,21 +176,21 @@ class ConvertGenoFile:
print(" Row is:", convertob.latest_row_value)
break
- #def process_snps_file(cls, snps_file, new_directory):
+ # def process_snps_file(cls, snps_file, new_directory):
# output_file = os.path.join(new_directory, "mouse_families.json")
# print("%s -> %s" % (snps_file, output_file))
# convertob = ConvertGenoFile(input_file, output_file)
-if __name__=="__main__":
+if __name__ == "__main__":
Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json"""
#Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
#Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
#convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
- #convertob.convert()
+ # convertob.convert()
ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
- #ConvertGenoFiles(Geno_Directory)
+ # ConvertGenoFiles(Geno_Directory)
#process_csv(Input_File, Output_File)
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 701b2b50..6751a8e5 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -20,10 +20,10 @@ def parse_db_uri():
parsed_uri = urllib.parse.urlparse(SQL_URI)
db_conn_info = dict(
- db = parsed_uri.path[1:],
- host = parsed_uri.hostname,
- user = parsed_uri.username,
- passwd = parsed_uri.password)
+ db=parsed_uri.path[1:],
+ host=parsed_uri.hostname,
+ user=parsed_uri.username,
+ passwd=parsed_uri.password)
print(db_conn_info)
return db_conn_info
@@ -35,16 +35,16 @@ def create_dataframe(input_file):
input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols)))
return pd.DataFrame(input_array)
-#This function taken from https://github.com/ShawnLYU/Quantile_Normalize
+# This function taken from https://github.com/ShawnLYU/Quantile_Normalize
def quantileNormalize(df_input):
df = df_input.copy()
- #compute rank
+ # compute rank
dic = {}
for col in df:
- dic.update({col : sorted(df[col])})
+ dic.update({col: sorted(df[col])})
sorted_df = pd.DataFrame(dic)
- rank = sorted_df.mean(axis = 1).tolist()
- #sort
+ rank = sorted_df.mean(axis=1).tolist()
+ # sort
for col in df:
t = np.searchsorted(np.sort(df[col]), df[col])
df[col] = [rank[i] for i in t]
@@ -65,8 +65,8 @@ def set_data(dataset_name):
for i, sample in enumerate(sample_names):
this_sample = {
"name": sample,
- "value": line1.split('\t')[i+1],
- "qnorm": line2.split('\t')[i+1]
+ "value": line1.split('\t')[i + 1],
+ "qnorm": line2.split('\t')[i + 1]
}
sample_list.append(this_sample)
query = """SELECT Species.SpeciesName, InbredSet.InbredSetName, ProbeSetFreeze.FullName
@@ -99,9 +99,9 @@ if __name__ == '__main__':
Conn = MySQLdb.Connect(**parse_db_uri())
Cursor = Conn.cursor()
- #es = Elasticsearch([{
+ # es = Elasticsearch([{
# "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
- #}], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+ # }], timeout=60) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
es = get_elasticsearch_connection(for_user=False)
@@ -116,8 +116,8 @@ if __name__ == '__main__':
success, _ = bulk(es, set_data(sys.argv[1]))
response = es.search(
- index = "traits", doc_type = "trait", body = {
- "query": { "match": { "name": "ENSMUSG00000028982" } }
+ index="traits", doc_type="trait", body = {
+ "query": {"match": {"name": "ENSMUSG00000028982"}}
}
)
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 4177c124..286094dd 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -43,10 +43,10 @@ def parse_db_uri():
parsed_uri = urllib.parse.urlparse(SQL_URI)
db_conn_info = dict(
- db = parsed_uri.path[1:],
- host = parsed_uri.hostname,
- user = parsed_uri.username,
- passwd = parsed_uri.password)
+ db=parsed_uri.path[1:],
+ host=parsed_uri.hostname,
+ user=parsed_uri.username,
+ passwd=parsed_uri.password)
print(db_conn_info)
return db_conn_info
@@ -63,14 +63,14 @@ def insert_probeset_resources(default_owner_id):
resource_ob = {}
resource_ob['name'] = resource[1]
resource_ob['owner_id'] = default_owner_id
- resource_ob['data'] = { "dataset" : str(resource[0])}
+ resource_ob['data'] = {"dataset": str(resource[0])}
resource_ob['type'] = "dataset-probeset"
if resource[2] < 1 and resource[3] > 0:
- resource_ob['default_mask'] = { "data": "view",
+ resource_ob['default_mask'] = {"data": "view",
"metadata": "view",
"admin": "not-admin"}
else:
- resource_ob['default_mask'] = { "data": "no-access",
+ resource_ob['default_mask'] = {"data": "no-access",
"metadata": "no-access",
"admin": "not-admin"}
resource_ob['group_masks'] = {}
@@ -97,10 +97,10 @@ def insert_publish_resources(default_owner_id):
else:
resource_ob['name'] = str(resource[0])
resource_ob['owner_id'] = default_owner_id
- resource_ob['data'] = { "dataset" : str(resource[1]) ,
- "trait" : str(resource[0])}
+ resource_ob['data'] = {"dataset": str(resource[1]),
+ "trait": str(resource[0])}
resource_ob['type'] = "dataset-publish"
- resource_ob['default_mask'] = { "data": "view",
+ resource_ob['default_mask'] = {"data": "view",
"metadata": "view",
"admin": "not-admin"}
@@ -125,14 +125,14 @@ def insert_geno_resources(default_owner_id):
resource_ob['owner_id'] = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae"
else:
resource_ob['owner_id'] = default_owner_id
- resource_ob['data'] = { "dataset" : str(resource[0]) }
+ resource_ob['data'] = {"dataset": str(resource[0])}
resource_ob['type'] = "dataset-geno"
if resource[2] < 1:
- resource_ob['default_mask'] = { "data": "view",
+ resource_ob['default_mask'] = {"data": "view",
"metadata": "view",
"admin": "not-admin"}
else:
- resource_ob['default_mask'] = { "data": "no-access",
+ resource_ob['default_mask'] = {"data": "no-access",
"metadata": "no-access",
"admin": "not-admin"}
resource_ob['group_masks'] = {}
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index d0264b87..bd99838d 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -127,9 +127,9 @@ class TestCorrelations(unittest.TestCase):
expected_pearsonr = [-0.21618688834430866, 0.680771605997119, 6]
expected_spearmanr = [-0.11595420713048969, 0.826848213385815, 6]
for i, val in enumerate(expected_pearsonr):
- self.assertAlmostEqual(val, results_pearsonr[i],4)
+ self.assertAlmostEqual(val, results_pearsonr[i], 4)
for i, val in enumerate(expected_spearmanr):
- self.assertAlmostEqual(val, results_spearmanr[i],4)
+ self.assertAlmostEqual(val, results_spearmanr[i], 4)
self.assertEqual(results_num_overlap, None)
@mock.patch("wqflask.api.correlation.do_literature_correlation_for_all_traits")
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index fe2569b8..f194c6c9 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -47,11 +47,11 @@ class TestGemmaMapping(unittest.TestCase):
@mock.patch("wqflask.marker_regression.run_mapping.random.choice")
@mock.patch("wqflask.marker_regression.gemma_mapping.os")
@mock.patch("wqflask.marker_regression.gemma_mapping.gen_pheno_txt_file")
- def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files,mock_parse_loco):
+ def test_run_gemma_firstrun_set_true(self, mock_gen_pheno_txt, mock_os, mock_choice, mock_gen_covar, mock_flat_files, mock_parse_loco):
"""add tests for run_gemma where first run is set to true"""
- this_chromosomes={}
+ this_chromosomes = {}
for i in range(1, 5):
- this_chromosomes[f'CH{i}']=(AttributeSetter({"name": f"CH{i}"}))
+ this_chromosomes[f'CH{i}'] = (AttributeSetter({"name": f"CH{i}"}))
chromosomes = AttributeSetter({"chromosomes": this_chromosomes})
dataset_group = MockGroup(
@@ -68,9 +68,9 @@ class TestGemmaMapping(unittest.TestCase):
mock_parse_loco.return_value = []
results = run_gemma(this_trait=trait, this_dataset=dataset, samples=[
], vals=[], covariates="", use_loco=True)
- self.assertEqual(mock_os.system.call_count,2)
+ self.assertEqual(mock_os.system.call_count, 2)
mock_gen_pheno_txt.assert_called_once()
- mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR",True)
+ mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR", True)
mock_os.path.isfile.assert_called_once_with(
('/home/user/imgfile_output.assoc.txt'))
self.assertEqual(mock_flat_files.call_count, 4)
@@ -144,7 +144,7 @@ class TestGemmaMapping(unittest.TestCase):
"files": [["file_name", "user", "~/file1"],
["file_name", "user", "~/file2"]]
}
- return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t
+ return_file = """X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t
chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5
Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7
X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
@@ -159,7 +159,7 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
mock_open.side_effect = handles
results = parse_loco_output(
this_dataset={}, gwa_output_filename=".xw/")
- expected_results= [
+ expected_results = [
{'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727},
{'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812},
{'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432},
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index b47f877a..bbb79f98 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -1,20 +1,20 @@
import unittest
-from unittest import mock
-from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
+from unittest import mock
+from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
-#issues some methods in genofile object are not defined
-#modify samples should equal to vals
+# issues some methods in genofile object are not defined
+# modify samples should equal to vals
class TestQtlReaperMapping(unittest.TestCase):
@mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
- def test_gen_pheno_txt_file(self):
- vals=["V1","x","V4","V3","x"]
- samples=["S1","S2","S3","S4","S5"]
- trait_filename="trait_file"
+ def test_gen_pheno_txt_file(self):
+ vals = ["V1", "x", "V4", "V3","x"]
+ samples = ["S1", "S2", "S3", "S4","S5"]
+ trait_filename = "trait_file"
with mock.patch("builtins.open", mock.mock_open())as mock_open:
- gen_pheno_txt_file(samples=samples,vals=vals,trait_filename=trait_filename)
- mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt","w")
- filehandler=mock_open()
- write_calls= [mock.call('Trait\t'),mock.call('S1\tS3\tS4\n'),mock.call('T1\t'),mock.call('V1\tV4\tV3')]
+ gen_pheno_txt_file(samples=samples, vals=vals, trait_filename=trait_filename)
+ mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w")
+ filehandler = mock_open()
+ write_calls = [mock.call('Trait\t'), mock.call('S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
filehandler.write.assert_has_calls(write_calls)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index c585f1df..0e617e93 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -8,7 +8,7 @@ from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names
class TestRqtlMapping(unittest.TestCase):
def setUp(self):
- self.app_context=app.app_context()
+ self.app_context = app.app_context()
self.app_context.push()
def tearDown(self):
@@ -17,28 +17,28 @@ class TestRqtlMapping(unittest.TestCase):
@mock.patch("wqflask.marker_regression.rqtl_mapping.g")
@mock.patch("wqflask.marker_regression.rqtl_mapping.logger")
- def test_get_trait_data(self,mock_logger,mock_db):
+ def test_get_trait_data(self, mock_logger, mock_db):
"""test for getting trait data_type return True"""
- query_value="""SELECT value FROM TraitMetadata WHERE type='trait_data_type'"""
- mock_db.db.execute.return_value.fetchone.return_value=["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
- results=get_trait_data_type("traid_id")
+ query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'"""
+ mock_db.db.execute.return_value.fetchone.return_value = ["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
+ results = get_trait_data_type("traid_id")
mock_db.db.execute.assert_called_with(query_value)
- self.assertEqual(results,"fer434f")
+ self.assertEqual(results, "fer434f")
def test_sanitize_rqtl_phenotype(self):
"""test for sanitizing rqtl phenotype"""
- vals=['f',"x","r","x","x"]
- results=sanitize_rqtl_phenotype(vals)
- expected_phenotype_string='c(f,NA,r,NA,NA)'
+ vals = ['f', "x", "r", "x","x"]
+ results = sanitize_rqtl_phenotype(vals)
+ expected_phenotype_string = 'c(f,NA,r,NA,NA)'
- self.assertEqual(results,expected_phenotype_string)
+ self.assertEqual(results, expected_phenotype_string)
def test_sanitize_rqtl_names(self):
"""test for sanitzing rqtl names"""
- vals=['f',"x","r","x","x"]
- expected_sanitized_name="c('f',NA,'r',NA,NA)"
- results=sanitize_rqtl_names(vals)
- self.assertEqual(expected_sanitized_name,results)
+ vals = ['f', "x", "r", "x","x"]
+ expected_sanitized_name = "c('f',NA,'r',NA,NA)"
+ results = sanitize_rqtl_names(vals)
+ self.assertEqual(expected_sanitized_name, results)
diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/wqflask/tests/wqflask/show_trait/testSampleList.py
index 34c51e3e..441a88a7 100644
--- a/wqflask/tests/wqflask/show_trait/testSampleList.py
+++ b/wqflask/tests/wqflask/show_trait/testSampleList.py
@@ -10,7 +10,7 @@ class TestSampleList(unittest.TestCase):
characters_list = ["z", "f", "q", "s", "t", "a", "g"]
names_list = ["temp1", "publish", "Sample", "Dataset"]
- sorted_list_a=natural_sort(characters_list)
- sorted_list_b=natural_sort(names_list)
+ sorted_list_a = natural_sort(characters_list)
+ sorted_list_b = natural_sort(names_list)
self.assertEqual(sorted_list_a, ["a", "f", "g", "q", "s", "t", "z"])
- self.assertEqual(sorted_list_b,["Dataset", "Sample", "publish", "temp1"])
+ self.assertEqual(sorted_list_b, ["Dataset", "Sample", "publish", "temp1"])
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 61f408d2..68c2cb72 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -34,7 +34,7 @@ import utility.corestats as corestats
from base import webqtlConfig
from utility.pillow_utils import draw_rotated_text
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
# ---- Define common colours ---- #
BLUE = ImageColor.getrgb("blue")
@@ -74,7 +74,7 @@ def frange(start, end=None, inc=1.0):
end = start + 0.0
start = 0.0
else:
- start += 0.0 # force it to be a float
+ start += 0.0 # force it to be a float
count = int((end - start) / inc)
if start + count * inc != end:
# Need to adjust the count. AFAICT, it always comes up one short.
@@ -119,13 +119,13 @@ def find_outliers(vals):
# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)
-def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
+def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset=(60, 20, 40, 40), zoom=1):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- if plotHeight<=0 or plotWidth<=0:
+ if plotHeight <= 0 or plotWidth <= 0:
return
if len(data) < 2:
@@ -133,15 +133,15 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
max_D = max(data)
min_D = min(data)
- #add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
- if max_D == float('inf') or max_D>webqtlConfig.MAXLRS:
- max_D=webqtlConfig.MAXLRS #maximum LRS value
+ # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
+ if max_D == float('inf') or max_D > webqtlConfig.MAXLRS:
+ max_D = webqtlConfig.MAXLRS # maximum LRS value
xLow, xTop, stepX = detScale(min_D, max_D)
- #reduce data
- #ZS: Used to determine number of bins for permutation output
- step = ceil((xTop-xLow)/50.0)
+ # reduce data
+ # ZS: Used to determine number of bins for permutation output
+ step = ceil((xTop - xLow) / 50.0)
j = xLow
dataXY = []
Count = []
@@ -151,122 +151,122 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
j += step
for i, item in enumerate(data):
- if item == float('inf') or item>webqtlConfig.MAXLRS:
- item = webqtlConfig.MAXLRS #maximum LRS value
- j = int((item-xLow)/step)
+ if item == float('inf') or item > webqtlConfig.MAXLRS:
+ item = webqtlConfig.MAXLRS # maximum LRS value
+ j = int((item - xLow) / step)
Count[j] += 1
- yLow, yTop, stepY=detScale(0, max(Count))
+ yLow, yTop, stepY = detScale(0, max(Count))
- #draw data
- xScale = plotWidth/(xTop-xLow)
- yScale = plotHeight/(yTop-yLow)
- barWidth = xScale*step
+ # draw data
+ xScale = plotWidth / (xTop - xLow)
+ yScale = plotHeight / (yTop - yLow)
+ barWidth = xScale * step
for i, count in enumerate(Count):
if count:
- xc = (dataXY[i]-xLow)*xScale+xLeftOffset
- yc =-(count-yLow)*yScale+yTopOffset+plotHeight
+ xc = (dataXY[i] - xLow) * xScale + xLeftOffset
+ yc = -(count - yLow) * yScale + yTopOffset + plotHeight
im_drawer.rectangle(
- xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)),
+ xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)),
outline=barColor, fill=barColor)
- #draw drawing region
+ # draw drawing region
im_drawer.rectangle(
- xy=((xLeftOffset, yTopOffset), (xLeftOffset+plotWidth, yTopOffset+plotHeight))
+ xy=((xLeftOffset, yTopOffset), (xLeftOffset + plotWidth, yTopOffset + plotHeight))
)
- #draw scale
- scaleFont=ImageFont.truetype(font=COUR_FILE, size=11)
- x=xLow
- for i in range(int(stepX)+1):
- xc=xLeftOffset+(x-xLow)*xScale
+ # draw scale
+ scaleFont = ImageFont.truetype(font=COUR_FILE, size=11)
+ x = xLow
+ for i in range(int(stepX) + 1):
+ xc = xLeftOffset + (x - xLow) * xScale
im_drawer.line(
- xy=((xc, yTopOffset+plotHeight), (xc, yTopOffset+plotHeight+5)),
+ xy=((xc, yTopOffset + plotHeight), (xc, yTopOffset + plotHeight + 5)),
fill=axesColor)
strX = cformat(d=x, rank=0)
im_drawer.text(
text=strX,
- xy=(xc-im_drawer.textsize(strX, font=scaleFont)[0]/2,
- yTopOffset+plotHeight+14), font=scaleFont)
- x+= (xTop - xLow)/stepX
-
- y=yLow
- for i in range(int(stepY)+1):
- yc=yTopOffset+plotHeight-(y-yLow)*yScale
- im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset-5, yc)), fill=axesColor)
- strY = "%d" %y
+ xy=(xc - im_drawer.textsize(strX, font=scaleFont)[0] / 2,
+ yTopOffset + plotHeight + 14), font=scaleFont)
+ x += (xTop - xLow) / stepX
+
+ y = yLow
+ for i in range(int(stepY) + 1):
+ yc = yTopOffset + plotHeight - (y - yLow) * yScale
+ im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor)
+ strY = "%d" % y
im_drawer.text(
text=strY,
- xy=(xLeftOffset-im_drawer.textsize(strY, font=scaleFont)[0]-6, yc+5),
+ xy=(xLeftOffset - im_drawer.textsize(strY, font=scaleFont)[0] - 6, yc + 5),
font=scaleFont)
- y+= (yTop - yLow)/stepY
+ y += (yTop - yLow) / stepY
- #draw label
- labelFont=ImageFont.truetype(font=TAHOMA_FILE, size=17)
+ # draw label
+ labelFont = ImageFont.truetype(font=TAHOMA_FILE, size=17)
if XLabel:
im_drawer.text(
text=XLabel,
- xy=(xLeftOffset+(
- plotWidth-im_drawer.textsize(XLabel, font=labelFont)[0])/2.0,
- yTopOffset+plotHeight+yBottomOffset-10),
+ xy=(xLeftOffset + (
+ plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0,
+ yTopOffset + plotHeight + yBottomOffset-10),
font=labelFont, fill=labelColor)
if YLabel:
draw_rotated_text(canvas, text=YLabel,
xy=(19,
- yTopOffset+plotHeight-(
- plotHeight-im_drawer.textsize(
- YLabel, font=labelFont)[0])/2.0),
+ yTopOffset + plotHeight - (
+ plotHeight - im_drawer.textsize(
+ YLabel, font=labelFont)[0]) / 2.0),
font=labelFont, fill=labelColor, angle=90)
- labelFont=ImageFont.truetype(font=VERDANA_FILE, size=16)
+ labelFont = ImageFont.truetype(font=VERDANA_FILE, size=16)
if title:
im_drawer.text(
text=title,
- xy=(xLeftOffset+(plotWidth-im_drawer.textsize(
- title, font=labelFont)[0])/2.0,
+ xy=(xLeftOffset + (plotWidth - im_drawer.textsize(
+ title, font=labelFont)[0]) / 2.0,
20),
font=labelFont, fill=labelColor)
# This function determines the scale of the plot
def detScaleOld(min, max):
- if min>=max:
+ if min >= max:
return None
elif min == -1.0 and max == 1.0:
return [-1.2, 1.2, 12]
else:
- a=max-min
- b=floor(log10(a))
- c=pow(10.0, b)
- if a < c*5.0:
- c/=2.0
- #print a,b,c
- low=c*floor(min/c)
- high=c*ceil(max/c)
- return [low, high, round((high-low)/c)]
-
-def detScale(min=0,max=0):
-
- if min>=max:
+ a = max - min
+ b = floor(log10(a))
+ c = pow(10.0, b)
+ if a < c * 5.0:
+ c /= 2.0
+ # print a,b,c
+ low = c * floor(min / c)
+ high = c * ceil(max / c)
+ return [low, high, round((high - low) / c)]
+
+def detScale(min=0, max=0):
+
+ if min >= max:
return None
elif min == -1.0 and max == 1.0:
return [-1.2, 1.2, 12]
else:
- a=max-min
+ a = max - min
if max != 0:
- max += 0.1*a
+ max += 0.1 * a
if min != 0:
- if min > 0 and min < 0.1*a:
+ if min > 0 and min < 0.1 * a:
min = 0.0
else:
- min -= 0.1*a
- a=max-min
- b=floor(log10(a))
- c=pow(10.0, b)
- low=c*floor(min/c)
- high=c*ceil(max/c)
- n = round((high-low)/c)
+ min -= 0.1 * a
+ a = max - min
+ b = floor(log10(a))
+ c = pow(10.0, b)
+ low = c * floor(min / c)
+ high = c * ceil(max / c)
+ n = round((high - low) / c)
div = 2.0
while n < 5 or n > 15:
if n < 5:
@@ -274,23 +274,23 @@ def detScale(min=0,max=0):
else:
c *= div
if div == 2.0:
- div =5.0
+ div = 5.0
else:
- div =2.0
- low=c*floor(min/c)
- high=c*ceil(max/c)
- n = round((high-low)/c)
+ div = 2.0
+ low = c * floor(min / c)
+ high = c * ceil(max / c)
+ n = round((high - low) / c)
return [low, high, n]
def bluefunc(x):
- return 1.0 / (1.0 + exp(-10*(x-0.6)))
+ return 1.0 / (1.0 + exp(-10 * (x - 0.6)))
def redfunc(x):
- return 1.0 / (1.0 + exp(10*(x-0.5)))
+ return 1.0 / (1.0 + exp(10 * (x - 0.5)))
def greenfunc(x):
- return 1 - pow(redfunc(x+0.2), 2) - bluefunc(x-0.3)
+ return 1 - pow(redfunc(x + 0.2), 2) - bluefunc(x - 0.3)
def colorSpectrum(n=100):
multiple = 10
@@ -303,17 +303,17 @@ def colorSpectrum(n=100):
return [ImageColor.getrgb("rgb(100%,0%,0%)"),
ImageColor.getrgb("rgb(0%,100%,0%)"),
ImageColor.getrgb("rgb(0%,0%,100%)")]
- N = n*multiple
- out = [None]*N;
+ N = n * multiple
+ out = [None] * N;
for i in range(N):
- x = float(i)/N
+ x = float(i) / N
out[i] = ImageColor.getrgb("rgb({}%,{}%,{}%".format(
- *[int(i*100) for i in (
+ *[int(i * 100) for i in (
redfunc(x), greenfunc(x), bluefunc(x))]))
out2 = [out[0]]
- step = N/float(n-1)
+ step = N / float(n - 1)
j = 0
- for i in range(n-2):
+ for i in range(n - 2):
j += step
out2.append(out[int(j)])
out2.append(out[-1])
@@ -324,5 +324,5 @@ def _test():
doctest.testmod()
-if __name__=="__main__":
+if __name__ == "__main__":
_test()
diff --git a/wqflask/utility/TDCell.py b/wqflask/utility/TDCell.py
index 8de8e050..4b0f4b1d 100644
--- a/wqflask/utility/TDCell.py
+++ b/wqflask/utility/TDCell.py
@@ -33,9 +33,9 @@
class TDCell:
def __init__(self, html="", text="", val=0.0):
- self.html = html #html, for web page
- self.text = text #text value, for output to a text file
- self.val = val #sort by value
+ self.html = html # html, for web page
+ self.text = text # text value, for output to a text file
+ self.val = val # sort by value
def __str__(self):
return self.text
diff --git a/wqflask/utility/THCell.py b/wqflask/utility/THCell.py
index dde221b5..f533dcb8 100644
--- a/wqflask/utility/THCell.py
+++ b/wqflask/utility/THCell.py
@@ -33,10 +33,10 @@
class THCell:
def __init__(self, html="", text="", sort=1, idx=-1):
- self.html = html #html, for web page
- self.text = text #Column text value
- self.sort = sort #0: not sortable, 1: yes
- self.idx = idx #sort by value
+ self.html = html # html, for web page
+ self.text = text # Column text value
+ self.sort = sort # 0: not sortable, 1: yes
+ self.idx = idx # sort by value
def __str__(self):
return self.text
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index df926884..ec7e72d0 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -4,7 +4,7 @@ from pprint import pformat as pf
class Bunch:
"""Like a dictionary but using object notation"""
- def __init__(self, **kw):
+ def __init__(self, **kw):
self.__dict__ = kw
def __repr__(self):
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 91ea91e8..3d40a3b8 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -4,7 +4,7 @@ import time
from utility.tools import LOG_BENCH
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
class Bench:
entries = collections.OrderedDict()
@@ -39,7 +39,7 @@ class Bench:
total_time = sum((time_taken for time_taken in list(cls.entries.values())))
print("\nTiming report\n")
for name, time_taken in list(cls.entries.items()):
- percent = int(round((time_taken/total_time) * 100))
+ percent = int(round((time_taken / total_time) * 100))
print("[{}%] {}: {}".format(percent, name, time_taken))
print()
diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py
index 9a7db102..484b5de6 100644
--- a/wqflask/utility/chunks.py
+++ b/wqflask/utility/chunks.py
@@ -26,6 +26,6 @@ def divide_into_chunks(the_list, number_chunks):
chunks = []
for counter in range(0, length, chunksize):
- chunks.append(the_list[counter:counter+chunksize])
+ chunks.append(the_list[counter:counter + chunksize])
return chunks
diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py
index 67ca3ad3..15d1cb8d 100644
--- a/wqflask/utility/corestats.py
+++ b/wqflask/utility/corestats.py
@@ -15,7 +15,7 @@
import sys
-#ZS: Should switch to using some third party library for this; maybe scipy has an equivalent
+# ZS: Should switch to using some third party library for this; maybe scipy has an equivalent
class Stats:
def __init__(self, sequence):
@@ -63,7 +63,7 @@ class Stats:
if len(self.sequence) < 1:
value = None
elif (percentile >= 100):
- sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n'% percentile)
+ sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n' % percentile)
value = None
else:
element_idx = int(len(self.sequence) * (percentile / 100.0))
@@ -80,4 +80,4 @@ class Stats:
# stats = corestats.Stats(sequence)
# print stats.avg()
# print stats.percentile(90)
-# -------------------------------------------
\ No newline at end of file
+# -------------------------------------------
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index a5580811..ae1181e4 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -48,7 +48,7 @@ logger = getLogger(__name__)
from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
def test_elasticsearch_connection():
- es = Elasticsearch(['http://'+ELASTICSEARCH_HOST+":"+str(ELASTICSEARCH_PORT)+'/'], verify_certs=True)
+ es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True)
if not es.ping():
logger.warning("Elasticsearch is DOWN")
@@ -97,8 +97,8 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
item_details = None
try:
response = es.search(
- index = index, doc_type = doc_type, body = {
- "query": { "match": { column_name: column_value } }
+ index=index, doc_type=doc_type, body = {
+ "query": {"match": {column_name: column_value}}
})
if len(response["hits"]["hits"]) > 0:
item_details = response["hits"]["hits"][0]["_source"]
@@ -109,4 +109,4 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
def es_save_data(es, index, doc_type, data_item, data_id,):
from time import sleep
es.create(index, doc_type, body=data_item, id=data_id)
- sleep(1) # Delay 1 second to allow indexing
+ sleep(1) # Delay 1 second to allow indexing
diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py
index 50afea08..c1bf4043 100644
--- a/wqflask/utility/external.py
+++ b/wqflask/utility/external.py
@@ -6,4 +6,4 @@ import subprocess
def shell(command):
if subprocess.call(command, shell=True) != 0:
- raise Exception("ERROR: failed on "+command)
+ raise Exception("ERROR: failed on " + command)
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 0a381c9b..9cfa39f9 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,5 +1,5 @@
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
class genotype:
"""
@@ -18,7 +18,7 @@ class genotype:
self.filler = False
self.mb_exists = False
- #ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary
+ # ZS: This is because I'm not sure if some files switch the column that contains Mb/cM positions; might be unnecessary
self.cm_column = 2
self.mb_column = 3
@@ -36,14 +36,14 @@ class genotype:
return len(self.chromosomes)
def read_rdata_output(self, qtl_results):
- #ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results
- self.chromosomes = [] #ZS: Overwriting since the .geno file's contents are just placeholders
+ # ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results
+ self.chromosomes = [] # ZS: Overwriting since the .geno file's contents are just placeholders
- this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers
+ this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers
chr_ob = None
for marker in qtl_results:
locus = Locus(self)
- if (str(marker['chr']) != this_chr) and this_chr != "X": #ZS: This is really awkward but works as a temporary fix
+ if (str(marker['chr']) != this_chr) and this_chr != "X": # ZS: This is really awkward but works as a temporary fix
if this_chr != "":
self.chromosomes.append(chr_ob)
this_chr = str(marker['chr'])
@@ -68,7 +68,7 @@ class genotype:
with open(filename, 'r') as geno_file:
lines = geno_file.readlines()
- this_chr = "" #ZS: This is so it can track when the chromosome changes as it iterates through markers
+ this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers
chr_ob = None
for line in lines:
if line[0] == "#":
@@ -141,7 +141,7 @@ class Chr:
self.loci.append(Locus(self.geno_ob, marker_row))
class Locus:
- def __init__(self, geno_ob, marker_row = None):
+ def __init__(self, geno_ob, marker_row=None):
self.chr = None
self.name = None
self.cM = None
@@ -175,5 +175,5 @@ class Locus:
for allele in marker_row[start_pos:]:
if allele in list(geno_table.keys()):
self.genotype.append(geno_table[allele])
- else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown
+ else: # ZS: Some genotype appears that isn't specified in the metadata, make it unknown
self.genotype.append("U")
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 12fd6be5..ecc075ae 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -39,7 +39,7 @@ def get_trait_db_obs(self, trait_db_list):
for trait in trait_db_list:
data, _separator, hmac_string = trait.rpartition(':')
data = data.strip()
- assert hmac_string==hmac.hmac_creation(data), "Data tampering?"
+ assert hmac_string == hmac.hmac_creation(data), "Data tampering?"
trait_name, dataset_name = data.split(":")[:2]
if dataset_name == "Temp":
dataset_ob = data_set.create_dataset(
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index e904eb94..16912e58 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -49,14 +49,14 @@ class GNLogger:
"""Set the undelying log level"""
self.logger.setLevel(value)
- def debug(self,*args):
+ def debug(self, *args):
"""Call logging.debug for multiple args. Use (lazy) debugf and
level=num to filter on LOG_LEVEL_DEBUG.
"""
self.collect(self.logger.debug, *args)
- def debug20(self,*args):
+ def debug20(self, *args):
"""Call logging.debug for multiple args. Use level=num to filter on
LOG_LEVEL_DEBUG (NYI).
@@ -65,29 +65,29 @@ LOG_LEVEL_DEBUG (NYI).
if self.logger.getEffectiveLevel() < 20:
self.collect(self.logger.debug, *args)
- def info(self,*args):
+ def info(self, *args):
"""Call logging.info for multiple args"""
self.collect(self.logger.info, *args)
- def warning(self,*args):
+ def warning(self, *args):
"""Call logging.warning for multiple args"""
self.collect(self.logger.warning, *args)
# self.logger.warning(self.collect(*args))
- def error(self,*args):
+ def error(self, *args):
"""Call logging.error for multiple args"""
now = datetime.datetime.utcnow()
time_str = now.strftime('%H:%M:%S UTC %Y%m%d')
- l = [time_str]+list(args)
+ l = [time_str] + list(args)
self.collect(self.logger.error, *l)
- def infof(self,*args):
+ def infof(self, *args):
"""Call logging.info for multiple args lazily"""
# only evaluate function when logging
if self.logger.getEffectiveLevel() < 30:
self.collectf(self.logger.debug, *args)
- def debugf(self,level=0,*args):
+ def debugf(self, level=0, *args):
"""Call logging.debug for multiple args lazily and handle
LOG_LEVEL_DEBUG correctly
@@ -97,7 +97,7 @@ LOG_LEVEL_DEBUG (NYI).
if self.logger.getEffectiveLevel() < 20:
self.collectf(self.logger.debug, *args)
- def sql(self, sqlcommand, fun = None):
+ def sql(self, sqlcommand, fun=None):
"""Log SQL command, optionally invoking a timed fun"""
if LOG_SQL:
caller = stack()[1][3]
@@ -110,11 +110,11 @@ LOG_LEVEL_DEBUG (NYI).
self.info(result)
return result
- def collect(self,fun,*args):
+ def collect(self, fun, *args):
"""Collect arguments and use fun to output"""
- out = "."+stack()[2][3]
+ out = "." + stack()[2][3]
for a in args:
- if len(out)>1:
+ if len(out) > 1:
out += ": "
if isinstance(a, str):
out = out + a
@@ -122,11 +122,11 @@ LOG_LEVEL_DEBUG (NYI).
out = out + pf(a, width=160)
fun(out)
- def collectf(self,fun,*args):
+ def collectf(self, fun, *args):
"""Collect arguments and use fun to output one by one"""
- out = "."+stack()[2][3]
+ out = "." + stack()[2][3]
for a in args:
- if len(out)>1:
+ if len(out) > 1:
out += ": "
if isfunction(a):
out += a()
@@ -139,7 +139,7 @@ LOG_LEVEL_DEBUG (NYI).
# Get the module logger. You can override log levels at the
# module level
-def getLogger(name, level = None):
+def getLogger(name, level=None):
gnlogger = GNLogger(name)
logger = gnlogger.logger
@@ -148,5 +148,5 @@ def getLogger(name, level = None):
else:
logger.setLevel(LOG_LEVEL)
- logger.info("Log level of "+name+" set to "+logging.getLevelName(logger.getEffectiveLevel()))
+ logger.info("Log level of " + name + " set to " + logging.getLevelName(logger.getEffectiveLevel()))
return gnlogger
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index c486abba..6e95beb0 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -3,7 +3,7 @@ from PIL import Image, ImageColor, ImageDraw, ImageFont
from utility.tools import TEMPDIR
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
BLACK = ImageColor.getrgb("black")
WHITE = ImageColor.getrgb("white")
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index f1aaebb6..f22f4b14 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -3,12 +3,12 @@ from wqflask import app
from utility.tools import WEBSERVER_MODE, show_settings, get_setting_int, get_setting, get_setting_bool
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
-BLUE = '\033[94m'
+BLUE = '\033[94m'
GREEN = '\033[92m'
-BOLD = '\033[1m'
-ENDC = '\033[0m'
+BOLD = '\033[1m'
+ENDC = '\033[0m'
def app_config():
app.config['SESSION_TYPE'] = 'filesystem'
@@ -27,7 +27,7 @@ def app_config():
port = get_setting_int("SERVER_PORT")
if get_setting_bool("USE_GN_SERVER"):
- print(("GN2 API server URL is ["+BLUE+get_setting("GN_SERVER_URL")+ENDC+"]"))
+ print(("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]"))
import requests
page = requests.get(get_setting("GN_SERVER_URL"))
if page.status_code != 200:
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index b92cc2d1..4c478c36 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -172,7 +172,7 @@ def _viewboxlist(a):
"""formats a tuple"""
s = ''
for e in a:
- s += str(e)+' '
+ s += str(e) + ' '
return s
@@ -189,7 +189,7 @@ class pathdata:
def __init__(self, x=None, y=None):
self.path = []
if x is not None and y is not None:
- self.path.append('M '+str(x)+' '+str(y))
+ self.path.append('M ' + str(x) + ' ' + str(y))
def closepath(self):
"""ends the path"""
@@ -197,79 +197,79 @@ class pathdata:
def move(self, x, y):
"""move to absolute"""
- self.path.append('M '+str(x)+' '+str(y))
+ self.path.append('M ' + str(x) + ' ' + str(y))
def relmove(self, x, y):
"""move to relative"""
- self.path.append('m '+str(x)+' '+str(y))
+ self.path.append('m ' + str(x) + ' ' + str(y))
def line(self, x, y):
"""line to absolute"""
- self.path.append('L '+str(x)+' '+str(y))
+ self.path.append('L ' + str(x) + ' ' + str(y))
def relline(self, x, y):
"""line to relative"""
- self.path.append('l '+str(x)+' '+str(y))
+ self.path.append('l ' + str(x) + ' ' + str(y))
def hline(self, x):
"""horizontal line to absolute"""
- self.path.append('H'+str(x))
+ self.path.append('H' + str(x))
def relhline(self, x):
"""horizontal line to relative"""
- self.path.append('h'+str(x))
+ self.path.append('h' + str(x))
def vline(self, y):
"""verical line to absolute"""
- self.path.append('V'+str(y))
+ self.path.append('V' + str(y))
def relvline(self, y):
"""vertical line to relative"""
- self.path.append('v'+str(y))
+ self.path.append('v' + str(y))
def bezier(self, x1, y1, x2, y2, x, y):
"""bezier with xy1 and xy2 to xy absolut"""
- self.path.append('C'+str(x1)+','+str(y1)+' '+str(x2) +
- ','+str(y2)+' '+str(x)+','+str(y))
+ self.path.append('C' + str(x1) + ','+str(y1)+' '+str(x2) +
+ ',' + str(y2) + ' '+str(x)+','+str(y))
def relbezier(self, x1, y1, x2, y2, x, y):
"""bezier with xy1 and xy2 to xy relative"""
- self.path.append('c'+str(x1)+','+str(y1)+' '+str(x2) +
- ','+str(y2)+' '+str(x)+','+str(y))
+ self.path.append('c' + str(x1) + ','+str(y1)+' '+str(x2) +
+ ',' + str(y2) + ' '+str(x)+','+str(y))
def smbezier(self, x2, y2, x, y):
"""smooth bezier with xy2 to xy absolut"""
- self.path.append('S'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
+ self.path.append('S' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
def relsmbezier(self, x2, y2, x, y):
"""smooth bezier with xy2 to xy relative"""
- self.path.append('s'+str(x2)+','+str(y2)+' '+str(x)+','+str(y))
+ self.path.append('s' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
def qbezier(self, x1, y1, x, y):
"""quadratic bezier with xy1 to xy absolut"""
- self.path.append('Q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
+ self.path.append('Q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y))
def relqbezier(self, x1, y1, x, y):
"""quadratic bezier with xy1 to xy relative"""
- self.path.append('q'+str(x1)+','+str(y1)+' '+str(x)+','+str(y))
+ self.path.append('q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y))
def smqbezier(self, x, y):
"""smooth quadratic bezier to xy absolut"""
- self.path.append('T'+str(x)+','+str(y))
+ self.path.append('T' + str(x) + ',' + str(y))
def relsmqbezier(self, x, y):
"""smooth quadratic bezier to xy relative"""
- self.path.append('t'+str(x)+','+str(y))
+ self.path.append('t' + str(x) + ',' + str(y))
def ellarc(self, rx, ry, xrot, laf, sf, x, y):
"""elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut"""
- self.path.append('A'+str(rx)+','+str(ry)+' '+str(xrot) +
- ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
+ self.path.append('A' + str(rx) + ','+str(ry)+' '+str(xrot) +
+ ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
def relellarc(self, rx, ry, xrot, laf, sf, x, y):
"""elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative"""
- self.path.append('a'+str(rx)+','+str(ry)+' '+str(xrot) +
- ' '+str(laf)+' '+str(sf)+' '+str(x)+' '+str(y))
+ self.path.append('a' + str(rx) + ','+str(ry)+' '+str(xrot) +
+ ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
def __repr__(self):
return ' '.join(self.path)
@@ -312,10 +312,10 @@ class SVGelement:
self.elements.append(SVGelement)
def toXml(self, level, f):
- f.write('\t'*level)
- f.write('<'+self.type)
+ f.write('\t' * level)
+ f.write('<' + self.type)
for attkey in list(self.attributes.keys()):
- f.write(' '+_escape(str(attkey))+'=' +
+ f.write(' ' + _escape(str(attkey)) + '=' +
_quoteattr(str(self.attributes[attkey])))
if self.namespace:
f.write(' xmlns="' + _escape(str(self.namespace)) +
@@ -325,23 +325,23 @@ class SVGelement:
if self.elements:
f.write('\n')
for element in self.elements:
- element.toXml(level+1, f)
+ element.toXml(level + 1, f)
if self.cdata:
- f.write('\n'+'\t'*(level+1)+'\n')
+ f.write('\n' + '\t' * (level + 2) + line)
+ f.write('\n' + '\t' * (level + 1) + ']]>\n')
if self.text:
if isinstance(self.text, type('')): # If the text is only text
f.write(_escape(str(self.text)))
else: # If the text is a spannedtext class
f.write(str(self.text))
if self.elements:
- f.write('\t'*level+'\n')
+ f.write('\t' * level + '\n')
elif self.text:
- f.write('\n')
+ f.write('\n')
elif self.cdata:
- f.write('\t'*level+'\n')
+ f.write('\t' * level + '\n')
else:
f.write('/>\n')
@@ -447,38 +447,38 @@ class rect(SVGelement):
if width == None or height == None:
raise ValueError('both height and width are required')
- SVGelement.__init__(self, 'rect', {'width':width,'height':height}, **args)
- if x!=None:
- self.attributes['x']=x
- if y!=None:
- self.attributes['y']=y
- if fill!=None:
- self.attributes['fill']=fill
- if stroke!=None:
- self.attributes['stroke']=stroke
- if stroke_width!=None:
- self.attributes['stroke-width']=stroke_width
+ SVGelement.__init__(self, 'rect', {'width': width, 'height': height}, **args)
+ if x != None:
+ self.attributes['x'] = x
+ if y != None:
+ self.attributes['y'] = y
+ if fill != None:
+ self.attributes['fill'] = fill
+ if stroke != None:
+ self.attributes['stroke'] = stroke
+ if stroke_width != None:
+ self.attributes['stroke-width'] = stroke_width
class ellipse(SVGelement):
"""e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
an ellipse is defined as a center and a x and y radius.
"""
- def __init__(self,cx=None,cy=None,rx=None,ry=None,fill=None,stroke=None,stroke_width=None,**args):
- if rx==None or ry== None:
+ def __init__(self, cx=None, cy=None, rx=None, ry=None,fill=None,stroke=None,stroke_width=None,**args):
+ if rx == None or ry == None:
raise ValueError('both rx and ry are required')
- SVGelement.__init__(self, 'ellipse', {'rx':rx,'ry':ry}, **args)
- if cx!=None:
- self.attributes['cx']=cx
- if cy!=None:
- self.attributes['cy']=cy
- if fill!=None:
- self.attributes['fill']=fill
- if stroke!=None:
- self.attributes['stroke']=stroke
- if stroke_width!=None:
- self.attributes['stroke-width']=stroke_width
+ SVGelement.__init__(self, 'ellipse', {'rx': rx, 'ry': ry}, **args)
+ if cx != None:
+ self.attributes['cx'] = cx
+ if cy != None:
+ self.attributes['cy'] = cy
+ if fill != None:
+ self.attributes['fill'] = fill
+ if stroke != None:
+ self.attributes['stroke'] = stroke
+ if stroke_width != None:
+ self.attributes['stroke-width'] = stroke_width
class circle(SVGelement):
@@ -486,20 +486,20 @@ class circle(SVGelement):
The circle creates an element using a x, y and radius values eg
"""
- def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args):
- if r==None:
+ def __init__(self, cx=None, cy=None, r=None, fill=None,stroke=None,stroke_width=None,**args):
+ if r == None:
raise ValueError('r is required')
- SVGelement.__init__(self, 'circle', {'r':r}, **args)
- if cx!=None:
- self.attributes['cx']=cx
- if cy!=None:
- self.attributes['cy']=cy
- if fill!=None:
- self.attributes['fill']=fill
- if stroke!=None:
- self.attributes['stroke']=stroke
- if stroke_width!=None:
- self.attributes['stroke-width']=stroke_width
+ SVGelement.__init__(self, 'circle', {'r': r}, **args)
+ if cx != None:
+ self.attributes['cx'] = cx
+ if cy != None:
+ self.attributes['cy'] = cy
+ if fill != None:
+ self.attributes['fill'] = fill
+ if stroke != None:
+ self.attributes['stroke'] = stroke
+ if stroke_width != None:
+ self.attributes['stroke-width'] = stroke_width
class point(circle):
"""p=point(x,y,color)
@@ -507,7 +507,7 @@ class point(circle):
A point is defined as a circle with a size 1 radius. It may be more efficient to use a
very small rectangle if you use many points because a circle is difficult to render.
"""
- def __init__(self,x,y,fill='black',**args):
+ def __init__(self, x, y, fill='black', **args):
circle.__init__(self, x, y, 1, fill, **args)
class line(SVGelement):
@@ -515,64 +515,64 @@ class line(SVGelement):
A line is defined by a begin x,y pair and an end x,y pair
"""
- def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args):
+ def __init__(self, x1=None, y1=None, x2=None, y2=None,stroke=None,stroke_width=None,**args):
SVGelement.__init__(self, 'line', **args)
- if x1!=None:
- self.attributes['x1']=x1
- if y1!=None:
- self.attributes['y1']=y1
- if x2!=None:
- self.attributes['x2']=x2
- if y2!=None:
- self.attributes['y2']=y2
- if stroke_width!=None:
- self.attributes['stroke-width']=stroke_width
- if stroke!=None:
- self.attributes['stroke']=stroke
+ if x1 != None:
+ self.attributes['x1'] = x1
+ if y1 != None:
+ self.attributes['y1'] = y1
+ if x2 != None:
+ self.attributes['x2'] = x2
+ if y2 != None:
+ self.attributes['y2'] = y2
+ if stroke_width != None:
+ self.attributes['stroke-width'] = stroke_width
+ if stroke != None:
+ self.attributes['stroke'] = stroke
class polyline(SVGelement):
"""pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
a polyline is defined by a list of xy pairs
"""
- def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
- SVGelement.__init__(self, 'polyline', {'points':_xypointlist(points)}, **args)
- if fill!=None:
- self.attributes['fill']=fill
- if stroke_width!=None:
- self.attributes['stroke-width']=stroke_width
- if stroke!=None:
- self.attributes['stroke']=stroke
+ def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
+ SVGelement.__init__(self, 'polyline', {'points': _xypointlist(points)}, **args)
+ if fill != None:
+ self.attributes['fill'] = fill
+ if stroke_width != None:
+ self.attributes['stroke-width'] = stroke_width
+ if stroke != None:
+ self.attributes['stroke'] = stroke
class polygon(SVGelement):
"""pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
a polygon is defined by a list of xy pairs
"""
- def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
- SVGelement.__init__(self, 'polygon', {'points':_xypointlist(points)}, **args)
- if fill!=None:
- self.attributes['fill']=fill
- if stroke_width!=None:
- self.attributes['stroke-width']=stroke_width
- if stroke!=None:
- self.attributes['stroke']=stroke
+ def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
+ SVGelement.__init__(self, 'polygon', {'points': _xypointlist(points)}, **args)
+ if fill != None:
+ self.attributes['fill'] = fill
+ if stroke_width != None:
+ self.attributes['stroke-width'] = stroke_width
+ if stroke != None:
+ self.attributes['stroke'] = stroke
class path(SVGelement):
"""p=path(path,fill,stroke,stroke_width,**args)
a path is defined by a path object and optional width, stroke and fillcolor
"""
- def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args):
- SVGelement.__init__(self, 'path', {'d':str(pathdata)}, **args)
- if stroke!=None:
- self.attributes['stroke']=stroke
- if fill!=None:
- self.attributes['fill']=fill
- if stroke_width!=None:
- self.attributes['stroke-width']=stroke_width
- if id!=None:
- self.attributes['id']=id
+ def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None,id=None,**args):
+ SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args)
+ if stroke != None:
+ self.attributes['stroke'] = stroke
+ if fill != None:
+ self.attributes['fill'] = fill
+ if stroke_width != None:
+ self.attributes['stroke-width'] = stroke_width
+ if id != None:
+ self.attributes['id'] = id
class text(SVGelement):
@@ -580,20 +580,20 @@ class text(SVGelement):
a text element can bge used for displaying text on the screen
"""
- def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args):
+ def __init__(self, x=None, y=None, text=None, font_size=None,font_family=None,text_anchor=None,**args):
SVGelement.__init__(self, 'text', **args)
- if x!=None:
- self.attributes['x']=x
- if y!=None:
- self.attributes['y']=y
- if font_size!=None:
- self.attributes['font-size']=font_size
- if font_family!=None:
- self.attributes['font-family']=font_family
- if text!=None:
- self.text=text
- if text_anchor!=None:
- self.attributes['text-anchor']=text_anchor
+ if x != None:
+ self.attributes['x'] = x
+ if y != None:
+ self.attributes['y'] = y
+ if font_size != None:
+ self.attributes['font-size'] = font_size
+ if font_family != None:
+ self.attributes['font-family'] = font_family
+ if text != None:
+ self.text = text
+ if text_anchor != None:
+ self.attributes['text-anchor'] = text_anchor
class textpath(SVGelement):
@@ -601,10 +601,10 @@ class textpath(SVGelement):
a textpath places a text on a path which is referenced by a link.
"""
- def __init__(self,link,text=None,**args):
- SVGelement.__init__(self, 'textPath', {'xlink:href':link}, **args)
- if text!=None:
- self.text=text
+ def __init__(self, link, text=None, **args):
+ SVGelement.__init__(self, 'textPath', {'xlink:href': link}, **args)
+ if text != None:
+ self.text = text
class pattern(SVGelement):
"""p=pattern(x,y,width,height,patternUnits,**args)
@@ -613,18 +613,18 @@ class pattern(SVGelement):
graphic object which can be replicated ("tiled") at fixed intervals
in x and y to cover the areas to be painted.
"""
- def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args):
+ def __init__(self, x=None, y=None, width=None, height=None,patternUnits=None,**args):
SVGelement.__init__(self, 'pattern', **args)
- if x!=None:
- self.attributes['x']=x
- if y!=None:
- self.attributes['y']=y
- if width!=None:
- self.attributes['width']=width
- if height!=None:
- self.attributes['height']=height
- if patternUnits!=None:
- self.attributes['patternUnits']=patternUnits
+ if x != None:
+ self.attributes['x'] = x
+ if y != None:
+ self.attributes['y'] = y
+ if width != None:
+ self.attributes['width'] = width
+ if height != None:
+ self.attributes['height'] = height
+ if patternUnits != None:
+ self.attributes['patternUnits'] = patternUnits
class title(SVGelement):
"""t=title(text,**args)
@@ -632,10 +632,10 @@ class title(SVGelement):
a title is a text element. The text is displayed in the title bar
add at least one to the root svg element
"""
- def __init__(self,text=None,**args):
+ def __init__(self, text=None, **args):
SVGelement.__init__(self, 'title', **args)
- if text!=None:
- self.text=text
+ if text != None:
+ self.text = text
class description(SVGelement):
"""d=description(text,**args)
@@ -643,10 +643,10 @@ class description(SVGelement):
a description can be added to any element and is used for a tooltip
Add this element before adding other elements.
"""
- def __init__(self,text=None,**args):
+ def __init__(self, text=None, **args):
SVGelement.__init__(self, 'desc', **args)
- if text!=None:
- self.text=text
+ if text != None:
+ self.text = text
class lineargradient(SVGelement):
"""lg=lineargradient(x1,y1,x2,y2,id,**args)
@@ -654,18 +654,18 @@ class lineargradient(SVGelement):
defines a lineargradient using two xy pairs.
stop elements van be added to define the gradient colors.
"""
- def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args):
+ def __init__(self, x1=None, y1=None, x2=None, y2=None,id=None,**args):
SVGelement.__init__(self, 'linearGradient', **args)
- if x1!=None:
- self.attributes['x1']=x1
- if y1!=None:
- self.attributes['y1']=y1
- if x2!=None:
- self.attributes['x2']=x2
- if y2!=None:
- self.attributes['y2']=y2
- if id!=None:
- self.attributes['id']=id
+ if x1 != None:
+ self.attributes['x1'] = x1
+ if y1 != None:
+ self.attributes['y1'] = y1
+ if x2 != None:
+ self.attributes['x2'] = x2
+ if y2 != None:
+ self.attributes['y2'] = y2
+ if id != None:
+ self.attributes['id'] = id
class radialgradient(SVGelement):
"""rg=radialgradient(cx,cy,r,fx,fy,id,**args)
@@ -673,38 +673,38 @@ class radialgradient(SVGelement):
defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint.
stop elements van be added to define the gradient colors.
"""
- def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args):
+ def __init__(self, cx=None, cy=None, r=None, fx=None,fy=None,id=None,**args):
SVGelement.__init__(self, 'radialGradient', **args)
- if cx!=None:
- self.attributes['cx']=cx
- if cy!=None:
- self.attributes['cy']=cy
- if r!=None:
- self.attributes['r']=r
- if fx!=None:
- self.attributes['fx']=fx
- if fy!=None:
- self.attributes['fy']=fy
- if id!=None:
- self.attributes['id']=id
+ if cx != None:
+ self.attributes['cx'] = cx
+ if cy != None:
+ self.attributes['cy'] = cy
+ if r != None:
+ self.attributes['r'] = r
+ if fx != None:
+ self.attributes['fx'] = fx
+ if fy != None:
+ self.attributes['fy'] = fy
+ if id != None:
+ self.attributes['id'] = id
class stop(SVGelement):
"""st=stop(offset,stop_color,**args)
Puts a stop color at the specified radius
"""
- def __init__(self,offset,stop_color=None,**args):
- SVGelement.__init__(self, 'stop', {'offset':offset}, **args)
- if stop_color!=None:
- self.attributes['stop-color']=stop_color
+ def __init__(self, offset, stop_color=None, **args):
+ SVGelement.__init__(self, 'stop', {'offset': offset}, **args)
+ if stop_color != None:
+ self.attributes['stop-color'] = stop_color
class style(SVGelement):
"""st=style(type,cdata=None,**args)
Add a CDATA element to this element for defing in line stylesheets etc..
"""
- def __init__(self,type,cdata=None,**args):
- SVGelement.__init__(self, 'style', {'type':type}, cdata=cdata, **args)
+ def __init__(self, type, cdata=None, **args):
+ SVGelement.__init__(self, 'style', {'type': type}, cdata=cdata, **args)
class image(SVGelement):
@@ -712,22 +712,22 @@ class image(SVGelement):
adds an image to the drawing. Supported formats are .png, .jpg and .svg.
"""
- def __init__(self,url,x=None,y=None,width=None,height=None,**args):
- if width==None or height==None:
+ def __init__(self, url, x=None, y=None, width=None,height=None,**args):
+ if width == None or height == None:
raise ValueError('both height and width are required')
- SVGelement.__init__(self, 'image', {'xlink:href':url,'width':width,'height':height}, **args)
- if x!=None:
- self.attributes['x']=x
- if y!=None:
- self.attributes['y']=y
+ SVGelement.__init__(self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args)
+ if x != None:
+ self.attributes['x'] = x
+ if y != None:
+ self.attributes['y'] = y
class cursor(SVGelement):
"""c=cursor(url,**args)
defines a custom cursor for a element or a drawing
"""
- def __init__(self,url,**args):
- SVGelement.__init__(self, 'cursor', {'xlink:href':url}, **args)
+ def __init__(self, url, **args):
+ SVGelement.__init__(self, 'cursor', {'xlink:href': url}, **args)
class marker(SVGelement):
@@ -736,20 +736,20 @@ class marker(SVGelement):
defines a marker which can be used as an endpoint for a line or other pathtypes
add an element to it which should be used as a marker.
"""
- def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args):
+ def __init__(self, id=None, viewBox=None, refx=None, refy=None,markerWidth=None,markerHeight=None,**args):
SVGelement.__init__(self, 'marker', **args)
- if id!=None:
- self.attributes['id']=id
- if viewBox!=None:
- self.attributes['viewBox']=_viewboxlist(viewBox)
- if refx!=None:
- self.attributes['refX']=refx
- if refy!=None:
- self.attributes['refY']=refy
- if markerWidth!=None:
- self.attributes['markerWidth']=markerWidth
- if markerHeight!=None:
- self.attributes['markerHeight']=markerHeight
+ if id != None:
+ self.attributes['id'] = id
+ if viewBox != None:
+ self.attributes['viewBox'] = _viewboxlist(viewBox)
+ if refx != None:
+ self.attributes['refX'] = refx
+ if refy != None:
+ self.attributes['refY'] = refy
+ if markerWidth != None:
+ self.attributes['markerWidth'] = markerWidth
+ if markerHeight != None:
+ self.attributes['markerHeight'] = markerHeight
class group(SVGelement):
"""g=group(id,**args)
@@ -757,10 +757,10 @@ class group(SVGelement):
a group is defined by an id and is used to contain elements
g.addElement(SVGelement)
"""
- def __init__(self,id=None,**args):
+ def __init__(self, id=None, **args):
SVGelement.__init__(self, 'g', **args)
- if id!=None:
- self.attributes['id']=id
+ if id != None:
+ self.attributes['id'] = id
class symbol(SVGelement):
"""sy=symbol(id,viewbox,**args)
@@ -771,19 +771,19 @@ class symbol(SVGelement):
sy.addElement(SVGelement)
"""
- def __init__(self,id=None,viewBox=None,**args):
+ def __init__(self, id=None, viewBox=None, **args):
SVGelement.__init__(self, 'symbol', **args)
- if id!=None:
- self.attributes['id']=id
- if viewBox!=None:
- self.attributes['viewBox']=_viewboxlist(viewBox)
+ if id != None:
+ self.attributes['id'] = id
+ if viewBox != None:
+ self.attributes['viewBox'] = _viewboxlist(viewBox)
class defs(SVGelement):
"""d=defs(**args)
container for defining elements
"""
- def __init__(self,**args):
+ def __init__(self, **args):
SVGelement.__init__(self, 'defs', **args)
class switch(SVGelement):
@@ -793,7 +793,7 @@ class switch(SVGelement):
requiredFeatures, requiredExtensions and systemLanguage.
Refer to the SVG specification for details.
"""
- def __init__(self,**args):
+ def __init__(self, **args):
SVGelement.__init__(self, 'switch', **args)
@@ -802,17 +802,17 @@ class use(SVGelement):
references a symbol by linking to its id and its position, height and width
"""
- def __init__(self,link,x=None,y=None,width=None,height=None,**args):
- SVGelement.__init__(self, 'use', {'xlink:href':link}, **args)
- if x!=None:
- self.attributes['x']=x
- if y!=None:
- self.attributes['y']=y
+ def __init__(self, link, x=None, y=None, width=None,height=None,**args):
+ SVGelement.__init__(self, 'use', {'xlink:href': link}, **args)
+ if x != None:
+ self.attributes['x'] = x
+ if y != None:
+ self.attributes['y'] = y
- if width!=None:
- self.attributes['width']=width
- if height!=None:
- self.attributes['height']=height
+ if width != None:
+ self.attributes['width'] = width
+ if height != None:
+ self.attributes['height'] = height
class link(SVGelement):
@@ -821,17 +821,17 @@ class link(SVGelement):
a link is defined by a hyperlink. add elements which have to be linked
a.addElement(SVGelement)
"""
- def __init__(self,link='',**args):
- SVGelement.__init__(self, 'a', {'xlink:href':link}, **args)
+ def __init__(self, link='', **args):
+ SVGelement.__init__(self, 'a', {'xlink:href': link}, **args)
class view(SVGelement):
"""v=view(id,**args)
a view can be used to create a view with different attributes"""
- def __init__(self,id=None,**args):
+ def __init__(self, id=None, **args):
SVGelement.__init__(self, 'view', **args)
- if id!=None:
- self.attributes['id']=id
+ if id != None:
+ self.attributes['id'] = id
class script(SVGelement):
"""sc=script(type,type,cdata,**args)
@@ -839,77 +839,77 @@ class script(SVGelement):
adds a script element which contains CDATA to the SVG drawing
"""
- def __init__(self,type,cdata=None,**args):
- SVGelement.__init__(self, 'script', {'type':type}, cdata=cdata, **args)
+ def __init__(self, type, cdata=None, **args):
+ SVGelement.__init__(self, 'script', {'type': type}, cdata=cdata, **args)
class animate(SVGelement):
"""an=animate(attribute,from,to,during,**args)
animates an attribute.
"""
- def __init__(self,attribute,fr=None,to=None,dur=None,**args):
- SVGelement.__init__(self, 'animate', {'attributeName':attribute}, **args)
- if fr!=None:
- self.attributes['from']=fr
- if to!=None:
- self.attributes['to']=to
- if dur!=None:
- self.attributes['dur']=dur
+ def __init__(self, attribute, fr=None, to=None, dur=None,**args):
+ SVGelement.__init__(self, 'animate', {'attributeName': attribute}, **args)
+ if fr != None:
+ self.attributes['from'] = fr
+ if to != None:
+ self.attributes['to'] = to
+ if dur != None:
+ self.attributes['dur'] = dur
class animateMotion(SVGelement):
"""an=animateMotion(pathdata,dur,**args)
animates a SVGelement over the given path in dur seconds
"""
- def __init__(self,pathdata,dur,**args):
+ def __init__(self, pathdata, dur, **args):
SVGelement.__init__(self, 'animateMotion', **args)
- if pathdata!=None:
- self.attributes['path']=str(pathdata)
- if dur!=None:
- self.attributes['dur']=dur
+ if pathdata != None:
+ self.attributes['path'] = str(pathdata)
+ if dur != None:
+ self.attributes['dur'] = dur
class animateTransform(SVGelement):
"""antr=animateTransform(type,from,to,dur,**args)
transform an element from and to a value.
"""
- def __init__(self,type=None,fr=None,to=None,dur=None,**args):
- SVGelement.__init__(self, 'animateTransform', {'attributeName':'transform'}, **args)
+ def __init__(self, type=None, fr=None, to=None, dur=None,**args):
+ SVGelement.__init__(self, 'animateTransform', {'attributeName': 'transform'}, **args)
# As far as I know the attributeName is always transform
- if type!=None:
- self.attributes['type']=type
- if fr!=None:
- self.attributes['from']=fr
- if to!=None:
- self.attributes['to']=to
- if dur!=None:
- self.attributes['dur']=dur
+ if type != None:
+ self.attributes['type'] = type
+ if fr != None:
+ self.attributes['from'] = fr
+ if to != None:
+ self.attributes['to'] = to
+ if dur != None:
+ self.attributes['dur'] = dur
class animateColor(SVGelement):
"""ac=animateColor(attribute,type,from,to,dur,**args)
Animates the color of a element
"""
- def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args):
- SVGelement.__init__(self, 'animateColor', {'attributeName':attribute}, **args)
- if type!=None:
- self.attributes['type']=type
- if fr!=None:
- self.attributes['from']=fr
- if to!=None:
- self.attributes['to']=to
- if dur!=None:
- self.attributes['dur']=dur
+ def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args):
+ SVGelement.__init__(self, 'animateColor', {'attributeName': attribute}, **args)
+ if type != None:
+ self.attributes['type'] = type
+ if fr != None:
+ self.attributes['from'] = fr
+ if to != None:
+ self.attributes['to'] = to
+ if dur != None:
+ self.attributes['dur'] = dur
class set(SVGelement):
"""st=set(attribute,to,during,**args)
sets an attribute to a value for a
"""
- def __init__(self,attribute,to=None,dur=None,**args):
- SVGelement.__init__(self, 'set', {'attributeName':attribute}, **args)
- if to!=None:
- self.attributes['to']=to
- if dur!=None:
- self.attributes['dur']=dur
+ def __init__(self, attribute, to=None, dur=None, **args):
+ SVGelement.__init__(self, 'set', {'attributeName': attribute}, **args)
+ if to != None:
+ self.attributes['to'] = to
+ if dur != None:
+ self.attributes['dur'] = dur
@@ -928,15 +928,15 @@ class svg(SVGelement):
d.setSVG(s)
d.toXml()
"""
- def __init__(self,viewBox=None, width=None, height=None,**args):
+ def __init__(self, viewBox=None, width=None, height=None, **args):
SVGelement.__init__(self, 'svg', **args)
- if viewBox!=None:
- self.attributes['viewBox']=_viewboxlist(viewBox)
- if width!=None:
- self.attributes['width']=width
- if height!=None:
- self.attributes['height']=height
- self.namespace="http://www.w3.org/2000/svg"
+ if viewBox != None:
+ self.attributes['viewBox'] = _viewboxlist(viewBox)
+ if width != None:
+ self.attributes['width'] = width
+ if height != None:
+ self.attributes['height'] = height
+ self.namespace = "http://www.w3.org/2000/svg"
class drawing:
"""d=drawing()
@@ -950,15 +950,15 @@ class drawing:
"""
def __init__(self, entity={}):
- self.svg=None
+ self.svg = None
self.entity = entity
def setSVG(self, svg):
- self.svg=svg
+ self.svg = svg
# Voeg een element toe aan de grafiek toe.
- if use_dom_implementation==0:
- def toXml(self, filename='',compress=False):
+ if use_dom_implementation == 0:
+ def toXml(self, filename='', compress=False):
import io
- xml=io.StringIO()
+ xml = io.StringIO()
xml.write("\n")
xml.write("to the screen
drawing.toXml(filename)---->to the file
writes a svg drawing to the screen or to a file
@@ -1002,35 +1002,35 @@ class drawing:
global root
# root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
# that is a bit messy.
- root=implementation.createDocument(None, None, doctype)
+ root = implementation.createDocument(None, None, doctype)
# Create the xml document.
global appender
def appender(element, elementroot):
"""This recursive function appends elements to an element and sets the attributes
and type. It stops when alle elements have been appended"""
if element.namespace:
- e=root.createElementNS(element.namespace, element.type)
+ e = root.createElementNS(element.namespace, element.type)
else:
- e=root.createElement(element.type)
+ e = root.createElement(element.type)
if element.text:
- textnode=root.createTextNode(element.text)
+ textnode = root.createTextNode(element.text)
e.appendChild(textnode)
- for attribute in list(element.attributes.keys()): #in element.attributes is supported from python 2.2
+ for attribute in list(element.attributes.keys()): # in element.attributes is supported from python 2.2
e.setAttribute(attribute, str(element.attributes[attribute]))
if element.elements:
for el in element.elements:
- e=appender(el, e)
+ e = appender(el, e)
elementroot.appendChild(e)
return elementroot
- root=appender(self.svg, root)
+ root = appender(self.svg, root)
if not filename:
import io
- xml=io.StringIO()
+ xml = io.StringIO()
PrettyPrint(root, xml)
if compress:
import gzip
- f=io.StringIO()
- zf=gzip.GzipFile(fileobj=f, mode='wb')
+ f = io.StringIO()
+ zf = gzip.GzipFile(fileobj=f, mode='wb')
zf.write(xml.getvalue())
zf.close()
f.seek(0)
@@ -1039,16 +1039,16 @@ class drawing:
return xml.getvalue()
else:
try:
- if filename[-4:]=='svgz':
+ if filename[-4:] == 'svgz':
import gzip
import io
- xml=io.StringIO()
+ xml = io.StringIO()
PrettyPrint(root, xml)
- f=gzip.GzipFile(filename=filename, mode='wb', compresslevel=9)
+ f = gzip.GzipFile(filename=filename, mode='wb', compresslevel=9)
f.write(xml.getvalue())
f.close()
else:
- f=open(filename, 'w')
+ f = open(filename, 'w')
PrettyPrint(root, f)
f.close()
except:
@@ -1058,44 +1058,44 @@ class drawing:
import xml.parsers.xmlproc.xmlval
except:
raise exceptions.ImportError('PyXml is required for validating SVG')
- svg=self.toXml()
- xv=xml.parsers.xmlproc.xmlval.XMLValidator()
+ svg = self.toXml()
+ xv = xml.parsers.xmlproc.xmlval.XMLValidator()
try:
xv.feed(svg)
except:
raise Exception("SVG is not well formed, see messages above")
else:
print("SVG well formed")
-if __name__=='__main__':
+if __name__ == '__main__':
- d=drawing()
- s=svg((0, 0, 100, 100))
- r=rect(-100, -100, 300, 300, 'cyan')
+ d = drawing()
+ s = svg((0, 0, 100, 100))
+ r = rect(-100, -100, 300, 300, 'cyan')
s.addElement(r)
- t=title('SVGdraw Demo')
+ t = title('SVGdraw Demo')
s.addElement(t)
- g=group('animations')
- e=ellipse(0, 0, 5, 2)
+ g = group('animations')
+ e = ellipse(0, 0, 5, 2)
g.addElement(e)
- c=circle(0, 0, 1, 'red')
+ c = circle(0, 0, 1, 'red')
g.addElement(c)
- pd=pathdata(0, -10)
+ pd = pathdata(0, -10)
for i in range(6):
pd.relsmbezier(10, 5, 0, 10)
pd.relsmbezier(-10, 5, 0, 10)
- an=animateMotion(pd, 10)
- an.attributes['rotate']='auto-reverse'
- an.attributes['repeatCount']="indefinite"
+ an = animateMotion(pd, 10)
+ an.attributes['rotate'] = 'auto-reverse'
+ an.attributes['repeatCount'] = "indefinite"
g.addElement(an)
s.addElement(g)
for i in range(20, 120, 20):
- u=use('#animations', i, 0)
+ u = use('#animations', i, 0)
s.addElement(u)
for i in range(0, 120, 20):
for j in range(5, 105, 10):
- c=circle(i, j, 1, 'red', 'black', .5)
+ c = circle(i, j, 1, 'red', 'black', .5)
s.addElement(c)
d.setSVG(s)
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index b2cbd458..2088ba9a 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -11,7 +11,7 @@ class TempData:
def store(self, field, value):
self.redis.hset(self.key, field, value)
- self.redis.expire(self.key, 60*15) # Expire in 15 minutes
+ self.redis.expire(self.key, 60 * 15) # Expire in 15 minutes
def get_all(self):
return self.redis.hgetall(self.key)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 65df59c3..9b751344 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -9,7 +9,7 @@ from wqflask import app
# Use the standard logger here to avoid a circular dependency
import logging
-logger = logging.getLogger(__name__ )
+logger = logging.getLogger(__name__)
OVERRIDES = {}
@@ -18,7 +18,7 @@ def app_set(command_id, value):
app.config.setdefault(command_id, value)
return value
-def get_setting(command_id,guess=None):
+def get_setting(command_id, guess=None):
"""Resolve a setting from the environment or the global settings in
app.config, with valid_path is a function checking whether the
path points to an expected directory and returns the full path to
@@ -54,7 +54,7 @@ def get_setting(command_id,guess=None):
# print("Looking for "+command_id+"\n")
command = value(os.environ.get(command_id))
if command is None or command == "":
- command = OVERRIDES.get(command_id) # currently not in use
+ command = OVERRIDES.get(command_id) # currently not in use
if command is None:
# ---- Check whether setting exists in app
command = value(app.config.get(command_id))
@@ -62,7 +62,7 @@ def get_setting(command_id,guess=None):
command = value(guess)
if command is None or command == "":
# print command
- raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).')
+ raise Exception(command_id + ' setting unknown or faulty (update default_settings.py?).')
# print("Set "+command_id+"="+str(command))
return command
@@ -99,13 +99,13 @@ def js_path(module=None):
"""
Find the JS module in the two paths
"""
- try_gn = get_setting("JS_GN_PATH")+"/"+module
+ try_gn = get_setting("JS_GN_PATH") + "/" + module
if valid_path(try_gn):
return try_gn
- try_guix = get_setting("JS_GUIX_PATH")+"/"+module
+ try_guix = get_setting("JS_GUIX_PATH") + "/" + module
if valid_path(try_guix):
return try_guix
- raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
+ raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)"
def reaper_command(guess=None):
return get_setting("REAPER_COMMAND", guess)
@@ -121,28 +121,28 @@ def plink_command(guess=None):
def flat_file_exists(subdir):
base = get_setting("GENENETWORK_FILES")
- return valid_path(base+"/"+subdir)
+ return valid_path(base + "/" + subdir)
def flat_files(subdir=None):
base = get_setting("GENENETWORK_FILES")
if subdir:
- return assert_dir(base+"/"+subdir)
+ return assert_dir(base + "/" + subdir)
return assert_dir(base)
def assert_bin(fn):
if not valid_bin(fn):
- raise Exception("ERROR: can not find binary "+fn)
+ raise Exception("ERROR: can not find binary " + fn)
return fn
def assert_dir(dir):
if not valid_path(dir):
- raise Exception("ERROR: can not find directory "+dir)
+ raise Exception("ERROR: can not find directory " + dir)
return dir
def assert_writable_dir(dir):
try:
fn = dir + "/test.txt"
- fh = open( fn, 'w' )
+ fh = open(fn, 'w')
fh.write("I am writing this text to the file\n")
fh.close()
os.remove(fn)
@@ -152,7 +152,7 @@ def assert_writable_dir(dir):
def assert_file(fn):
if not valid_file(fn):
- raise Exception('Unable to find file '+fn)
+ raise Exception('Unable to find file ' + fn)
return fn
def mk_dir(dir):
@@ -168,19 +168,19 @@ def locate(name, subdir=None):
"""
base = get_setting("GENENETWORK_FILES")
if subdir:
- base = base+"/"+subdir
+ base = base + "/" + subdir
if valid_path(base):
lookfor = base + "/" + name
if valid_file(lookfor):
- logger.info("Found: file "+lookfor+"\n")
+ logger.info("Found: file " + lookfor + "\n")
return lookfor
else:
- raise Exception("Can not locate "+lookfor)
+ raise Exception("Can not locate " + lookfor)
if subdir: sys.stderr.write(subdir)
- raise Exception("Can not locate "+name+" in "+base)
+ raise Exception("Can not locate " + name + " in " + base)
def locate_phewas(name, subdir=None):
- return locate(name, '/phewas/'+subdir)
+ return locate(name, '/phewas/' + subdir)
def locate_ignore_error(name, subdir=None):
"""
@@ -191,13 +191,13 @@ def locate_ignore_error(name, subdir=None):
"""
base = get_setting("GENENETWORK_FILES")
if subdir:
- base = base+"/"+subdir
+ base = base + "/" + subdir
if valid_path(base):
lookfor = base + "/" + name
if valid_file(lookfor):
- logger.debug("Found: file "+name+"\n")
+ logger.debug("Found: file " + name + "\n")
return lookfor
- logger.info("WARNING: file "+name+" not found\n")
+ logger.info("WARNING: file " + name + " not found\n")
return None
def tempdir():
@@ -206,20 +206,20 @@ def tempdir():
"""
return valid_path(get_setting("TMPDIR", "/tmp"))
-BLUE = '\033[94m'
+BLUE = '\033[94m'
GREEN = '\033[92m'
-BOLD = '\033[1m'
-ENDC = '\033[0m'
+BOLD = '\033[1m'
+ENDC = '\033[0m'
def show_settings():
from utility.tools import LOG_LEVEL
- print(("Set global log level to "+BLUE+LOG_LEVEL+ENDC))
+ print(("Set global log level to " + BLUE + LOG_LEVEL + ENDC))
log_level = getattr(logging, LOG_LEVEL.upper())
logging.basicConfig(level=log_level)
logger.info(OVERRIDES)
- logger.info(BLUE+"Mr. Mojo Risin 2"+ENDC)
+ logger.info(BLUE + "Mr. Mojo Risin 2" + ENDC)
keylist = list(app.config.keys())
print("runserver.py: ****** Webserver configuration - k,v pairs from app.config ******")
keylist.sort()
@@ -231,35 +231,35 @@ def show_settings():
# Cached values
-GN_VERSION = get_setting('GN_VERSION')
-HOME = get_setting('HOME')
-SERVER_PORT = get_setting('SERVER_PORT')
-WEBSERVER_MODE = get_setting('WEBSERVER_MODE')
-GN2_BASE_URL = get_setting('GN2_BASE_URL')
-GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL')
-GN_SERVER_URL = get_setting('GN_SERVER_URL')
-SERVER_PORT = get_setting_int('SERVER_PORT')
-SQL_URI = get_setting('SQL_URI')
-LOG_LEVEL = get_setting('LOG_LEVEL')
-LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG')
-LOG_SQL = get_setting_bool('LOG_SQL')
-LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY')
-LOG_BENCH = get_setting_bool('LOG_BENCH')
-LOG_FORMAT = "%(message)s" # not yet in use
-USE_REDIS = get_setting_bool('USE_REDIS')
-USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
-
-GENENETWORK_FILES = get_setting('GENENETWORK_FILES')
-JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
+GN_VERSION = get_setting('GN_VERSION')
+HOME = get_setting('HOME')
+SERVER_PORT = get_setting('SERVER_PORT')
+WEBSERVER_MODE = get_setting('WEBSERVER_MODE')
+GN2_BASE_URL = get_setting('GN2_BASE_URL')
+GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL')
+GN_SERVER_URL = get_setting('GN_SERVER_URL')
+SERVER_PORT = get_setting_int('SERVER_PORT')
+SQL_URI = get_setting('SQL_URI')
+LOG_LEVEL = get_setting('LOG_LEVEL')
+LOG_LEVEL_DEBUG = get_setting_int('LOG_LEVEL_DEBUG')
+LOG_SQL = get_setting_bool('LOG_SQL')
+LOG_SQL_ALCHEMY = get_setting_bool('LOG_SQL_ALCHEMY')
+LOG_BENCH = get_setting_bool('LOG_BENCH')
+LOG_FORMAT = "%(message)s" # not yet in use
+USE_REDIS = get_setting_bool('USE_REDIS')
+USE_GN_SERVER = get_setting_bool('USE_GN_SERVER')
+
+GENENETWORK_FILES = get_setting('GENENETWORK_FILES')
+JS_GUIX_PATH = get_setting('JS_GUIX_PATH')
assert_dir(JS_GUIX_PATH)
-JS_GN_PATH = get_setting('JS_GN_PATH')
+JS_GN_PATH = get_setting('JS_GN_PATH')
# assert_dir(JS_GN_PATH)
GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID')
GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET')
if GITHUB_CLIENT_ID != 'UNKNOWN' and GITHUB_CLIENT_SECRET:
GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id=" + \
- GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET
+ GITHUB_CLIENT_ID + "&client_secret=" + GITHUB_CLIENT_SECRET
GITHUB_API_URL = get_setting('GITHUB_API_URL')
ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID')
@@ -267,7 +267,7 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
ORCID_AUTH_URL = None
if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \
- ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
+ ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
@@ -279,28 +279,28 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT')
SMTP_USERNAME = get_setting('SMTP_USERNAME')
SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
-REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command())
-GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command())
+REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command())
+GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command())
assert(GEMMA_COMMAND is not None)
-PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command())
+PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command())
GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
-TEMPDIR = tempdir() # defaults to UNIX TMPDIR
+TEMPDIR = tempdir() # defaults to UNIX TMPDIR
assert_dir(TEMPDIR)
# ---- Handle specific JS modules
JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
assert_dir(JS_GUIX_PATH)
-assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
+assert_dir(JS_GUIX_PATH + '/cytoscape-panzoom')
CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS
# assert_dir(JS_PATH)
JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher"))
assert_dir(JS_TWITTER_POST_FETCHER_PATH)
-assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
+assert_file(JS_TWITTER_POST_FETCHER_PATH + "/js/twitterFetcher_min.js")
JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape"))
assert_dir(JS_CYTOSCAPE_PATH)
-assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js')
+assert_file(JS_CYTOSCAPE_PATH + '/cytoscape.min.js')
# assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData")
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
index 6b029317..662bf794 100644
--- a/wqflask/utility/type_checking.py
+++ b/wqflask/utility/type_checking.py
@@ -23,19 +23,19 @@ def is_str(value):
except:
return False
-def get_float(vars_obj,name,default=None):
+def get_float(vars_obj, name, default=None):
if name in vars_obj:
if is_float(vars_obj[name]):
return float(vars_obj[name])
return default
-def get_int(vars_obj,name,default=None):
+def get_int(vars_obj, name, default=None):
if name in vars_obj:
if is_int(vars_obj[name]):
return float(vars_obj[name])
return default
-def get_string(vars_obj,name,default=None):
+def get_string(vars_obj, name, default=None):
if name in vars_obj:
if not vars_obj[name] is None:
return str(vars_obj[name])
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 5681fadf..ed59b0eb 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -33,38 +33,38 @@ from math import *
from base import webqtlConfig
# NL, 07/27/2010. moved from webqtlForm.py
-#Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
-ParInfo ={
-'BXH':['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'],
-'AKXD':['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
-'BXD':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'],
-'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
-'BHHBF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
-'BHF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
-'B6D2F2':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'BDF2-1999':['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
-'BDF2-2005':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'CTB6F2':['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
-'CXB':['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
-'AXBXA':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
-'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
-'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
-'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'],
-'HXBBXH':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
-'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
-'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
-'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
-'SXM':['SMF1', 'MSF1', 'Steptoe', 'Morex'],
-'HRDP':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
+# Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
+ParInfo = {
+'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'],
+'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
+'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+'C57BL-6JxC57BL-6NJF2': ['', '', 'C57BL/6J', 'C57BL/6NJ'],
+'BXD300': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+'B6BTBRF2': ['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
+'BHHBF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
+'BHF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
+'B6D2F2': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+'BDF2-1999': ['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
+'BDF2-2005': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+'CTB6F2': ['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
+'CXB': ['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
+'AXBXA': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
+'AXB': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
+'BXA': ['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
+'LXS': ['LSF1', 'SLF1', 'ISS', 'ILS'],
+'HXBBXH': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
+'BayXSha': ['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
+'ColXBur': ['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
+'ColXCvi': ['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
+'SXM': ['SMF1', 'MSF1', 'Steptoe', 'Morex'],
+'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
}
#########################################
# Accessory Functions
#########################################
-def genRandStr(prefix = "", length=8, chars=string.ascii_letters+string.digits):
+def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits):
from random import choice
_str = prefix[:]
for i in range(length):
@@ -83,12 +83,12 @@ def ListNotNull(lst):
return 1
return None
-def readLineCSV(line): ### dcrowell July 2008
+def readLineCSV(line): # dcrowell July 2008
"""Parses a CSV string of text and returns a list containing each element as a string.
Used by correlationPage"""
returnList = line.split('","')
- returnList[-1]=returnList[-1][:-2]
- returnList[0]=returnList[0][1:]
+ returnList[-1] = returnList[-1][:-2]
+ returnList[0] = returnList[0][1:]
return returnList
def cmpEigenValue(A, B):
@@ -107,7 +107,7 @@ def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users)
if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
access_to_confidential_phenotype_trait = 1
else:
- AuthorizedUsersList=[x.strip() for x in authorized_users.split(',')]
+ AuthorizedUsersList = [x.strip() for x in authorized_users.split(',')]
if userName in AuthorizedUsersList:
access_to_confidential_phenotype_trait = 1
return access_to_confidential_phenotype_trait
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 0564cfa7..bab87115 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -7,11 +7,11 @@ from flask import g
from flask import Flask
from utility import formatting
from wqflask.markdown_routes import glossary_blueprint
-from wqflask.markdown_routes import references_blueprint
-from wqflask.markdown_routes import links_blueprint
+from wqflask.markdown_routes import references_blueprint
+from wqflask.markdown_routes import links_blueprint
from wqflask.markdown_routes import policies_blueprint
-from wqflask.markdown_routes import environments_blueprint
-from wqflask.markdown_routes import facilities_blueprint
+from wqflask.markdown_routes import environments_blueprint
+from wqflask.markdown_routes import facilities_blueprint
app = Flask(__name__)
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index f5b50dcd..e0b7fea0 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -16,16 +16,16 @@ from utility import webqtlUtil, helper_functions, corr_result_helpers
from utility.benchmark import Bench
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
def do_correlation(start_vars):
assert('db' in start_vars)
assert('target_db' in start_vars)
assert('trait_id' in start_vars)
- this_dataset = data_set.create_dataset(dataset_name = start_vars['db'])
- target_dataset = data_set.create_dataset(dataset_name = start_vars['target_db'])
- this_trait = create_trait(dataset = this_dataset, name = start_vars['trait_id'])
+ this_dataset = data_set.create_dataset(dataset_name=start_vars['db'])
+ target_dataset = data_set.create_dataset(dataset_name=start_vars['target_db'])
+ this_trait = create_trait(dataset=this_dataset, name=start_vars['trait_id'])
this_trait = retrieve_sample_data(this_trait, this_dataset)
corr_params = init_corr_params(start_vars)
@@ -38,26 +38,26 @@ def do_correlation(start_vars):
if corr_params['type'] == "tissue":
[sample_r, num_overlap, sample_p, symbol] = corr_results[trait]
result_dict = {
- "trait" : trait,
- "sample_r" : sample_r,
- "#_strains" : num_overlap,
- "p_value" : sample_p,
- "symbol" : symbol
+ "trait": trait,
+ "sample_r": sample_r,
+ "#_strains": num_overlap,
+ "p_value": sample_p,
+ "symbol": symbol
}
elif corr_params['type'] == "literature" or corr_params['type'] == "lit":
[gene_id, sample_r] = corr_results[trait]
result_dict = {
- "trait" : trait,
- "sample_r" : sample_r,
- "gene_id" : gene_id
+ "trait": trait,
+ "sample_r": sample_r,
+ "gene_id": gene_id
}
else:
[sample_r, sample_p, num_overlap] = corr_results[trait]
result_dict = {
- "trait" : trait,
- "sample_r" : sample_r,
- "#_strains" : num_overlap,
- "p_value" : sample_p
+ "trait": trait,
+ "sample_r": sample_r,
+ "#_strains": num_overlap,
+ "p_value": sample_p
}
final_results.append(result_dict)
@@ -76,7 +76,7 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params)
sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
key=lambda t: -abs(t[1][1])))
- elif corr_params['type'] == "literature" or corr_params['type'] == "lit": #ZS: Just so a user can use either "lit" or "literature"
+ elif corr_params['type'] == "literature" or corr_params['type'] == "lit": # ZS: Just so a user can use either "lit" or "literature"
trait_geneid_dict = this_dataset.retrieve_genes("GeneId")
corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params)
sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
@@ -92,8 +92,8 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
return sorted_results
def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1):
- #Gets tissue expression values for the primary trait
- primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list = [this_trait.symbol])
+ # Gets tissue expression values for the primary trait
+ primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=[this_trait.symbol])
if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()]
@@ -227,9 +227,9 @@ def init_corr_params(start_vars):
return_count = int(start_vars['return_count'])
corr_params = {
- 'method' : method,
- 'type' : type,
- 'return_count' : return_count
+ 'method': method,
+ 'type': type,
+ 'return_count': return_count
}
return corr_params
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index eaddecd7..a64524dd 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -87,14 +87,14 @@ def phenotypes_exist(group_name):
results = g.db.execute(
("SELECT Name FROM PublishFreeze "
"WHERE PublishFreeze.Name = "
- "'{}'").format(group_name+"Publish")).fetchone()
+ "'{}'").format(group_name + "Publish")).fetchone()
return bool(results)
def genotypes_exist(group_name):
results = g.db.execute(
("SELECT Name FROM GenoFreeze " +
- "WHERE GenoFreeze.Name = '{}'").format(group_name+"Geno")).fetchone()
+ "WHERE GenoFreeze.Name = '{}'").format(group_name + "Geno")).fetchone()
return bool(results)
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index d59a69df..fbfbc879 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -8,15 +8,15 @@ from utility import helper_functions
from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
def do_mapping_for_api(start_vars):
assert('db' in start_vars)
assert('trait_id' in start_vars)
- dataset = data_set.create_dataset(dataset_name = start_vars['db'])
+ dataset = data_set.create_dataset(dataset_name=start_vars['db'])
dataset.group.get_markers()
- this_trait = create_trait(dataset = dataset, name = start_vars['trait_id'])
+ this_trait = create_trait(dataset=dataset, name=start_vars['trait_id'])
this_trait = retrieve_sample_data(this_trait, dataset)
samples = []
@@ -36,11 +36,11 @@ def do_mapping_for_api(start_vars):
mapping_params = initialize_parameters(start_vars, dataset, this_trait)
- covariates = "" #ZS: It seems to take an empty string as default. This should probably be changed.
+ covariates = "" # ZS: It seems to take an empty string as default. This should probably be changed.
if mapping_params['mapping_method'] == "gemma":
header_row = ["name", "chr", "Mb", "lod_score", "p_value"]
- if mapping_params['use_loco'] == "True": #ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api
+ if mapping_params['use_loco'] == "True": # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api
result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0]
else:
result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])
@@ -118,7 +118,7 @@ def initialize_parameters(start_vars, dataset, this_trait):
mapping_params['maf'] = 0.01
if 'maf' in start_vars:
- mapping_params['maf'] = start_vars['maf'] # Minor allele frequency
+ mapping_params['maf'] = start_vars['maf'] # Minor allele frequency
mapping_params['use_loco'] = True
if 'use_loco' in start_vars:
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 60e163f2..b0559a07 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -23,13 +23,13 @@ from wqflask.api import correlation, mapping, gen_menu
from utility.tools import flat_files
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
version = "pre1"
@app.route("/api/v_{}/".format(version))
def hello_world():
- return flask.jsonify({"hello":"world"})
+ return flask.jsonify({"hello": "world"})
@app.route("/api/v_{}/species".format(version))
def get_species_list():
@@ -38,10 +38,10 @@ def get_species_list():
species_list = []
for species in the_species:
species_dict = {
- "Id" : species[0],
- "Name" : species[1],
- "FullName" : species[2],
- "TaxonomyId" : species[3]
+ "Id": species[0],
+ "Name": species[1],
+ "FullName": species[2],
+ "TaxonomyId": species[3]
}
species_list.append(species_dict)
@@ -49,17 +49,17 @@ def get_species_list():
@app.route("/api/v_{}/species/".format(version))
@app.route("/api/v_{}/species/.".format(version))
-def get_species_info(species_name, file_format = "json"):
+def get_species_info(species_name, file_format="json"):
results = g.db.execute("""SELECT SpeciesId, Name, FullName, TaxonomyId
FROM Species
WHERE (Name="{0}" OR FullName="{0}" OR SpeciesName="{0}");""".format(species_name))
the_species = results.fetchone()
species_dict = {
- "Id" : the_species[0],
- "Name" : the_species[1],
- "FullName" : the_species[2],
- "TaxonomyId" : the_species[3]
+ "Id": the_species[0],
+ "Name": the_species[1],
+ "FullName": the_species[2],
+ "TaxonomyId": the_species[3]
}
return flask.jsonify(species_dict)
@@ -87,14 +87,14 @@ def get_groups_list(species_name=None):
groups_list = []
for group in the_groups:
group_dict = {
- "Id" : group[0],
- "SpeciesId" : group[1],
- "DisplayName" : group[2],
- "Name" : group[3],
- "FullName" : group[4],
- "public" : group[5],
- "MappingMethodId" : group[6],
- "GeneticType" : group[7]
+ "Id": group[0],
+ "SpeciesId": group[1],
+ "DisplayName": group[2],
+ "Name": group[3],
+ "FullName": group[4],
+ "public": group[5],
+ "MappingMethodId": group[6],
+ "GeneticType": group[7]
}
groups_list.append(group_dict)
@@ -106,7 +106,7 @@ def get_groups_list(species_name=None):
@app.route("/api/v_{}/group/.".format(version))
@app.route("/api/v_{}/group//".format(version))
@app.route("/api/v_{}/group//.".format(version))
-def get_group_info(group_name, species_name = None, file_format = "json"):
+def get_group_info(group_name, species_name=None, file_format="json"):
if species_name:
results = g.db.execute("""SELECT InbredSet.InbredSetId, InbredSet.SpeciesId, InbredSet.InbredSetName,
InbredSet.Name, InbredSet.FullName, InbredSet.public,
@@ -131,14 +131,14 @@ def get_group_info(group_name, species_name = None, file_format = "json"):
group = results.fetchone()
if group:
group_dict = {
- "Id" : group[0],
- "SpeciesId" : group[1],
- "DisplayName" : group[2],
- "Name" : group[3],
- "FullName" : group[4],
- "public" : group[5],
- "MappingMethodId" : group[6],
- "GeneticType" : group[7]
+ "Id": group[0],
+ "SpeciesId": group[1],
+ "DisplayName": group[2],
+ "Name": group[3],
+ "FullName": group[4],
+ "public": group[5],
+ "MappingMethodId": group[6],
+ "GeneticType": group[7]
}
return flask.jsonify(group_dict)
@@ -179,17 +179,17 @@ def get_datasets_for_group(group_name, species_name=None):
datasets_list = []
for dataset in the_datasets:
dataset_dict = {
- "Id" : dataset[0],
- "ProbeFreezeId" : dataset[1],
- "AvgID" : dataset[2],
- "Short_Abbreviation" : dataset[3],
- "Long_Abbreviation" : dataset[4],
- "FullName" : dataset[5],
- "ShortName" : dataset[6],
- "CreateTime" : dataset[7],
- "public" : dataset[8],
- "confidentiality" : dataset[9],
- "DataScale" : dataset[10]
+ "Id": dataset[0],
+ "ProbeFreezeId": dataset[1],
+ "AvgID": dataset[2],
+ "Short_Abbreviation": dataset[3],
+ "Long_Abbreviation": dataset[4],
+ "FullName": dataset[5],
+ "ShortName": dataset[6],
+ "CreateTime": dataset[7],
+ "public": dataset[8],
+ "confidentiality": dataset[9],
+ "DataScale": dataset[10]
}
datasets_list.append(dataset_dict)
@@ -201,10 +201,10 @@ def get_datasets_for_group(group_name, species_name=None):
@app.route("/api/v_{}/dataset/.".format(version))
@app.route("/api/v_{}/dataset//".format(version))
@app.route("/api/v_{}/dataset//.".format(version))
-def get_dataset_info(dataset_name, group_name = None, file_format="json"):
- #ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets
+def get_dataset_info(dataset_name, group_name=None, file_format="json"):
+ # ZS: First get ProbeSet (mRNA expression) datasets and then get Phenotype datasets
- datasets_list = [] #ZS: I figure I might as well return a list if there are multiple matches, though I don"t know if this will actually happen in practice
+ datasets_list = [] # ZS: I figure I might as well return a list if there are multiple matches, though I don"t know if this will actually happen in practice
probeset_query = """
SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName,
@@ -235,16 +235,16 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"):
if dataset:
dataset_dict = {
- "dataset_type" : "mRNA expression",
- "id" : dataset[0],
- "name" : dataset[1],
- "full_name" : dataset[2],
- "short_name" : dataset[3],
- "data_scale" : dataset[4],
- "tissue_id" : dataset[5],
- "tissue" : dataset[6],
- "public" : dataset[7],
- "confidential" : dataset[8]
+ "dataset_type": "mRNA expression",
+ "id": dataset[0],
+ "name": dataset[1],
+ "full_name": dataset[2],
+ "short_name": dataset[3],
+ "data_scale": dataset[4],
+ "tissue_id": dataset[5],
+ "tissue": dataset[6],
+ "public": dataset[7],
+ "confidential": dataset[8]
}
datasets_list.append(dataset_dict)
@@ -272,25 +272,25 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"):
if dataset:
if dataset[5]:
dataset_dict = {
- "dataset_type" : "phenotype",
- "id" : dataset[0],
- "name" : dataset[1],
- "description" : dataset[2],
- "pubmed_id" : dataset[5],
- "title" : dataset[6],
- "year" : dataset[7]
+ "dataset_type": "phenotype",
+ "id": dataset[0],
+ "name": dataset[1],
+ "description": dataset[2],
+ "pubmed_id": dataset[5],
+ "title": dataset[6],
+ "year": dataset[7]
}
elif dataset[4]:
dataset_dict = {
- "dataset_type" : "phenotype",
- "id" : dataset[0],
- "name" : dataset[3],
- "description" : dataset[4]
+ "dataset_type": "phenotype",
+ "id": dataset[0],
+ "name": dataset[3],
+ "description": dataset[4]
}
else:
dataset_dict = {
- "dataset_type" : "phenotype",
- "id" : dataset[0]
+ "dataset_type": "phenotype",
+ "id": dataset[0]
}
datasets_list.append(dataset_dict)
@@ -304,7 +304,7 @@ def get_dataset_info(dataset_name, group_name = None, file_format="json"):
@app.route("/api/v_{}/traits/".format(version), methods=("GET",))
@app.route("/api/v_{}/traits/.".format(version), methods=("GET",))
-def fetch_traits(dataset_name, file_format = "json"):
+def fetch_traits(dataset_name, file_format="json"):
trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args)
if ("ids_only" in request.args) and (len(trait_ids) > 0):
if file_format == "json":
@@ -432,7 +432,7 @@ def fetch_traits(dataset_name, file_format = "json"):
@app.route("/api/v_{}/sample_data/".format(version))
@app.route("/api/v_{}/sample_data/.".format(version))
-def all_sample_data(dataset_name, file_format = "csv"):
+def all_sample_data(dataset_name, file_format="csv"):
trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args)
if len(trait_ids) > 0:
@@ -538,7 +538,7 @@ def all_sample_data(dataset_name, file_format = "csv"):
@app.route("/api/v_{}/sample_data//".format(version))
@app.route("/api/v_{}/sample_data//.".format(version))
-def trait_sample_data(dataset_name, trait_name, file_format = "json"):
+def trait_sample_data(dataset_name, trait_name, file_format="json"):
probeset_query = """
SELECT
Strain.Name, Strain.Name2, ProbeSetData.value, ProbeSetData.Id, ProbeSetSE.error
@@ -610,10 +610,10 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
sample_list = []
for sample in sample_data:
sample_dict = {
- "sample_name" : sample[0],
- "sample_name_2" : sample[1],
- "value" : sample[2],
- "data_id" : sample[3]
+ "sample_name": sample[0],
+ "sample_name_2": sample[1],
+ "value": sample[2],
+ "data_id": sample[3]
}
if sample[4]:
sample_dict["se"] = sample[4]
@@ -629,7 +629,7 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
@app.route("/api/v_{}/trait//.".format(version))
@app.route("/api/v_{}/trait_info//".format(version))
@app.route("/api/v_{}/trait_info//.".format(version))
-def get_trait_info(dataset_name, trait_name, file_format = "json"):
+def get_trait_info(dataset_name, trait_name, file_format="json"):
probeset_query = """
SELECT
ProbeSet.Id, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, ProbeSet.Mb, ProbeSet.alias,
@@ -648,24 +648,24 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"):
trait_info = probeset_results.fetchone()
if trait_info:
trait_dict = {
- "id" : trait_info[0],
- "name" : trait_info[1],
- "symbol" : trait_info[2],
- "description" : trait_info[3],
- "chr" : trait_info[4],
- "mb" : trait_info[5],
- "alias" :trait_info[6],
- "mean" : trait_info[7],
- "se" : trait_info[8],
- "locus" : trait_info[9],
- "lrs" : trait_info[10],
- "p_value" : trait_info[11],
- "additive" : trait_info[12]
+ "id": trait_info[0],
+ "name": trait_info[1],
+ "symbol": trait_info[2],
+ "description": trait_info[3],
+ "chr": trait_info[4],
+ "mb": trait_info[5],
+ "alias": trait_info[6],
+ "mean": trait_info[7],
+ "se": trait_info[8],
+ "locus": trait_info[9],
+ "lrs": trait_info[10],
+ "p_value": trait_info[11],
+ "additive": trait_info[12]
}
return flask.jsonify(trait_dict)
else:
- if "Publish" in dataset_name: #ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish"
+ if "Publish" in dataset_name: # ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish"
dataset_name = dataset_name.replace("Publish", "")
group_id = get_group_id(dataset_name)
@@ -684,10 +684,10 @@ def get_trait_info(dataset_name, trait_name, file_format = "json"):
trait_info = pheno_results.fetchone()
if trait_info:
trait_dict = {
- "id" : trait_info[0],
- "locus" : trait_info[1],
- "lrs" : trait_info[2],
- "additive" : trait_info[3]
+ "id": trait_info[0],
+ "locus": trait_info[1],
+ "lrs": trait_info[2],
+ "additive": trait_info[3]
}
return flask.jsonify(trait_dict)
@@ -699,7 +699,7 @@ def get_corr_results():
results = correlation.do_correlation(request.args)
if len(results) > 0:
- return flask.jsonify(results) #ZS: I think flask.jsonify expects a dict/list instead of JSON
+ return flask.jsonify(results) # ZS: I think flask.jsonify expects a dict/list instead of JSON
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
@@ -754,7 +754,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
output_lines.append(line.split())
i += 1
- csv_writer = csv.writer(si, delimiter = "\t", escapechar = "\\", quoting = csv.QUOTE_NONE)
+ csv_writer = csv.writer(si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE)
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
elif file_format == "rqtl2":
@@ -802,7 +802,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
output_lines.append([line.strip() for line in line.split(",")])
i += 1
- csv_writer = csv.writer(si, delimiter = ",")
+ csv_writer = csv.writer(si, delimiter=",")
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
@@ -826,8 +826,8 @@ def return_error(code, source, title, details):
json_ob = {"errors": [
{
"status": code,
- "source": { "pointer": source },
- "title" : title,
+ "source": {"pointer": source},
+ "title": title,
"detail": details
}
]}
@@ -842,8 +842,8 @@ def get_dataset_trait_ids(dataset_name, start_vars):
limit_string = ""
if "Geno" in dataset_name:
- data_type = "Geno" #ZS: Need to pass back the dataset type
- query = """
+ data_type = "Geno" # ZS: Need to pass back the dataset type
+ query = """
SELECT
GenoXRef.GenoId, Geno.Name, GenoXRef.GenoFreezeId
FROM
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 0291f2b8..6a1b88ca 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -68,18 +68,18 @@ def collections_add():
uc_id = g.user_session.add_collection(collection_name, set())
collections = g.user_session.user_collections
- #ZS: One of these might be unnecessary
+ # ZS: One of these might be unnecessary
if 'traits' in request.args:
- traits=request.args['traits']
+ traits = request.args['traits']
return render_template("collections/add.html",
- traits = traits,
- collections = collections,
+ traits=traits,
+ collections=collections,
)
else:
hash = request.args['hash']
return render_template("collections/add.html",
- hash = hash,
- collections = collections,
+ hash=hash,
+ collections=collections,
)
@app.route("/collections/new")
@@ -139,8 +139,8 @@ def list_collections():
user_collections = list(g.user_session.user_collections)
return render_template("collections/list.html",
- params = params,
- collections = user_collections,
+ params=params,
+ collections=user_collections,
)
@app.route("/collections/remove", methods=('POST',))
@@ -196,7 +196,7 @@ def view_collection():
name, dataset_name = atrait.split(':')
if dataset_name == "Temp":
group = name.split("_")[2]
- dataset = create_dataset(dataset_name, dataset_type = "Temp", group_name = group)
+ dataset = create_dataset(dataset_name, dataset_type="Temp", group_name=group)
trait_ob = create_trait(name=name, dataset=dataset)
else:
dataset = create_dataset(dataset_name)
@@ -207,7 +207,7 @@ def view_collection():
json_version.append(jsonable(trait_ob))
collection_info = dict(trait_obs=trait_obs,
- uc = uc)
+ uc=uc)
if "json" in params:
return json.dumps(json_version)
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 5855ccf0..c135faa3 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -1,4 +1,4 @@
-## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
@@ -23,7 +23,7 @@ from pprint import pformat as pf
from base.trait import create_trait
from base import data_set
from utility import webqtlUtil, helper_functions, corr_result_helpers
-import utility.webqtlUtil #this is for parallel computing only.
+import utility.webqtlUtil # this is for parallel computing only.
from wqflask.correlation import correlation_functions
from MySQLdb import escape_string as escape
@@ -41,7 +41,7 @@ class ComparisonBarChart:
self.all_sample_list = []
self.traits = []
self.insufficient_shared_samples = False
- this_group = self.trait_list[0][1].group.name #ZS: Getting initial group name before verifying all traits are in the same group in the following loop
+ this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop
for trait_db in self.trait_list:
if trait_db[1].group.name != this_group:
@@ -74,9 +74,9 @@ class ComparisonBarChart:
this_trait_vals.append('')
self.sample_data.append(this_trait_vals)
- self.js_data = dict(traits = [trait.name for trait in self.traits],
- samples = self.all_sample_list,
- sample_data = self.sample_data,)
+ self.js_data = dict(traits=[trait.name for trait in self.traits],
+ samples=self.all_sample_list,
+ sample_data=self.sample_data,)
def get_trait_db_obs(self, trait_db_list):
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index d5dc26f5..22941ad5 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -9,18 +9,18 @@ from scipy import stats
import numpy as np
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
class CorrScatterPlot:
"""Page that displays a correlation scatterplot with a line fitted to it"""
def __init__(self, params):
if "Temp" in params['dataset_1']:
- self.dataset_1 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_1'].split("_")[1])
+ self.dataset_1 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1])
else:
self.dataset_1 = data_set.create_dataset(params['dataset_1'])
if "Temp" in params['dataset_2']:
- self.dataset_2 = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = params['dataset_2'].split("_")[1])
+ self.dataset_2 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1])
else:
self.dataset_2 = data_set.create_dataset(params['dataset_2'])
@@ -60,8 +60,8 @@ class CorrScatterPlot:
else:
slope_string = '%.3f' % slope
- x_buffer = (max(vals_1) - min(vals_1))*0.1
- y_buffer = (max(vals_2) - min(vals_2))*0.1
+ x_buffer = (max(vals_1) - min(vals_1)) * 0.1
+ y_buffer = (max(vals_2) - min(vals_2)) * 0.1
x_range = [min(vals_1) - x_buffer, max(vals_1) + x_buffer]
y_range = [min(vals_2) - y_buffer, max(vals_2) + y_buffer]
@@ -80,8 +80,8 @@ class CorrScatterPlot:
else:
srslope_string = '%.3f' % srslope
- x_buffer = (max(rx) - min(rx))*0.1
- y_buffer = (max(ry) - min(ry))*0.1
+ x_buffer = (max(rx) - min(rx)) * 0.1
+ y_buffer = (max(ry) - min(ry)) * 0.1
sr_range = [min(rx) - x_buffer, max(rx) + x_buffer]
@@ -92,33 +92,33 @@ class CorrScatterPlot:
self.collections_exist = "True"
self.js_data = dict(
- data = self.data,
- rdata = self.rdata,
- indIDs = self.indIDs,
- trait_1 = self.trait_1.dataset.name + ": " + str(self.trait_1.name),
- trait_2 = self.trait_2.dataset.name + ": " + str(self.trait_2.name),
- samples_1 = samples_1,
- samples_2 = samples_2,
- num_overlap = num_overlap,
- vals_1 = vals_1,
- vals_2 = vals_2,
- x_range = x_range,
- y_range = y_range,
- sr_range = sr_range,
- intercept_coords = intercept_coords,
- sr_intercept_coords = sr_intercept_coords,
-
- slope = slope,
- slope_string = slope_string,
- intercept = intercept,
- r_value = r_value,
- p_value = p_value,
-
- srslope = srslope,
- srslope_string = srslope_string,
- srintercept = srintercept,
- srr_value = srr_value,
- srp_value = srp_value
+ data=self.data,
+ rdata=self.rdata,
+ indIDs=self.indIDs,
+ trait_1=self.trait_1.dataset.name + ": " + str(self.trait_1.name),
+ trait_2=self.trait_2.dataset.name + ": " + str(self.trait_2.name),
+ samples_1=samples_1,
+ samples_2=samples_2,
+ num_overlap=num_overlap,
+ vals_1=vals_1,
+ vals_2=vals_2,
+ x_range=x_range,
+ y_range=y_range,
+ sr_range=sr_range,
+ intercept_coords=intercept_coords,
+ sr_intercept_coords=sr_intercept_coords,
+
+ slope=slope,
+ slope_string=slope_string,
+ intercept=intercept,
+ r_value=r_value,
+ p_value=p_value,
+
+ srslope=srslope,
+ srslope_string=srslope_string,
+ srintercept=srintercept,
+ srr_value=srr_value,
+ srp_value=srp_value
#trait3 = self.trait_3.data,
#vals_3 = vals_3
@@ -129,10 +129,10 @@ class CorrScatterPlot:
def get_intercept_coords(slope, intercept, x_range, y_range):
intercept_coords = []
- y1 = slope*x_range[0] + intercept
- y2 = slope*x_range[1] + intercept
- x1 = (y1-intercept)/slope
- x2 = (y2-intercept)/slope
+ y1 = slope * x_range[0] + intercept
+ y2 = slope * x_range[1] + intercept
+ x1 = (y1 - intercept) / slope
+ x2 = (y2 - intercept) / slope
intercept_coords.append([x1, y1])
intercept_coords.append([x2, y2])
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index fd7691d4..0f24241a 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -34,19 +34,19 @@ from flask import Flask, g
#####################################################################################
-#Input: primaryValue(list): one list of expression values of one probeSet,
+# Input: primaryValue(list): one list of expression values of one probeSet,
# targetValue(list): one list of expression values of one probeSet,
# method(string): indicate correlation method ('pearson' or 'spearman')
-#Output: corr_result(list): first item is Correlation Value, second item is tissue number,
+# Output: corr_result(list): first item is Correlation Value, second item is tissue number,
# third item is PValue
-#Function: get correlation value,Tissue quantity ,p value result by using R;
-#Note : This function is special case since both primaryValue and targetValue are from
-#the same dataset. So the length of these two parameters is the same. They are pairs.
-#Also, in the datatable TissueProbeSetData, all Tissue values are loaded based on
-#the same tissue order
+# Function: get correlation value,Tissue quantity ,p value result by using R;
+# Note : This function is special case since both primaryValue and targetValue are from
+# the same dataset. So the length of these two parameters is the same. They are pairs.
+# Also, in the datatable TissueProbeSetData, all Tissue values are loaded based on
+# the same tissue order
#####################################################################################
-def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pearson'):
+def cal_zero_order_corr_for_tiss(primaryValue=[], targetValue=[], method='pearson'):
R_primary = rpy2.robjects.FloatVector(list(range(len(primaryValue))))
N = len(primaryValue)
@@ -55,27 +55,27 @@ def cal_zero_order_corr_for_tiss (primaryValue=[], targetValue=[], method='pears
R_target = rpy2.robjects.FloatVector(list(range(len(targetValue))))
for i in range(len(targetValue)):
- R_target[i]=targetValue[i]
+ R_target[i] = targetValue[i]
R_corr_test = rpy2.robjects.r['cor.test']
- if method =='spearman':
+ if method == 'spearman':
R_result = R_corr_test(R_primary, R_target, method='spearman')
else:
R_result = R_corr_test(R_primary, R_target)
- corr_result =[]
- corr_result.append( R_result[3][0])
- corr_result.append( N )
- corr_result.append( R_result[2][0])
+ corr_result = []
+ corr_result.append(R_result[3][0])
+ corr_result.append(N)
+ corr_result.append(R_result[2][0])
return corr_result
########################################################################################################
-#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
-#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
+# input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
+# output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
# key is symbol, value is one list of expression values of one probeSet.
-#function: wrapper function for getSymbolValuePairDict function
+# function: wrapper function for getSymbolValuePairDict function
# build gene symbol list if necessary, cut it into small lists if necessary,
# then call getSymbolValuePairDict function and merge the results.
########################################################################################################
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index cb341e79..051ac1cb 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -1,4 +1,4 @@
-## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
@@ -78,7 +78,7 @@ class CorrelationResults:
with Bench("Doing correlations"):
if start_vars['dataset'] == "Temp":
- self.dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = start_vars['group'])
+ self.dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group'])
self.trait_id = start_vars['trait_id']
self.this_trait = create_trait(dataset=self.dataset,
name=self.trait_id,
@@ -109,8 +109,8 @@ class CorrelationResults:
self.get_formatted_corr_type()
self.return_number = int(start_vars['corr_return_results'])
- #The two if statements below append samples to the sample list based upon whether the user
- #rselected Primary Samples Only, Other Samples Only, or All Samples
+ # The two if statements below append samples to the sample list based upon whether the user
+ # rselected Primary Samples Only, Other Samples Only, or All Samples
primary_samples = self.dataset.group.samplelist
if self.dataset.group.parlist != None:
@@ -118,13 +118,13 @@ class CorrelationResults:
if self.dataset.group.f1list != None:
primary_samples += self.dataset.group.f1list
- #If either BXD/whatever Only or All Samples, append all of that group's samplelist
+ # If either BXD/whatever Only or All Samples, append all of that group's samplelist
if corr_samples_group != 'samples_other':
self.process_samples(start_vars, primary_samples)
- #If either Non-BXD/whatever or All Samples, get all samples from this_trait.data and
- #exclude the primary samples (because they would have been added in the previous
- #if statement if the user selected All Samples)
+ # If either Non-BXD/whatever or All Samples, get all samples from this_trait.data and
+ # exclude the primary samples (because they would have been added in the previous
+ # if statement if the user selected All Samples)
if corr_samples_group != 'samples_primary':
if corr_samples_group == 'samples_other':
primary_samples = [x for x in primary_samples if x not in (
@@ -173,7 +173,7 @@ class CorrelationResults:
key=lambda t: -abs(t[1][0])))
- #ZS: Convert min/max chromosome to an int for the location range option
+ # ZS: Convert min/max chromosome to an int for the location range option
range_chr_as_int = None
for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
if 'loc_chr' in start_vars:
@@ -259,15 +259,15 @@ class CorrelationResults:
def do_tissue_correlation_for_trait_list(self, tissue_dataset_id=1):
"""Given a list of correlation results (self.correlation_results), gets the tissue correlation value for each"""
- #Gets tissue expression values for the primary trait
+ # Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
- symbol_list = [self.this_trait.symbol])
+ symbol_list=[self.this_trait.symbol])
if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
gene_symbol_list = [trait.symbol for trait in self.correlation_results if trait.symbol]
- corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
+ corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=gene_symbol_list)
for trait in self.correlation_results:
@@ -282,15 +282,15 @@ class CorrelationResults:
trait.tissue_pvalue = result[2]
def do_tissue_correlation_for_all_traits(self, tissue_dataset_id=1):
- #Gets tissue expression values for the primary trait
+ # Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
- symbol_list = [self.this_trait.symbol])
+ symbol_list=[self.this_trait.symbol])
if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
#print("trait_gene_symbols: ", pf(trait_gene_symbols.values()))
- corr_result_tissue_vals_dict= correlation_functions.get_trait_symbol_and_tissue_values(
+ corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=list(self.trait_symbol_dict.values()))
#print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
@@ -443,7 +443,7 @@ class CorrelationResults:
self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals)
if num_overlap > 5:
- #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/
+ # ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/
if self.corr_method == 'bicor':
sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals)
elif self.corr_method == 'pearson':
@@ -475,16 +475,16 @@ def do_bicor(this_trait_vals, target_trait_vals):
r_library("WGCNA")
r_bicor = ro.r["bicorAndPvalue"] # Map the bicorAndPvalue function
- r_options(stringsAsFactors = False)
+ r_options(stringsAsFactors=False)
this_vals = ro.Vector(this_trait_vals)
target_vals = ro.Vector(target_trait_vals)
- the_r, the_p, _fisher_transform, _the_t, _n_obs = [numpy.asarray(x) for x in r_bicor(x = this_vals, y = target_vals)]
+ the_r, the_p, _fisher_transform, _the_t, _n_obs = [numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)]
return the_r, the_p
-def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api = False):
+def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False):
results_list = []
for i, trait in enumerate(corr_results):
if trait.view == False:
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index d0b4a156..94c8931f 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -1,4 +1,4 @@
-## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
@@ -52,7 +52,7 @@ class CorrelationMatrix:
self.traits = []
self.insufficient_shared_samples = False
self.do_PCA = True
- this_group = self.trait_list[0][1].group.name #ZS: Getting initial group name before verifying all traits are in the same group in the following loop
+ this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop
for trait_db in self.trait_list:
this_group = trait_db[1].group.name
this_trait = trait_db[0]
@@ -76,10 +76,10 @@ class CorrelationMatrix:
this_trait_vals.append('')
self.sample_data.append(this_trait_vals)
- if len(this_trait_vals) < len(self.trait_list): #Shouldn't do PCA if there are more traits than observations/samples
+ if len(this_trait_vals) < len(self.trait_list): # Shouldn't do PCA if there are more traits than observations/samples
self.do_PCA = False
- self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
+ self.lowest_overlap = 8 # ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
self.corr_results = []
self.pca_corr_results = []
@@ -93,7 +93,7 @@ class CorrelationMatrix:
corr_result_row = []
pca_corr_result_row = []
- is_spearman = False #ZS: To determine if it's above or below the diagonal
+ is_spearman = False # ZS: To determine if it's above or below the diagonal
for target in self.trait_list:
target_trait = target[0]
target_db = target[1]
@@ -168,12 +168,12 @@ class CorrelationMatrix:
except:
self.pca_works = "False"
- self.js_data = dict(traits = [trait.name for trait in self.traits],
- groups = groups,
- cols = list(range(len(self.traits))),
- rows = list(range(len(self.traits))),
- samples = self.all_sample_list,
- sample_data = self.sample_data,)
+ self.js_data = dict(traits=[trait.name for trait in self.traits],
+ groups=groups,
+ cols=list(range(len(self.traits))),
+ rows=list(range(len(self.traits))),
+ samples=self.all_sample_list,
+ sample_data=self.sample_data,)
def calculate_pca(self, cols, corr_eigen_value, corr_eigen_vectors):
base = importr('base')
@@ -183,7 +183,7 @@ class CorrelationMatrix:
m = robjects.r.matrix(corr_results_to_list, nrow=len(cols))
eigen = base.eigen(m)
- pca = stats.princomp(m, cor = "TRUE")
+ pca = stats.princomp(m, cor="TRUE")
self.loadings = pca.rx('loadings')
self.scores = pca.rx('scores')
self.scale = pca.rx('scale')
@@ -193,15 +193,15 @@ class CorrelationMatrix:
pca_traits = []
for i, vector in enumerate(trait_array_vectors):
- #ZS: Check if below check is necessary
- #if corr_eigen_value[i-1] > 100.0/len(self.trait_list):
- pca_traits.append((vector*-1.0).tolist())
+ # ZS: Check if below check is necessary
+ # if corr_eigen_value[i-1] > 100.0/len(self.trait_list):
+ pca_traits.append((vector * -1.0).tolist())
this_group_name = self.trait_list[0][1].group.name
- temp_dataset = data_set.create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = this_group_name)
+ temp_dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = this_group_name)
temp_dataset.group.get_samplelist()
for i, pca_trait in enumerate(pca_traits):
- trait_id = "PCA" + str(i+1) + "_" + temp_dataset.group.species + "_" + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
+ trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
this_vals_string = ""
position = 0
for sample in temp_dataset.group.all_samples_ordered():
@@ -228,7 +228,7 @@ class CorrelationMatrix:
else:
the_range = 2
for j in range(the_range):
- position = i + len(self.trait_list)*j
+ position = i + len(self.trait_list) * j
loadings_row.append(self.loadings[0][position])
loadings_array.append(loadings_row)
return loadings_array
@@ -271,14 +271,14 @@ def zScore(trait_data_array):
i = 0
for data in trait_data_array:
N = len(data)
- S = reduce(lambda x, y: x+y, data, 0.)
- SS = reduce(lambda x, y: x+y*y, data, 0.)
- mean = S/N
- var = SS - S*S/N
- stdev = math.sqrt(var/(N-1))
+ S = reduce(lambda x, y: x + y, data, 0.)
+ SS = reduce(lambda x, y: x + y * y, data, 0.)
+ mean = S / N
+ var = SS - S * S / N
+ stdev = math.sqrt(var / (N - 1))
if stdev == 0:
stdev = 1e-100
- data2 = [(x-mean)/stdev for x in data]
+ data2 = [(x - mean) / stdev for x in data]
trait_data_array[i] = data2
i += 1
return trait_data_array
@@ -298,8 +298,8 @@ def sortEigenVectors(vector):
for item in combines:
A.append(item[0])
B.append(item[1])
- sum = reduce(lambda x, y: x+y, A, 0.0)
- A = [x*100.0/sum for x in A]
+ sum = reduce(lambda x, y: x + y, A, 0.0)
+ A = [x * 100.0 / sum for x in A]
return [A, B]
except:
return []
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 1556e370..2fa90a93 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -25,33 +25,33 @@ from utility.tools import locate, GN2_BRANCH_URL
from rpy2.robjects.packages import importr
import utility.logger
-logger = utility.logger.getLogger(__name__ )
-
-## Get pointers to some common R functions
-r_library = ro.r["library"] # Map the library function
-r_options = ro.r["options"] # Map the options function
-r_t = ro.r["t"] # Map the t function
-r_unlist = ro.r["unlist"] # Map the unlist function
-r_list = ro.r.list # Map the list function
-r_png = ro.r["png"] # Map the png function for plotting
-r_dev_off = ro.r["dev.off"] # Map the dev.off function
-r_write_table = ro.r["write.table"] # Map the write.table function
-r_data_frame = ro.r["data.frame"] # Map the write.table function
-r_as_numeric = ro.r["as.numeric"] # Map the write.table function
+logger = utility.logger.getLogger(__name__)
+
+# Get pointers to some common R functions
+r_library = ro.r["library"] # Map the library function
+r_options = ro.r["options"] # Map the options function
+r_t = ro.r["t"] # Map the t function
+r_unlist = ro.r["unlist"] # Map the unlist function
+r_list = ro.r.list # Map the list function
+r_png = ro.r["png"] # Map the png function for plotting
+r_dev_off = ro.r["dev.off"] # Map the dev.off function
+r_write_table = ro.r["write.table"] # Map the write.table function
+r_data_frame = ro.r["data.frame"] # Map the write.table function
+r_as_numeric = ro.r["as.numeric"] # Map the write.table function
class CTL:
def __init__(self):
logger.info("Initialization of CTL")
#log = r_file("/tmp/genenetwork_ctl.log", open = "wt")
- #r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file
+ # r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file
#r_sink(log, type = "message")
r_library("ctl") # Load CTL - Should only be done once, since it is quite expensive
- r_options(stringsAsFactors = False)
+ r_options(stringsAsFactors=False)
logger.info("Initialization of CTL done, package loaded in R session")
- self.r_CTLscan = ro.r["CTLscan"] # Map the CTLscan function
- self.r_CTLsignificant = ro.r["CTLsignificant"] # Map the CTLsignificant function
- self.r_lineplot = ro.r["ctl.lineplot"] # Map the ctl.lineplot function
- self.r_plotCTLobject = ro.r["plot.CTLobject"] # Map the CTLsignificant function
+ self.r_CTLscan = ro.r["CTLscan"] # Map the CTLscan function
+ self.r_CTLsignificant = ro.r["CTLsignificant"] # Map the CTLsignificant function
+ self.r_lineplot = ro.r["ctl.lineplot"] # Map the ctl.lineplot function
+ self.r_plotCTLobject = ro.r["plot.CTLobject"] # Map the CTLsignificant function
self.nodes_list = []
self.edges_list = []
logger.info("Obtained pointers to CTL functions")
@@ -59,23 +59,23 @@ class CTL:
self.gn2_url = GN2_BRANCH_URL
def addNode(self, gt):
- node_dict = { 'data' : {'id' : str(gt.name) + ":" + str(gt.dataset.name),
- 'sid' : str(gt.name),
- 'dataset' : str(gt.dataset.name),
- 'label' : gt.name,
- 'symbol' : gt.symbol,
- 'geneid' : gt.geneid,
- 'omim' : gt.omim } }
+ node_dict = {'data': {'id': str(gt.name) + ":" + str(gt.dataset.name),
+ 'sid': str(gt.name),
+ 'dataset': str(gt.dataset.name),
+ 'label': gt.name,
+ 'symbol': gt.symbol,
+ 'geneid': gt.geneid,
+ 'omim': gt.omim}}
self.nodes_list.append(node_dict)
def addEdge(self, gtS, gtT, significant, x):
- edge_data = {'id' : str(gtS.symbol) + '_' + significant[1][x] + '_' + str(gtT.symbol),
- 'source' : str(gtS.name) + ":" + str(gtS.dataset.name),
- 'target' : str(gtT.name) + ":" + str(gtT.dataset.name),
- 'lod' : significant[3][x],
- 'color' : "#ff0000",
- 'width' : significant[3][x] }
- edge_dict = { 'data' : edge_data }
+ edge_data = {'id': str(gtS.symbol) + '_' + significant[1][x] + '_' + str(gtT.symbol),
+ 'source': str(gtS.name) + ":" + str(gtS.dataset.name),
+ 'target': str(gtT.name) + ":" + str(gtT.dataset.name),
+ 'lod': significant[3][x],
+ 'color': "#ff0000",
+ 'width': significant[3][x]}
+ edge_dict = {'data': edge_data}
self.edges_list.append(edge_dict)
def run_analysis(self, requestform):
@@ -114,7 +114,7 @@ class CTL:
genotypes = list(itertools.chain(*markers))
logger.debug(len(genotypes) / len(individuals), "==", len(parser.markers))
- rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames = r_list(markernames, individuals), byrow=True))
+ rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames=r_list(markernames, individuals), byrow=True))
# Create a phenotype matrix
traits = []
@@ -122,7 +122,7 @@ class CTL:
logger.debug("retrieving data for", trait)
if trait != "":
ts = trait.split(':')
- gt = create_trait(name = ts[0], dataset_name = ts[1])
+ gt = create_trait(name=ts[0], dataset_name=ts[1])
gt = retrieve_sample_data(gt, dataset, individuals)
for ind in individuals:
if ind in list(gt.data.keys()):
@@ -130,23 +130,23 @@ class CTL:
else:
traits.append("-999")
- rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames = r_list(self.trait_db_list, individuals), byrow=True))
+ rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True))
logger.debug(rPheno)
# Use a data frame to store the objects
- rPheno = r_data_frame(rPheno, check_names = False)
- rGeno = r_data_frame(rGeno, check_names = False)
+ rPheno = r_data_frame(rPheno, check_names=False)
+ rGeno = r_data_frame(rGeno, check_names=False)
# Debug: Print the genotype and phenotype files to disk
#r_write_table(rGeno, "~/outputGN/geno.csv")
#r_write_table(rPheno, "~/outputGN/pheno.csv")
# Perform the CTL scan
- res = self.r_CTLscan(rGeno, rPheno, strategy = strategy, nperm = nperm, parametric = parametric, nthreads=6)
+ res = self.r_CTLscan(rGeno, rPheno, strategy=strategy, nperm=nperm, parametric = parametric, nthreads=6)
# Get significant interactions
- significant = self.r_CTLsignificant(res, significance = significance)
+ significant = self.r_CTLsignificant(res, significance=significance)
# Create an image for output
self.results = {}
@@ -158,7 +158,7 @@ class CTL:
# Create the lineplot
r_png(self.results['imgloc1'], width=1000, height=600, type='cairo-png')
- self.r_lineplot(res, significance = significance)
+ self.r_lineplot(res, significance=significance)
r_dev_off()
n = 2 # We start from 2, since R starts from 1 :)
@@ -167,7 +167,7 @@ class CTL:
self.results['imgurl' + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png"
self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + self.results['imgurl' + str(n)]
r_png(self.results['imgloc' + str(n)], width=1000, height=600, type='cairo-png')
- self.r_plotCTLobject(res, (n-1), significance = significance, main='Phenotype ' + trait)
+ self.r_plotCTLobject(res, (n - 1), significance=significance, main='Phenotype ' + trait)
r_dev_off()
n = n + 1
@@ -180,8 +180,8 @@ class CTL:
logger.debug(significant[0][x], significant[1][x], significant[2][x]) # Debug to console
tsS = significant[0][x].split(':') # Source
tsT = significant[2][x].split(':') # Target
- gtS = create_trait(name = tsS[0], dataset_name = tsS[1]) # Retrieve Source info from the DB
- gtT = create_trait(name = tsT[0], dataset_name = tsT[1]) # Retrieve Target info from the DB
+ gtS = create_trait(name=tsS[0], dataset_name=tsS[1]) # Retrieve Source info from the DB
+ gtT = create_trait(name=tsT[0], dataset_name=tsT[1]) # Retrieve Target info from the DB
self.addNode(gtS)
self.addNode(gtT)
self.addEdge(gtS, gtT, significant, x)
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index adeed6ad..b6e85494 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -6,7 +6,7 @@ from sqlalchemy.ext.declarative import declarative_base
from utility.tools import SQL_URI
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
engine = create_engine(SQL_URI, encoding="latin1")
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 364a3eed..115182e4 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -32,7 +32,7 @@ class DoSearch:
self.search_type = search_type
if self.dataset:
- #Get group information for dataset and the species id
+ # Get group information for dataset and the species id
self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
def execute(self, query):
@@ -137,7 +137,7 @@ class MrnaAssaySearch(DoSearch):
return where_clause
- def compile_final_query(self, from_clause = '', where_clause = ''):
+ def compile_final_query(self, from_clause='', where_clause=''):
"""Generates the final query string"""
from_clause = self.normalize_spaces(from_clause)
@@ -153,7 +153,7 @@ class MrnaAssaySearch(DoSearch):
escape(str(self.dataset.id))))
return query
- def run_combined(self, from_clause = '', where_clause = ''):
+ def run_combined(self, from_clause='', where_clause=''):
"""Generates and runs a combined search of an mRNA expression dataset"""
logger.debug("Running ProbeSetSearch")
@@ -218,10 +218,10 @@ class PhenotypeSearch(DoSearch):
def get_where_clause(self):
"""Generate clause for WHERE portion of query"""
- #Todo: Zach will figure out exactly what both these lines mean
- #and comment here
+ # Todo: Zach will figure out exactly what both these lines mean
+ # and comment here
- #if "'" not in self.search_term[0]:
+ # if "'" not in self.search_term[0]:
search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]"
if "_" in self.search_term[0]:
if len(self.search_term[0].split("_")[0]) == 3:
@@ -236,7 +236,7 @@ class PhenotypeSearch(DoSearch):
return where_clause
- def compile_final_query(self, from_clause = '', where_clause = ''):
+ def compile_final_query(self, from_clause='', where_clause=''):
"""Generates the final query string"""
from_clause = self.normalize_spaces(from_clause)
@@ -292,7 +292,7 @@ class PhenotypeSearch(DoSearch):
def run(self):
"""Generates and runs a simple search of a phenotype dataset"""
- query = self.compile_final_query(where_clause = self.get_where_clause())
+ query = self.compile_final_query(where_clause=self.get_where_clause())
return self.execute(query)
@@ -334,7 +334,7 @@ class GenotypeSearch(DoSearch):
return where_clause
- def compile_final_query(self, from_clause = '', where_clause = ''):
+ def compile_final_query(self, from_clause='', where_clause=''):
"""Generates the final query string"""
from_clause = self.normalize_spaces(from_clause)
@@ -344,26 +344,26 @@ class GenotypeSearch(DoSearch):
query = (self.base_query +
"""WHERE Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
- and GenoFreeze.Id = %s"""% (escape(str(self.dataset.id))))
+ and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id))))
else:
query = (self.base_query +
"""WHERE %s
and Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
- and GenoFreeze.Id = %s"""% (where_clause,
+ and GenoFreeze.Id = %s""" % (where_clause,
escape(str(self.dataset.id))))
return query
def run(self):
"""Generates and runs a simple search of a genotype dataset"""
- #Todo: Zach will figure out exactly what both these lines mean
- #and comment here
+ # Todo: Zach will figure out exactly what both these lines mean
+ # and comment here
if self.search_term[0] == "*":
self.query = self.compile_final_query()
else:
- self.query = self.compile_final_query(where_clause = self.get_where_clause())
+ self.query = self.compile_final_query(where_clause=self.get_where_clause())
return self.execute(self.query)
@@ -393,7 +393,7 @@ class RifSearch(MrnaAssaySearch):
class WikiSearch(MrnaAssaySearch):
"""Searches GeneWiki for traits other people have annotated"""
- DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch"
+ DoSearch.search_types['ProbeSet_WIKI'] = "WikiSearch"
def get_from_clause(self):
return ", GeneRIF "
@@ -403,7 +403,7 @@ class WikiSearch(MrnaAssaySearch):
and GeneRIF.versionId=0 and GeneRIF.display>0
and (GeneRIF.comment REGEXP '%s' or GeneRIF.initial = '%s')
""" % (self.dataset.type,
- "[[:<:]]"+str(self.search_term[0])+"[[:>:]]",
+ "[[:<:]]" + str(self.search_term[0]) + "[[:>:]]",
str(self.search_term[0]))
return where_clause
@@ -418,7 +418,7 @@ class WikiSearch(MrnaAssaySearch):
class GoSearch(MrnaAssaySearch):
"""Searches for synapse-associated genes listed in the Gene Ontology."""
- DoSearch.search_types['ProbeSet_GO'] = "GoSearch"
+ DoSearch.search_types['ProbeSet_GO'] = "GoSearch"
def get_from_clause(self):
from_clause = """, db_GeneOntology.term as GOterm,
@@ -429,7 +429,7 @@ class GoSearch(MrnaAssaySearch):
def get_where_clause(self):
field = 'GOterm.acc'
- go_id = 'GO:' + ('0000000'+self.search_term[0])[-7:]
+ go_id = 'GO:' + ('0000000' + self.search_term[0])[-7:]
statements = ("""%s.symbol=GOgene_product.symbol and
GOassociation.gene_product_id=GOgene_product.id and
@@ -448,7 +448,7 @@ class GoSearch(MrnaAssaySearch):
return self.execute(query)
-#ZS: Not sure what the best way to deal with LRS searches is
+# ZS: Not sure what the best way to deal with LRS searches is
class LrsSearch(DoSearch):
"""Searches for genes with a QTL within the given LRS values
@@ -486,8 +486,8 @@ class LrsSearch(DoSearch):
assert isinstance(self.search_term, (list, tuple))
lrs_min, lrs_max = self.search_term[:2]
if self.search_type == "LOD":
- lrs_min = lrs_min*4.61
- lrs_max = lrs_max*4.61
+ lrs_min = lrs_min * 4.61
+ lrs_max = lrs_max * 4.61
where_clause = """ %sXRef.LRS > %s and
%sXRef.LRS < %s """ % self.mescape(self.dataset.type,
@@ -496,7 +496,7 @@ class LrsSearch(DoSearch):
max(lrs_min, lrs_max))
if len(self.search_term) > 2:
- #If the user typed, for example "Chr4", the "Chr" substring needs to be removed so that all search elements can be converted to floats
+ # If the user typed, for example "Chr4", the "Chr" substring needs to be removed so that all search elements can be converted to floats
chr_num = self.search_term[2]
if "chr" in self.search_term[2].lower():
chr_num = self.search_term[2].lower().replace("chr", "")
@@ -518,7 +518,7 @@ class LrsSearch(DoSearch):
logger.debug("self.search_term is:", self.search_term)
lrs_val = self.search_term[0]
if self.search_type == "LOD":
- lrs_val = lrs_val*4.61
+ lrs_val = lrs_val * 4.61
where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type,
self.search_operator,
@@ -546,7 +546,7 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(from_clause = self.from_clause, where_clause = self.where_clause)
+ self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause)
return self.execute(self.query)
@@ -560,7 +560,7 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(from_clause = self.from_clause, where_clause = self.where_clause)
+ self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause)
return self.execute(self.query)
@@ -599,7 +599,7 @@ class CisTransLrsSearch(DoSearch):
lrs_max = lrs_max * 4.61
sub_clause = """ %sXRef.LRS > %s and
- %sXRef.LRS < %s and """ % (
+ %sXRef.LRS < %s and """ % (
escape(self.dataset.type),
escape(str(min(lrs_min, lrs_max))),
escape(self.dataset.type),
@@ -607,7 +607,7 @@ class CisTransLrsSearch(DoSearch):
)
else:
# Deal with >, <, >=, and <=
- sub_clause = """ %sXRef.LRS %s %s and """ % (
+ sub_clause = """ %sXRef.LRS %s %s and """ % (
escape(self.dataset.type),
escape(self.search_operator),
escape(self.search_term[0])
@@ -667,7 +667,7 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""
for search_key in ('LRS', 'LOD'):
- DoSearch.search_types['ProbeSet_CIS'+search_key] = "CisLrsSearch"
+ DoSearch.search_types['ProbeSet_CIS' + search_key] = "CisLrsSearch"
def get_where_clause(self):
return CisTransLrsSearch.get_where_clause(self, "cis")
@@ -697,7 +697,7 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""
for search_key in ('LRS', 'LOD'):
- DoSearch.search_types['ProbeSet_TRANS'+search_key] = "TransLrsSearch"
+ DoSearch.search_types['ProbeSet_TRANS' + search_key] = "TransLrsSearch"
def get_where_clause(self):
return CisTransLrsSearch.get_where_clause(self, "trans")
@@ -740,7 +740,7 @@ class MeanSearch(MrnaAssaySearch):
self.where_clause = self.get_where_clause()
logger.debug("where_clause is:", pf(self.where_clause))
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -775,7 +775,7 @@ class RangeSearch(MrnaAssaySearch):
def run(self):
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -815,7 +815,7 @@ class PositionSearch(DoSearch):
def run(self):
self.get_where_clause()
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -823,12 +823,12 @@ class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
"""Searches for genes located within a specified range on a specified chromosome"""
for search_key in ('POSITION', 'POS', 'MB'):
- DoSearch.search_types['ProbeSet_'+search_key] = "MrnaPositionSearch"
+ DoSearch.search_types['ProbeSet_' + search_key] = "MrnaPositionSearch"
def run(self):
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -836,12 +836,12 @@ class GenotypePositionSearch(PositionSearch, GenotypeSearch):
"""Searches for genes located within a specified range on a specified chromosome"""
for search_key in ('POSITION', 'POS', 'MB'):
- DoSearch.search_types['Geno_'+search_key] = "GenotypePositionSearch"
+ DoSearch.search_types['Geno_' + search_key] = "GenotypePositionSearch"
def run(self):
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -873,7 +873,7 @@ class PvalueSearch(MrnaAssaySearch):
logger.debug("where_clause is:", pf(self.where_clause))
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
logger.sql(self.query)
return self.execute(self.query)
@@ -888,7 +888,7 @@ class AuthorSearch(PhenotypeSearch):
self.where_clause = """ Publication.Authors REGEXP "[[:<:]]%s[[:>:]]" and
""" % (self.search_term[0])
- self.query = self.compile_final_query(where_clause = self.where_clause)
+ self.query = self.compile_final_query(where_clause=self.where_clause)
return self.execute(self.query)
@@ -924,8 +924,8 @@ def get_aliases(symbol, species):
return filtered_aliases
if __name__ == "__main__":
- ### Usually this will be used as a library, but call it from the command line for testing
- ### And it runs the code below
+ # Usually this will be used as a library, but call it from the command line for testing
+ # And it runs the code below
import MySQLdb
import sys
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 6fb760e0..95c20673 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -13,7 +13,7 @@ from base.trait import create_trait, retrieve_trait_info
from pprint import pformat as pf
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
def export_search_results_csv(targs):
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index c5c79e98..9836eb9c 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -1,4 +1,4 @@
-## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
@@ -22,7 +22,7 @@ from base.trait import GeneralTrait
from utility import helper_functions, corr_result_helpers
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
class SendToBNW:
def __init__(self, start_vars):
@@ -40,7 +40,7 @@ class SendToBNW:
shared_samples = list(set(trait_samples_list[0]).intersection(*trait_samples_list))
- self.form_value = "" #ZS: string that is passed to BNW through form
+ self.form_value = "" # ZS: string that is passed to BNW through form
values_list = []
for trait_db in self.trait_list:
this_trait = trait_db[0]
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 47e4c53a..36f1b8e5 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -1,4 +1,4 @@
-## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
@@ -27,7 +27,7 @@ from base.species import TheSpecies
from utility import helper_functions, corr_result_helpers
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
class SendToGeneWeaver:
def __init__(self, start_vars):
@@ -74,7 +74,7 @@ def test_chip(trait_list):
FROM GeneChip, ProbeFreeze, ProbeSetFreeze
WHERE GeneChip.Id = ProbeFreeze.ChipId and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
- ProbeSetFreeze.Name = '%s'""" % dataset.name).fetchone()
+ ProbeSetFreeze.Name = '%s'""" % dataset.name).fetchone()
if result:
chip_name = result[0]
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index e1e5e655..f50eeb8b 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -1,4 +1,4 @@
-## Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
+# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License
@@ -27,7 +27,7 @@ from base.species import TheSpecies
from utility import helper_functions, corr_result_helpers
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
class SendToWebGestalt:
def __init__(self, start_vars):
@@ -47,16 +47,16 @@ class SendToWebGestalt:
id_type = "entrezgene"
self.hidden_vars = {
- 'gene_list' : "\n".join(gene_id_list),
- 'id_type' : "entrezgene",
- 'ref_set' : "genome",
- 'enriched_database_category' : "geneontology",
- 'enriched_database_name' : "Biological_Process",
- 'sig_method' : "fdr",
- 'sig_value' : "0.05",
- 'enrich_method' : "ORA",
- 'fdr_method' : "BH",
- 'min_num' : "2"
+ 'gene_list': "\n".join(gene_id_list),
+ 'id_type': "entrezgene",
+ 'ref_set': "genome",
+ 'enriched_database_category': "geneontology",
+ 'enriched_database_name': "Biological_Process",
+ 'sig_method': "fdr",
+ 'sig_value': "0.05",
+ 'enrich_method': "ORA",
+ 'fdr_method': "BH",
+ 'min_num': "2"
}
species = self.trait_list[0][1].group.species
@@ -78,7 +78,7 @@ def test_chip(trait_list):
FROM GeneChip, ProbeFreeze, ProbeSetFreeze
WHERE GeneChip.Id = ProbeFreeze.ChipId and
ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id and
- ProbeSetFreeze.Name = '%s'""" % dataset.name).fetchone()
+ ProbeSetFreeze.Name = '%s'""" % dataset.name).fetchone()
if result:
chip_name = result[0]
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index 69ee9623..f29c0e4d 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -40,8 +40,8 @@ def view_group():
user_info = get_user_by_unique_column("user_id", user_id)
members_info.append(user_info)
- #ZS: This whole part might not scale well with many resources
- resources_info = []
+ # ZS: This whole part might not scale well with many resources
+ resources_info = []
all_resources = get_resources()
for resource_id in all_resources:
resource_info = get_resource_info(resource_id)
@@ -82,10 +82,10 @@ def add_users(user_type='members'):
group_id = request.form['group_id']
if user_type == "admins":
user_emails = request.form['admin_emails_to_add'].split(",")
- add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = True)
+ add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=True)
elif user_type == "members":
user_emails = request.form['member_emails_to_add'].split(",")
- add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = False)
+ add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=False)
return redirect(url_for('view_group', id=group_id))
@@ -103,7 +103,7 @@ def add_or_edit_group():
if "group_name" in params:
member_user_ids = set()
admin_user_ids = set()
- admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin
+ admin_user_ids.add(g.user_session.user_id) # ZS: Always add the user creating the group as an admin
if "admin_emails_to_add" in params:
admin_emails = params['admin_emails_to_add'].split(",")
for email in admin_emails:
@@ -124,22 +124,22 @@ def add_or_edit_group():
else:
return render_template("admin/create_group.html")
-#ZS: Will integrate this later, for now just letting users be added directly
-def send_group_invites(group_id, user_email_list = [], user_type="members"):
+# ZS: Will integrate this later, for now just letting users be added directly
+def send_group_invites(group_id, user_email_list=[], user_type="members"):
for user_email in user_email_list:
user_details = get_user_by_unique_column("email_address", user_email)
if user_details:
group_info = get_group_info(group_id)
- #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here,
+ # ZS: Probably not necessary since the group should normally always exist if group_id is being passed here,
# but it's technically possible to hit it if Redis is cleared out before submitting the new users or something
if group_info:
- #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user,
+ # ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user,
# but do add them if they're a regular user and are added as an admin
if (user_details['user_id'] in group_info['admins']) or \
((user_type == "members") and (user_details['user_id'] in group_info['members'])):
continue
else:
- send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group")
+ send_verification_email(user_details, template_name="email/group_verification.txt", key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group")
else:
temp_password = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
user_details = {
@@ -152,4 +152,4 @@ def send_group_invites(group_id, user_email_list = [], user_type="members"):
save_user(user_details, user_details['user_id'])
send_invitation_email(user_email, temp_password)
-#@app.route()
+# @app.route()
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 9bf23d57..8cb81dcc 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -102,7 +102,7 @@ class GSearch:
this_trait['locus_chr'] = line[16]
this_trait['locus_mb'] = line[17]
- dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet",species=this_trait["species"])
+ dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"])
if dataset_ob.id not in dataset_to_permissions:
permissions = check_resource_availability(dataset_ob)
dataset_to_permissions[dataset_ob.id] = permissions
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 20e3559a..f8ef7028 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -12,7 +12,7 @@ from utility.logger import getLogger
Redis = Redis()
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
class Heatmap:
@@ -24,7 +24,7 @@ class Heatmap:
self.num_permutations = 5000
self.dataset = self.trait_list[0][1]
- self.json_data = {} #The dictionary that will be used to create the json object that contains all the data needed to create the figure
+ self.json_data = {} # The dictionary that will be used to create the json object that contains all the data needed to create the figure
self.all_sample_list = []
self.traits = []
@@ -83,7 +83,7 @@ class Heatmap:
self.json_data[trait] = self.trait_results[trait]
self.js_data = dict(
- json_data = self.json_data
+ json_data=self.json_data
)
def gen_reaper_results(self):
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index d0dd7aea..9779878e 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -2,14 +2,14 @@ import string
from flask import Flask, g
-#Just return a list of dictionaries
-#each dictionary contains sub-dictionary
+# Just return a list of dictionaries
+# each dictionary contains sub-dictionary
def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
- ##List All Species in the Gene Table
+ # List All Species in the Gene Table
speciesDict = {}
results = g.db.execute("""
SELECT Species.Name, GeneList.SpeciesId
@@ -20,7 +20,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
for item in results:
speciesDict[item[0]] = item[1]
- ##List current Species and other Species
+ # List current Species and other Species
speciesId = speciesDict[species]
otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())]
otherSpecies.remove([species, speciesId])
@@ -43,8 +43,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
newdict = {}
for j, item in enumerate(fetchFields):
newdict[item] = result[j]
- #count SNPs if possible
- if diffCol and species=='mouse':
+ # count SNPs if possible
+ if diffCol and species == 'mouse':
newdict["snpCount"] = g.db.execute("""
SELECT count(*)
FROM BXDSnpPosition
@@ -52,16 +52,16 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
Mb >= %2.6f AND Mb < %2.6f AND
StrainId1 = %d AND StrainId2 = %d
""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0]
- newdict["snpDensity"] = newdict["snpCount"]/(newdict["TxEnd"]-newdict["TxStart"])/1000.0
+ newdict["snpDensity"] = newdict["snpCount"] / (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0
else:
newdict["snpDensity"] = newdict["snpCount"] = 0
try:
- newdict['GeneLength'] = 1000.0*(newdict['TxEnd'] - newdict['TxStart'])
+ newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart'])
except:
pass
- #load gene from other Species by the same name
+ # load gene from other Species by the same name
for item in otherSpecies:
othSpec, othSpecId = item
newdict2 = {}
@@ -74,7 +74,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
for j, item in enumerate(fetchFields):
newdict2[item] = resultsOther[j]
- #count SNPs if possible, could be a separate function
+ # count SNPs if possible, could be a separate function
if diffCol and othSpec == 'mouse':
newdict2["snpCount"] = g.db.execute("""
SELECT count(*)
@@ -84,12 +84,12 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
StrainId1 = %d AND StrainId2 = %d
""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0]
- newdict2["snpDensity"] = newdict2["snpCount"]/(newdict2["TxEnd"]-newdict2["TxStart"])/1000.0
+ newdict2["snpDensity"] = newdict2["snpCount"] / (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0
else:
newdict2["snpDensity"] = newdict2["snpCount"] = 0
try:
- newdict2['GeneLength'] = 1000.0*(newdict2['TxEnd'] - newdict2['TxStart'])
+ newdict2['GeneLength'] = 1000.0 * (newdict2['TxEnd'] - newdict2['TxStart'])
except:
pass
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 4074f098..3753d1ce 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -51,7 +51,7 @@ try: # Only import this for Python3
from functools import reduce
except:
pass
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
RED = ImageColor.getrgb("red")
BLUE = ImageColor.getrgb("blue")
@@ -390,24 +390,24 @@ class DisplayMappingResults:
else:
self.genotype = self.dataset.group.read_genotype_file()
- #Darwing Options
+ # Darwing Options
try:
if self.selectedChr > -1:
- self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
+ self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
else:
- self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
+ self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
except:
if self.selectedChr > -1:
- self.graphWidth = self.GRAPH_DEFAULT_WIDTH
+ self.graphWidth = self.GRAPH_DEFAULT_WIDTH
else:
- self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH
+ self.graphWidth = self.MULT_GRAPH_DEFAULT_WIDTH
-## BEGIN HaplotypeAnalyst
+# BEGIN HaplotypeAnalyst
if 'haplotypeAnalystCheck' in list(start_vars.keys()):
self.haplotypeAnalystChecked = start_vars['haplotypeAnalystCheck']
else:
self.haplotypeAnalystChecked = False
-## END HaplotypeAnalyst
+# END HaplotypeAnalyst
self.graphHeight = self.GRAPH_DEFAULT_HEIGHT
self.dominanceChecked = False
@@ -446,7 +446,7 @@ class DisplayMappingResults:
except:
self.lrsMax = 0
- #Trait Infos
+ # Trait Infos
self.identification = ""
################################################################
@@ -471,10 +471,10 @@ class DisplayMappingResults:
Chr_Length.OrderId
""" % (self.dataset.group.name, ", ".join(["'%s'" % X[0] for X in self.ChrList[1:]])))
- self.ChrLengthMbList = [x[0]/1000000.0 for x in self.ChrLengthMbList]
- self.ChrLengthMbSum = reduce(lambda x, y:x+y, self.ChrLengthMbList, 0.0)
+ self.ChrLengthMbList = [x[0] / 1000000.0 for x in self.ChrLengthMbList]
+ self.ChrLengthMbSum = reduce(lambda x, y: x + y, self.ChrLengthMbList, 0.0)
if self.ChrLengthMbList:
- self.MbGraphInterval = self.ChrLengthMbSum/(len(self.ChrLengthMbList)*12) #Empirical Mb interval
+ self.MbGraphInterval = self.ChrLengthMbSum / (len(self.ChrLengthMbList) * 12) # Empirical Mb interval
else:
self.MbGraphInterval = 1
@@ -482,18 +482,18 @@ class DisplayMappingResults:
for i, _chr in enumerate(self.genotype):
self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM)
- self.ChrLengthCMSum = reduce(lambda x, y:x+y, self.ChrLengthCMList, 0.0)
+ self.ChrLengthCMSum = reduce(lambda x, y: x + y, self.ChrLengthCMList, 0.0)
if self.plotScale == 'physic':
- self.GraphInterval = self.MbGraphInterval #Mb
+ self.GraphInterval = self.MbGraphInterval # Mb
else:
- self.GraphInterval = self.cMGraphInterval #cM
+ self.GraphInterval = self.cMGraphInterval # cM
-## BEGIN HaplotypeAnalyst
-## count the amount of individuals to be plotted, and increase self.graphHeight
+# BEGIN HaplotypeAnalyst
+# count the amount of individuals to be plotted, and increase self.graphHeight
if self.haplotypeAnalystChecked and self.selectedChr > -1:
thisTrait = self.this_trait
- smd=[]
+ smd = []
for sample in self.sample_vals_dict.keys():
if self.sample_vals_dict[sample] != "x":
temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
@@ -501,19 +501,19 @@ class DisplayMappingResults:
else:
continue
samplelist = list(self.genotype.prgy)
- for j, _geno in enumerate (self.genotype[0][1].genotype):
+ for j, _geno in enumerate(self.genotype[0][1].genotype):
for item in smd:
if item.name == samplelist[j]:
self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
# default:
- self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS+10) * self.EACH_GENE_HEIGHT
-## END HaplotypeAnalyst
+ self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT
+# END HaplotypeAnalyst
#########################
- ## Get the sorting column
+ # Get the sorting column
#########################
RISet = self.dataset.group.name
if RISet in ('AXB', 'BXA', 'AXBXA'):
@@ -529,7 +529,7 @@ class DisplayMappingResults:
elif RISet in ('LXS'):
self.diffCol = ['ILS', 'ISS']
else:
- self.diffCol= []
+ self.diffCol = []
for i, strain in enumerate(self.diffCol):
self.diffCol[i] = g.db.execute("select Id from Strain where Symbol = %s", strain).fetchone()[0]
@@ -546,7 +546,7 @@ class DisplayMappingResults:
geneTable = ""
self.geneCol = None
- if self.plotScale == 'physic' and self.selectedChr > -1 and (self.intervalAnalystChecked or self.geneChecked):
+ if self.plotScale == 'physic' and self.selectedChr > -1 and (self.intervalAnalystChecked or self.geneChecked):
# Draw the genes for this chromosome / region of this chromosome
webqtldatabase = self.dataset.name
@@ -580,11 +580,11 @@ class DisplayMappingResults:
showLocusForm = ""
intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight))
with Bench("Drawing Plot"):
- gifmap = self.plotIntMapping(intCanvas, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm)
+ gifmap = self.plotIntMapping(intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm)
self.gifmap = gifmap.__str__()
- self.filename= webqtlUtil.genRandStr("Itvl_")
+ self.filename = webqtlUtil.genRandStr("Itvl_")
intCanvas.save(
"{}.png".format(
os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename)),
@@ -594,20 +594,20 @@ class DisplayMappingResults:
border="0", usemap='#WebQTLImageMap'
)
- #Scales plot differently for high resolution
+ # Scales plot differently for high resolution
if self.draw2X:
- intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2, self.graphHeight*2))
- gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
+ intCanvasX2 = Image.new("RGBA", size=(self.graphWidth * 2, self.graphHeight * 2))
+ gifmapX2 = self.plotIntMapping(intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2)
intCanvasX2.save(
"{}.png".format(
os.path.join(webqtlConfig.GENERATED_IMAGE_DIR,
- self.filename+"X2")),
+ self.filename + "X2")),
format='png')
################################################################
# Outputs goes here
################################################################
- #this form is used for opening Locus page or trait page, only available for genetic mapping
+ # this form is used for opening Locus page or trait page, only available for genetic mapping
if showLocusForm:
showLocusForm = HtmlGenWrapper.create_form_tag(
cgi=os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE),
@@ -615,7 +615,7 @@ class DisplayMappingResults:
name=showLocusForm,
submit=HtmlGenWrapper.create_input_tag(type_='hidden'))
- hddn = {'FormID':'showDatabase', 'ProbeSetID':'_','database':fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
+ hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
for key in hddn.keys():
showLocusForm.append(HtmlGenWrapper.create_input_tag(
name=key, value=hddn[key], type_='hidden'))
@@ -636,9 +636,9 @@ class DisplayMappingResults:
btminfo.append(HtmlGenWrapper.create_br_tag())
btminfo.append('Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
- def plotIntMapping(self, canvas, offset= (80, 120, 90, 100), zoom = 1, startMb = None, endMb = None, showLocusForm = ""):
+ def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb= None, endMb = None, showLocusForm = ""):
im_drawer = ImageDraw.Draw(canvas)
- #calculating margins
+ # calculating margins
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
if self.multipleInterval:
yTopOffset = max(90, yTopOffset)
@@ -659,34 +659,34 @@ class DisplayMappingResults:
xLeftOffset += 20
fontZoom = 1.5
- xLeftOffset = int(xLeftOffset*fontZoom)
- xRightOffset = int(xRightOffset*fontZoom)
- yBottomOffset = int(yBottomOffset*fontZoom)
+ xLeftOffset = int(xLeftOffset * fontZoom)
+ xRightOffset = int(xRightOffset * fontZoom)
+ yBottomOffset = int(yBottomOffset * fontZoom)
cWidth = canvas.size[0]
cHeight = canvas.size[1]
plotWidth = cWidth - xLeftOffset - xRightOffset
plotHeight = cHeight - yTopOffset - yBottomOffset
- #Drawing Area Height
+ # Drawing Area Height
drawAreaHeight = plotHeight
if self.plotScale == 'physic' and self.selectedChr > -1:
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
- drawAreaHeight -= 4*self.BAND_HEIGHT + 4*self.BAND_SPACING+ 10*zoom
+ drawAreaHeight -= 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING + 10 * zoom
else:
- drawAreaHeight -= 3*self.BAND_HEIGHT + 3*self.BAND_SPACING+ 10*zoom
+ drawAreaHeight -= 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom
if self.geneChecked:
- drawAreaHeight -= self.NUM_GENE_ROWS*self.EACH_GENE_HEIGHT + 3*self.BAND_SPACING + 10*zoom
+ drawAreaHeight -= self.NUM_GENE_ROWS * self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom
else:
if self.selectedChr > -1:
drawAreaHeight -= 20
else:
drawAreaHeight -= 30
-## BEGIN HaplotypeAnalyst
+# BEGIN HaplotypeAnalyst
if self.haplotypeAnalystChecked and self.selectedChr > -1:
- drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS+10) * 2 * zoom
-## END HaplotypeAnalyst
+ drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS + 10) * 2 * zoom
+# END HaplotypeAnalyst
if zoom == 2:
drawAreaHeight -= 60
@@ -696,42 +696,42 @@ class DisplayMappingResults:
newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
# Draw the alternating-color background first and get plotXScale
- plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+ plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
- #draw bootstap
+ # draw bootstap
if self.bootChecked and not self.multipleInterval:
- self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+ self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
# Draw clickable region and gene band if selected
if self.plotScale == 'physic' and self.selectedChr > -1:
- self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb)
+ self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
if self.geneChecked and self.geneCol:
- self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb)
+ self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
if self.SNPChecked:
- self.drawSNPTrackNew(canvas, offset=newoffset, zoom = 2*zoom, startMb=startMb, endMb = endMb)
-## BEGIN HaplotypeAnalyst
+ self.drawSNPTrackNew(canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb)
+# BEGIN HaplotypeAnalyst
if self.haplotypeAnalystChecked:
- self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb)
-## END HaplotypeAnalyst
+ self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
+# END HaplotypeAnalyst
# Draw X axis
- self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom = zoom, startMb=startMb, endMb = endMb)
+ self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
# Draw QTL curve
- self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom= zoom, startMb=startMb, endMb = endMb)
+ self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
- #draw legend
+ # draw legend
if self.multipleInterval:
self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset)
elif self.legendChecked:
- self.drawLegendPanel(canvas, offset=newoffset, zoom = zoom)
+ self.drawLegendPanel(canvas, offset=newoffset, zoom=zoom)
else:
pass
- #draw position, no need to use a separate function
- self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom = zoom)
+ # draw position, no need to use a separate function
+ self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom=zoom)
return gifmap
- def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -741,9 +741,9 @@ class DisplayMappingResults:
if zoom == 2:
fontZoom = 1.5
- bootHeightThresh = drawAreaHeight*3/4
+ bootHeightThresh = drawAreaHeight * 3 / 4
- #break bootstrap result into groups
+ # break bootstrap result into groups
BootCoord = []
i = 0
previous_chr = None
@@ -751,7 +751,7 @@ class DisplayMappingResults:
startX = xLeftOffset
BootChrCoord = []
- if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes
+ if self.selectedChr == -1: # ZS: If viewing full genome/all chromosomes
for i, result in enumerate(self.qtlresults):
if result['chr'] != previous_chr:
previous_chr = result['chr']
@@ -759,28 +759,28 @@ class DisplayMappingResults:
if previous_chr_as_int != 1:
BootCoord.append(BootChrCoord)
BootChrCoord = []
- startX += (self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval)*plotXScale
+ startX += (self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval) * plotXScale
if self.plotScale == 'physic':
- Xc = startX + (result['Mb']-self.startMb)*plotXScale
+ Xc = startX + (result['Mb'] - self.startMb) * plotXScale
else:
- Xc = startX + (result['cM']-self.qtlresults[0]['cM'])*plotXScale
+ Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale
BootChrCoord.append([Xc, self.bootResult[i]])
else:
for i, result in enumerate(self.qtlresults):
if str(result['chr']) == str(self.ChrList[self.selectedChr][0]):
if self.plotScale == 'physic':
- Xc = startX + (result['Mb']-self.startMb)*plotXScale
+ Xc = startX + (result['Mb'] - self.startMb) * plotXScale
else:
- Xc = startX + (result['cM']-self.qtlresults[0]['cM'])*plotXScale
+ Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale
BootChrCoord.append([Xc, self.bootResult[i]])
BootCoord = [BootChrCoord]
- #reduce bootResult
+ # reduce bootResult
if self.selectedChr > -1:
maxBootBar = 80.0
else:
maxBootBar = 200.0
- stepBootStrap = plotWidth/maxBootBar
+ stepBootStrap = plotWidth / maxBootBar
reducedBootCoord = []
maxBootCount = 0
@@ -801,8 +801,8 @@ class DisplayMappingResults:
bootCount = BootChrCoord[i][1]
# end else
# end for
- #add last piece
- if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap/2.0:
+ # add last piece
+ if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap / 2.0:
reducedBootCoord.append([bootStartPixX, BootChrCoord[-1][0], bootCount])
else:
reducedBootCoord[-1][2] += bootCount
@@ -815,64 +815,64 @@ class DisplayMappingResults:
if item[2] > 0:
if item[0] < xLeftOffset:
item[0] = xLeftOffset
- if item[0] > xLeftOffset+plotWidth:
- item[0] = xLeftOffset+plotWidth
+ if item[0] > xLeftOffset + plotWidth:
+ item[0] = xLeftOffset + plotWidth
if item[1] < xLeftOffset:
item[1] = xLeftOffset
- if item[1] > xLeftOffset+plotWidth:
- item[1] = xLeftOffset+plotWidth
+ if item[1] > xLeftOffset + plotWidth:
+ item[1] = xLeftOffset + plotWidth
if item[0] != item[1]:
im_drawer.rectangle(
xy=((item[0], yZero),
- (item[1], yZero - item[2]*bootHeightThresh/maxBootCount)),
+ (item[1], yZero - item[2] * bootHeightThresh / maxBootCount)),
fill=self.BOOTSTRAP_BOX_COLOR, outline=BLACK)
- ###draw boot scale
- highestPercent = (maxBootCount*100.0)/nboot
+ # draw boot scale
+ highestPercent = (maxBootCount * 100.0) / nboot
bootScale = Plot.detScale(0, highestPercent)
- bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1]/bootScale[2])
+ bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1] / bootScale[2])
bootScale = bootScale[:-1] + [highestPercent]
- bootOffset = 50*fontZoom
- bootScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=13*fontZoom)
+ bootOffset = 50 * fontZoom
+ bootScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=13 * fontZoom)
im_drawer.rectangle(
- xy=((canvas.size[0]-bootOffset, yZero-bootHeightThresh),
- (canvas.size[0]-bootOffset-15*zoom, yZero)),
- fill = YELLOW, outline=BLACK)
+ xy=((canvas.size[0] - bootOffset, yZero - bootHeightThresh),
+ (canvas.size[0] - bootOffset - 15*zoom, yZero)),
+ fill=YELLOW, outline=BLACK)
im_drawer.line(
- xy=((canvas.size[0]-bootOffset+4, yZero),
- (canvas.size[0]-bootOffset, yZero)),
+ xy=((canvas.size[0] - bootOffset + 4, yZero),
+ (canvas.size[0] - bootOffset, yZero)),
fill=BLACK)
TEXT_Y_DISPLACEMENT = -8
- im_drawer.text(xy=(canvas.size[0]-bootOffset+10, yZero+TEXT_Y_DISPLACEMENT), text='0%',
+ im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, yZero+TEXT_Y_DISPLACEMENT), text='0%',
font=bootScaleFont, fill=BLACK)
for item in bootScale:
if item == 0:
continue
- bootY = yZero-bootHeightThresh*item/highestPercent
+ bootY = yZero - bootHeightThresh * item / highestPercent
im_drawer.line(
- xy=((canvas.size[0]-bootOffset+4, bootY),
- (canvas.size[0]-bootOffset, bootY)),
+ xy=((canvas.size[0] - bootOffset + 4, bootY),
+ (canvas.size[0] - bootOffset, bootY)),
fill=BLACK)
- im_drawer.text(xy=(canvas.size[0]-bootOffset+10, bootY+TEXT_Y_DISPLACEMENT),
- text='%2.1f'%item, font=bootScaleFont, fill=BLACK)
+ im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, bootY+TEXT_Y_DISPLACEMENT),
+ text='%2.1f' % item, font=bootScaleFont, fill=BLACK)
if self.legendChecked:
if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'):
startPosY = 30
else:
startPosY = 15
- smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
+ smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom)
leftOffset = canvas.size[0] - xRightOffset - 190
im_drawer.rectangle(
- xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)),
+ xy=((leftOffset, startPosY - 6), (leftOffset + 12, startPosY + 6)),
fill=YELLOW, outline=BLACK)
- im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY+TEXT_Y_DISPLACEMENT),
+ im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY + TEXT_Y_DISPLACEMENT),
text='Frequency of the Peak LRS',
font=smallLabelFont, fill=BLACK)
- def drawProbeSetPosition(self, canvas, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ def drawProbeSetPosition(self, canvas, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
if len(self.traitList) != 1:
return
@@ -896,21 +896,21 @@ class DisplayMappingResults:
if self.plotScale == "physic":
this_chr = str(self.ChrList[self.selectedChr][0])
else:
- this_chr = str(self.ChrList[self.selectedChr][1]+1)
+ this_chr = str(self.ChrList[self.selectedChr][1] + 1)
if self.plotScale == 'physic':
if self.selectedChr > -1:
if this_chr != Chr or Mb < self.startMb or Mb > self.endMb:
return
else:
- locPixel = xLeftOffset + (Mb-self.startMb)*plotXScale
+ locPixel = xLeftOffset + (Mb - self.startMb) * plotXScale
else:
locPixel = xLeftOffset
for i, _chr in enumerate(self.ChrList[1:]):
if _chr[0] != Chr:
- locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+ locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale
else:
- locPixel += Mb*plotXScale
+ locPixel += Mb * plotXScale
break
else:
if self.selectedChr > -1:
@@ -918,33 +918,33 @@ class DisplayMappingResults:
if qtlresult['chr'] != self.selectedChr:
continue
- if i==0 and qtlresult['Mb'] >= Mb:
- locPixel=-1
+ if i == 0 and qtlresult['Mb'] >= Mb:
+ locPixel = -1
break
- #the trait's position is between two traits
- if i > 0 and self.qtlresults[i-1]['Mb'] < Mb and qtlresult['Mb'] >= Mb:
- locPixel = xLeftOffset + plotXScale*(self.qtlresults[i-1]['Mb']+(qtlresult['Mb']-self.qtlresults[i-1]['Mb'])*(Mb - self.qtlresults[i-1]['Mb'])/(qtlresult['Mb']-self.qtlresults[i-1]['Mb']))
+ # the trait's position is between two traits
+ if i > 0 and self.qtlresults[i - 1]['Mb'] < Mb and qtlresult['Mb'] >= Mb:
+ locPixel = xLeftOffset + plotXScale * (self.qtlresults[i - 1]['Mb'] + (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']) * (Mb - self.qtlresults[i - 1]['Mb']) / (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']))
break
- #the trait's position is on the right of the last genotype
- if i==len(self.qtlresults) and Mb>=qtlresult['Mb']:
+ # the trait's position is on the right of the last genotype
+ if i == len(self.qtlresults) and Mb >= qtlresult['Mb']:
locPixel = -1
else:
locPixel = xLeftOffset
for i, _chr in enumerate(self.ChrList):
- if i < (len(self.ChrList)-1):
+ if i < (len(self.ChrList) - 1):
if _chr != Chr:
- locPixel += (self.ChrLengthDistList[i] + self.GraphInterval)*plotXScale
+ locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale
else:
- locPixel += (Mb*(_chr[-1].cM-_chr[0].cM)/self.ChrLengthCMList[i])*plotXScale
+ locPixel += (Mb * (_chr[-1].cM - _chr[0].cM) / self.ChrLengthCMList[i]) * plotXScale
break
if locPixel >= 0 and self.plotScale == 'physic':
- traitPixel = ((locPixel, yZero), (locPixel-7, yZero+14), (locPixel+7, yZero+14))
+ traitPixel = ((locPixel, yZero), (locPixel - 7, yZero + 14), (locPixel + 7, yZero + 14))
draw_open_polygon(canvas, xy=traitPixel, outline=BLACK,
fill=self.TRANSCRIPT_LOCATION_COLOR)
- def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ def drawSNPTrackNew(self, canvas, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
return
@@ -963,36 +963,36 @@ class DisplayMappingResults:
#chrName = self.genotype[0].name
chrName = self.ChrList[self.selectedChr][0]
- stepMb = (endMb-startMb)/plotWidth
+ stepMb = (endMb - startMb) / plotWidth
strainId1, strainId2 = self.diffCol
SNPCounts = []
- while startMb= %2.6f AND Mb < %2.6f AND
StrainId1 = %d AND StrainId2 = %d
- """ % (chrName, startMb, startMb+stepMb, strainId1, strainId2)).fetchone()[0]
+ """ % (chrName, startMb, startMb + stepMb, strainId1, strainId2)).fetchone()[0]
SNPCounts.append(snp_count)
startMb += stepMb
if (len(SNPCounts) > 0):
maxCount = max(SNPCounts)
- if maxCount>0:
+ if maxCount > 0:
for i in range(xLeftOffset, xLeftOffset + plotWidth):
- snpDensity = float(SNPCounts[i-xLeftOffset]*SNP_HEIGHT_MODIFIER/maxCount)
+ snpDensity = float(SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount)
im_drawer.line(
- xy=((i, drawSNPLocationY+(snpDensity)*zoom),
- (i, drawSNPLocationY-(snpDensity)*zoom)),
+ xy=((i, drawSNPLocationY + (snpDensity) * zoom),
+ (i, drawSNPLocationY - (snpDensity) * zoom)),
fill=self.SNP_COLOR, width=1)
- def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1):
+ def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset=(40, 120, 80, 10), zoom=1):
nameWidths = []
yPaddingTop = 10
- colorFont=ImageFont.truetype(font=TREBUC_FILE, size=12)
- if len(self.qtlresults) >20 and self.selectedChr > -1:
+ colorFont = ImageFont.truetype(font=TREBUC_FILE, size=12)
+ if len(self.qtlresults) > 20 and self.selectedChr > -1:
rightShift = 20
rightShiftStep = 60
rectWidth = 10
@@ -1004,7 +1004,7 @@ class DisplayMappingResults:
for k, thisTrait in enumerate(self.traitList):
thisLRSColor = self.colorCollection[k]
kstep = k % 4
- if k!=0 and kstep==0:
+ if k != 0 and kstep == 0:
if nameWidths:
rightShiftStep = max(nameWidths[-4:]) + rectWidth + 20
rightShift += rightShiftStep
@@ -1014,19 +1014,19 @@ class DisplayMappingResults:
nameWidths.append(nameWidth)
im_drawer.rectangle(
- xy=((rightShift, yPaddingTop+kstep*15),
- (rectWidth+rightShift, yPaddingTop+10+kstep*15)),
+ xy=((rightShift, yPaddingTop + kstep * 15),
+ (rectWidth + rightShift, yPaddingTop + 10+kstep*15)),
fill=thisLRSColor, outline=BLACK)
im_drawer.text(
- text=name, xy=(rectWidth+2+rightShift, yPaddingTop+10+kstep*15),
+ text=name, xy=(rectWidth + 2 + rightShift, yPaddingTop + 10 + kstep * 15),
font=colorFont, fill=BLACK)
if thisTrait.db:
- COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,)
- HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
+ COORDS = "%d,%d,%d,%d" % (rectWidth + 2 + rightShift, yPaddingTop + kstep * 15, rectWidth + 2 + rightShift + nameWidth, yPaddingTop + 10 + kstep * 15,)
+ HREF = "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF)
- gifmap.append(Areas) ### TODO
+ gifmap.append(Areas) # TODO
- def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
+ def drawLegendPanel(self, canvas, offset=(40, 120, 80, 10), zoom=1):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -1037,80 +1037,80 @@ class DisplayMappingResults:
if zoom == 2:
fontZoom = 1.5
- labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
+ labelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom)
startPosY = 15
- stepPosY = 12*fontZoom
+ stepPosY = 12 * fontZoom
startPosX = canvas.size[0] - xRightOffset - 415
if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'):
startPosY = 15
nCol = 2
- smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
+ smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom)
leftOffset = canvas.size[0] - xRightOffset - 190
draw_open_polygon(
canvas,
xy=(
- (leftOffset + 6, startPosY-7),
- (leftOffset - 1, startPosY+7),
- (leftOffset + 13, startPosY+7)),
+ (leftOffset + 6, startPosY - 7),
+ (leftOffset - 1, startPosY + 7),
+ (leftOffset + 13, startPosY + 7)),
outline=BLACK, fill=self.TRANSCRIPT_LOCATION_COLOR
)
TEXT_Y_DISPLACEMENT = -8
im_drawer.text(
text="Sequence Site",
- xy=(leftOffset + 20, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
+ xy=(leftOffset + 20, startPosY + TEXT_Y_DISPLACEMENT), font=smallLabelFont,
fill=self.TOP_RIGHT_INFO_COLOR)
if self.manhattan_plot != True:
im_drawer.line(
- xy=((startPosX, startPosY), (startPosX+32, startPosY)),
+ xy=((startPosX, startPosY), (startPosX + 32, startPosY)),
fill=self.LRS_COLOR, width=2)
im_drawer.text(
- text=self.LRS_LOD, xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
+ text=self.LRS_LOD, xy=(startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT),
font=labelFont, fill=BLACK)
startPosY += stepPosY
if self.additiveChecked:
im_drawer.line(
- xy=((startPosX, startPosY), (startPosX+17, startPosY)),
+ xy=((startPosX, startPosY), (startPosX + 17, startPosY)),
fill=self.ADDITIVE_COLOR_POSITIVE, width=2)
im_drawer.line(
- xy=((startPosX+18, startPosY), (startPosX+32, startPosY)),
+ xy=((startPosX + 18, startPosY), (startPosX + 32, startPosY)),
fill=self.ADDITIVE_COLOR_NEGATIVE, width=2)
im_drawer.text(
- text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
+ text='Additive Effect', xy=(startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT),
font=labelFont, fill=BLACK)
startPosY += stepPosY
if self.genotype.type == 'intercross' and self.dominanceChecked:
im_drawer.line(
- xy=((startPosX, startPosY), (startPosX+17, startPosY)),
+ xy=((startPosX, startPosY), (startPosX + 17, startPosY)),
fill=self.DOMINANCE_COLOR_POSITIVE, width=4)
im_drawer.line(
- xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
+ xy=((startPosX + 18, startPosY), (startPosX + 35, startPosY)),
fill=self.DOMINANCE_COLOR_NEGATIVE, width=4)
im_drawer.text(
- text='Dominance Effect', xy=(startPosX+42, startPosY+5),
+ text='Dominance Effect', xy=(startPosX + 42, startPosY + 5),
font=labelFont, fill=BLACK)
startPosY += stepPosY
if self.haplotypeAnalystChecked:
im_drawer.line(
- xy=((startPosX-34, startPosY), (startPosX-17, startPosY)),
+ xy=((startPosX - 34, startPosY), (startPosX - 17, startPosY)),
fill=self.HAPLOTYPE_POSITIVE, width=4)
im_drawer.line(
- xy=((startPosX-17, startPosY), (startPosX, startPosY)),
+ xy=((startPosX - 17, startPosY), (startPosX, startPosY)),
fill=self.HAPLOTYPE_NEGATIVE, width=4)
im_drawer.line(
- xy=((startPosX, startPosY), (startPosX+17, startPosY)),
+ xy=((startPosX, startPosY), (startPosX + 17, startPosY)),
fill=self.HAPLOTYPE_HETEROZYGOUS, width=4)
im_drawer.line(
- xy=((startPosX+17, startPosY), (startPosX+34, startPosY)),
+ xy=((startPosX + 17, startPosY), (startPosX + 34, startPosY)),
fill=self.HAPLOTYPE_RECOMBINATION, width=4)
im_drawer.text(
text='Haplotypes (Pat, Mat, Het, Unk)',
- xy=(startPosX+41, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
+ xy=(startPosX + 41, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
startPosY += stepPosY
if self.permChecked and self.nperm > 0:
@@ -1118,20 +1118,20 @@ class DisplayMappingResults:
if self.multipleInterval and not self.bootChecked:
thisStartX = canvas.size[0] - xRightOffset - 205
im_drawer.line(
- xy=((thisStartX, startPosY), ( startPosX + 32, startPosY)),
+ xy=((thisStartX, startPosY), (startPosX + 32, startPosY)),
fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
im_drawer.line(
- xy=((thisStartX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)),
+ xy=((thisStartX, startPosY + stepPosY), (startPosX + 32, startPosY + stepPosY)),
fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
im_drawer.text(
text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant),
- xy=(thisStartX+40, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
+ xy=(thisStartX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
im_drawer.text(
text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
- xy=(thisStartX+40, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
+ xy=(thisStartX + 40, startPosY + TEXT_Y_DISPLACEMENT + stepPosY), font=labelFont,
fill=BLACK)
- labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom)
+ labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12 * fontZoom)
labelColor = BLACK
if self.dataset.type == "Publish" or self.dataset.type == "Geno":
@@ -1195,17 +1195,17 @@ class DisplayMappingResults:
identification += "Trait: %s" % (self.this_trait.name)
identification += " with %s samples" % (self.n_samples)
- d = 4+ max(
+ d = 4 + max(
im_drawer.textsize(identification, font=labelFont)[0],
im_drawer.textsize(string1, font=labelFont)[0],
im_drawer.textsize(string2, font=labelFont)[0])
im_drawer.text(
text=identification,
- xy=(xLeftOffset, y_constant*fontZoom), font=labelFont,
+ xy=(xLeftOffset, y_constant * fontZoom), font=labelFont,
fill=labelColor)
y_constant += 15
else:
- d = 4+ max(
+ d = 4 + max(
im_drawer.textsize(string1, font=labelFont)[0],
im_drawer.textsize(string2, font=labelFont)[0])
@@ -1223,28 +1223,28 @@ class DisplayMappingResults:
transform_text += "Invert +/-"
im_drawer.text(
- text=transform_text, xy=(xLeftOffset, y_constant*fontZoom),
+ text=transform_text, xy=(xLeftOffset, y_constant * fontZoom),
font=labelFont, fill=labelColor)
y_constant += 15
im_drawer.text(
- text=string1, xy=(xLeftOffset, y_constant*fontZoom),
+ text=string1, xy=(xLeftOffset, y_constant * fontZoom),
font=labelFont, fill=labelColor)
y_constant += 15
im_drawer.text(
- text=string2, xy=(xLeftOffset, y_constant*fontZoom),
+ text=string2, xy=(xLeftOffset, y_constant * fontZoom),
font=labelFont, fill=labelColor)
y_constant += 15
if string3 != '':
im_drawer.text(
- text=string3, xy=(xLeftOffset, y_constant*fontZoom),
+ text=string3, xy=(xLeftOffset, y_constant * fontZoom),
font=labelFont, fill=labelColor)
y_constant += 15
if string4 != '':
im_drawer.text(
- text=string4, xy=(xLeftOffset, y_constant*fontZoom),
+ text=string4, xy=(xLeftOffset, y_constant * fontZoom),
font=labelFont, fill=labelColor)
- def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
return
@@ -1264,9 +1264,9 @@ class DisplayMappingResults:
if self.dataset.group.species == "mouse":
txStart = theGO["TxStart"]
txEnd = theGO["TxEnd"]
- geneLength = (txEnd - txStart)*1000.0
- tenPercentLength = geneLength*0.0001
- SNPdensity = theGO["snpCount"]/geneLength
+ geneLength = (txEnd - txStart) * 1000.0
+ tenPercentLength = geneLength * 0.0001
+ SNPdensity = theGO["snpCount"] / geneLength
exonStarts = list(map(float, theGO['exonStarts'].split(",")[:-1]))
exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1]))
@@ -1277,23 +1277,23 @@ class DisplayMappingResults:
strand = theGO["Strand"]
exonCount = theGO["exonCount"]
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel
+ geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb)
+ geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel
if (geneEndPix < xLeftOffset):
- return; # this gene is not on the screen
+ return; # this gene is not on the screen
elif (geneEndPix > xLeftOffset + plotWidth):
- geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
+ geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
if (geneStartPix > xLeftOffset + plotWidth):
- return; # we are outside the valid on-screen range, so stop drawing genes
+ return; # we are outside the valid on-screen range, so stop drawing genes
elif (geneStartPix < xLeftOffset):
- geneStartPix = xLeftOffset; # clip the first in-range gene
+ geneStartPix = xLeftOffset; # clip the first in-range gene
- #color the gene based on SNP density
- #found earlier, needs to be recomputed as snps are added
- #always apply colors now, even if SNP Track not checked - Zach 11/24/2010
+ # color the gene based on SNP density
+ # found earlier, needs to be recomputed as snps are added
+ # always apply colors now, even if SNP Track not checked - Zach 11/24/2010
- densities=[1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
+ densities = [1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
if SNPdensity < densities[0]:
myColor = BLACK
elif SNPdensity < densities[1]:
@@ -1310,11 +1310,11 @@ class DisplayMappingResults:
myColor = DARKRED
outlineColor = myColor
- fillColor = myColor
+ fillColor = myColor
TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % (geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount)
# NL: 06-02-2011 Rob required to change this link for gene related
- HREF=geneNCBILink %geneSymbol
+ HREF = geneNCBILink % geneSymbol
elif self.dataset.group.species == "rat":
exonStarts = []
@@ -1327,85 +1327,85 @@ class DisplayMappingResults:
strand = theGO["Strand"]
exonCount = 0
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb)
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) #at least one pixel
+ geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb)
+ geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel
if (geneEndPix < xLeftOffset):
- return; # this gene is not on the screen
+ return; # this gene is not on the screen
elif (geneEndPix > xLeftOffset + plotWidth):
- geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
+ geneEndPix = xLeftOffset + plotWidth; # clip the last in-range gene
if (geneStartPix > xLeftOffset + plotWidth):
- return; # we are outside the valid on-screen range, so stop drawing genes
+ return; # we are outside the valid on-screen range, so stop drawing genes
elif (geneStartPix < xLeftOffset):
- geneStartPix = xLeftOffset; # clip the first in-range gene
+ geneStartPix = xLeftOffset; # clip the first in-range gene
outlineColor = DARKBLUE
fillColor = DARKBLUE
TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand)
# NL: 06-02-2011 Rob required to change this link for gene related
- HREF=geneNCBILink %geneSymbol
+ HREF = geneNCBILink % geneSymbol
else:
outlineColor = ORANGE
fillColor = ORANGE
TITLE = "Gene: %s" % geneSymbol
- #Draw Genes
- geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT*zoom
+ # Draw Genes
+ geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT * zoom
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
- geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING
+ geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING
else:
- geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING
+ geneYLocation += 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING
- #draw the detail view
+ # draw the detail view
if self.endMb - self.startMb <= self.DRAW_DETAIL_MB and geneEndPix - geneStartPix > self.EACH_GENE_ARROW_SPACING * 3:
utrColor = ImageColor.getrgb("rgb(66%, 66%, 66%)")
arrowColor = ImageColor.getrgb("rgb(70%, 70%, 70%)")
- #draw the line that runs the entire length of the gene
+ # draw the line that runs the entire length of the gene
im_drawer.line(
xy=(
- (geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom),
- ( geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT/2*zoom)),
+ (geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 * zoom),
+ (geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 *zoom)),
fill=outlineColor, width=1)
- #draw the arrows
+ # draw the arrows
if geneEndPix - geneStartPix < 1:
genePixRange = 1
else:
genePixRange = int(geneEndPix - geneStartPix)
for xCoord in range(0, genePixRange):
- if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix-geneStartPix) or xCoord == 0:
+ if (xCoord % self.EACH_GENE_ARROW_SPACING == 0 and xCoord + self.EACH_GENE_ARROW_SPACING < geneEndPix - geneStartPix) or xCoord == 0:
if strand == "+":
im_drawer.line(
xy=((geneStartPix + xCoord, geneYLocation),
(geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH,
- geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom)),
+ geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)),
fill=arrowColor, width=1)
im_drawer.line(
xy=((geneStartPix + xCoord,
- geneYLocation + self.EACH_GENE_HEIGHT*zoom),
- (geneStartPix + xCoord+self.EACH_GENE_ARROW_WIDTH,
+ geneYLocation + self.EACH_GENE_HEIGHT * zoom),
+ (geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH,
geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)),
fill=arrowColor, width=1)
else:
im_drawer.line(
xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH,
geneYLocation),
- ( geneStartPix + xCoord,
- geneYLocation +(self.EACH_GENE_HEIGHT / 2)*zoom)),
+ (geneStartPix + xCoord,
+ geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)),
fill=arrowColor, width=1)
im_drawer.line(
xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH,
- geneYLocation + self.EACH_GENE_HEIGHT*zoom),
- ( geneStartPix + xCoord,
- geneYLocation + (self.EACH_GENE_HEIGHT / 2)*zoom)),
+ geneYLocation + self.EACH_GENE_HEIGHT * zoom),
+ (geneStartPix + xCoord,
+ geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)),
fill=arrowColor, width=1)
- #draw the blocks for the exon regions
+ # draw the blocks for the exon regions
for i in range(0, len(exonStarts)):
- exonStartPix = (exonStarts[i]-startMb)*plotXScale + xLeftOffset
- exonEndPix = (exonEnds[i]-startMb)*plotXScale + xLeftOffset
+ exonStartPix = (exonStarts[i] - startMb) * plotXScale + xLeftOffset
+ exonEndPix = (exonEnds[i] - startMb) * plotXScale + xLeftOffset
if (exonStartPix < xLeftOffset):
exonStartPix = xLeftOffset
if (exonEndPix < xLeftOffset):
@@ -1416,13 +1416,13 @@ class DisplayMappingResults:
exonStartPix = xLeftOffset + plotWidth
im_drawer.rectangle(
xy=((exonStartPix, geneYLocation),
- (exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom))),
- outline = outlineColor, fill = fillColor)
+ (exonEndPix, (geneYLocation + self.EACH_GENE_HEIGHT * zoom))),
+ outline=outlineColor, fill=fillColor)
- #draw gray blocks for 3' and 5' UTR blocks
+ # draw gray blocks for 3' and 5' UTR blocks
if cdsStart and cdsEnd:
- utrStartPix = (txStart-startMb)*plotXScale + xLeftOffset
- utrEndPix = (cdsStart-startMb)*plotXScale + xLeftOffset
+ utrStartPix = (txStart - startMb) * plotXScale + xLeftOffset
+ utrEndPix = (cdsStart - startMb) * plotXScale + xLeftOffset
if (utrStartPix < xLeftOffset):
utrStartPix = xLeftOffset
if (utrEndPix < xLeftOffset):
@@ -1439,13 +1439,13 @@ class DisplayMappingResults:
labelText = "5'"
im_drawer.text(
text=labelText,
- xy=(utrStartPix-9, geneYLocation+self.EACH_GENE_HEIGHT),
+ xy=(utrStartPix - 9, geneYLocation + self.EACH_GENE_HEIGHT),
font=ImageFont.truetype(font=ARIAL_FILE, size=2))
- #the second UTR region
+ # the second UTR region
- utrStartPix = (cdsEnd-startMb)*plotXScale + xLeftOffset
- utrEndPix = (txEnd-startMb)*plotXScale + xLeftOffset
+ utrStartPix = (cdsEnd - startMb) * plotXScale + xLeftOffset
+ utrEndPix = (txEnd - startMb) * plotXScale + xLeftOffset
if (utrStartPix < xLeftOffset):
utrStartPix = xLeftOffset
if (utrEndPix < xLeftOffset):
@@ -1462,17 +1462,17 @@ class DisplayMappingResults:
labelText = "3'"
im_drawer.text(
text=labelText,
- xy=(utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT),
+ xy=(utrEndPix + 2, geneYLocation + self.EACH_GENE_HEIGHT),
font=ImageFont.truetype(font=ARIAL_FILE, size=2))
- #draw the genes as rectangles
+ # draw the genes as rectangles
else:
im_drawer.rectangle(
xy=((geneStartPix, geneYLocation),
- (geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT*zoom))),
- outline= outlineColor, fill = fillColor)
+ (geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT * zoom))),
+ outline=outlineColor, fill=fillColor)
- COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
+ COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
# NL: 06-02-2011 Rob required to display NCBI info in a new window
gifmap.append(
HtmlGenWrapper.create_area_tag(
@@ -1482,8 +1482,8 @@ class DisplayMappingResults:
title=TITLE,
target="_blank"))
-## BEGIN HaplotypeAnalyst
- def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+# BEGIN HaplotypeAnalyst
+ def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
return
@@ -1496,7 +1496,7 @@ class DisplayMappingResults:
samplelist = list(self.genotype.prgy)
- smd=[]
+ smd = []
for sample in self.sample_vals_dict.keys():
if self.sample_vals_dict[sample] != "x" and sample in samplelist:
temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
@@ -1504,24 +1504,24 @@ class DisplayMappingResults:
else:
continue
- smd.sort(key = lambda A: A.value)
+ smd.sort(key=lambda A: A.value)
smd.reverse()
oldgeneEndPix = -1
- #Initializing plotRight, error before
+ # Initializing plotRight, error before
plotRight = xRightOffset
im_drawer = ImageDraw.Draw(canvas)
-#### find out PlotRight
+# find out PlotRight
for _chr in self.genotype:
if _chr.name == self.ChrList[self.selectedChr][0]:
for i, _locus in enumerate(_chr):
txStart = _chr[i].Mb
- txEnd = _chr[i].Mb
+ txEnd = _chr[i].Mb
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) - 0
+ geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0
+ geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) - 0
drawit = 1
if (geneStartPix < xLeftOffset):
@@ -1530,27 +1530,27 @@ class DisplayMappingResults:
drawit = 0;
if drawit == 1:
- if _chr[i].name != " - " :
+ if _chr[i].name != " - ":
plotRight = geneEndPix + 4
-#### end find out PlotRight
+# end find out PlotRight
firstGene = 1
lastGene = 0
- #Sets the length to the length of the strain list. Beforehand, "oldgeno = self.genotype[0][i].genotype"
- #was the only place it was initialized, which worked as long as the very start (startMb = None/0) wasn't being mapped.
- #Now there should always be some value set for "oldgeno" - Zach 12/14/2010
- oldgeno = [None]*len(self.strainlist)
+ # Sets the length to the length of the strain list. Beforehand, "oldgeno = self.genotype[0][i].genotype"
+ # was the only place it was initialized, which worked as long as the very start (startMb = None/0) wasn't being mapped.
+ # Now there should always be some value set for "oldgeno" - Zach 12/14/2010
+ oldgeno = [None] * len(self.strainlist)
for i, _chr in enumerate(self.genotype):
if _chr.name == self.ChrList[self.selectedChr][0]:
for j, _locus in enumerate(_chr):
txStart = _chr[j].Mb
- txEnd = _chr[j].Mb
+ txEnd = _chr[j].Mb
- geneStartPix = xLeftOffset + plotXScale*(float(txStart) - startMb) - 0
- geneEndPix = xLeftOffset + plotXScale*(float(txEnd) - startMb) + 0
+ geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0
+ geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) + 0
if oldgeneEndPix >= xLeftOffset:
drawStart = oldgeneEndPix + 4
@@ -1582,36 +1582,36 @@ class DisplayMappingResults:
if drawit == 1:
myColor = DARKBLUE
outlineColor = myColor
- fillColor = myColor
+ fillColor = myColor
- maxind=0
+ maxind = 0
- #Draw Genes
+ # Draw Genes
- geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT)*zoom
+ geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT) * zoom
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
- geneYLocation += 4*self.BAND_HEIGHT + 4*self.BAND_SPACING
+ geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING
else:
- geneYLocation += 3*self.BAND_HEIGHT + 3*self.BAND_SPACING
+ geneYLocation += 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING
- if _chr[j].name != " - " :
+ if _chr[j].name != " - ":
if (firstGene == 1) and (lastGene != 1):
oldgeneEndPix = drawStart = xLeftOffset
oldgeno = _chr[j].genotype
continue
- for k, _geno in enumerate (_chr[j].genotype):
- plotbxd=0
+ for k, _geno in enumerate(_chr[j].genotype):
+ plotbxd = 0
if samplelist[k] in [item.name for item in smd]:
- plotbxd=1
+ plotbxd = 1
if (plotbxd == 1):
ind = 0
if samplelist[k] in [item.name for item in smd]:
ind = [item.name for item in smd].index(samplelist[k])
- maxind=max(ind, maxind)
+ maxind = max(ind, maxind)
# lines
if (oldgeno[k] == -1 and _geno == -1):
@@ -1621,27 +1621,27 @@ class DisplayMappingResults:
elif (oldgeno[k] == 0 and _geno == 0):
mylineColor = self.HAPLOTYPE_HETEROZYGOUS
else:
- mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown
+ mylineColor = self.HAPLOTYPE_RECOMBINATION # XZ: Unknown
im_drawer.line(
xy=((drawStart,
- geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
(drawEnd,
- geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom)),
- fill= mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
+ geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
+ fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
- fillColor=BLACK
- outlineColor=BLACK
+ fillColor = BLACK
+ outlineColor = BLACK
if lastGene == 0:
im_drawer.rectangle(
xy=((geneStartPix,
- geneYLocation+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 2 * ind*self.EACH_GENE_HEIGHT*zoom),
(geneEndPix,
- geneYLocation+2*ind*self.EACH_GENE_HEIGHT+ 2*self.EACH_GENE_HEIGHT*zoom)),
+ geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)),
outline=outlineColor, fill=fillColor)
- COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
+ COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT))
TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
HREF = ''
gifmap.append(
@@ -1658,10 +1658,10 @@ class DisplayMappingResults:
mylineColor = self.HAPLOTYPE_RECOMBINATION
im_drawer.line(
xy=((plotRight,
- geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
(drawEnd,
- geneYLocation+7+2*ind*self.EACH_GENE_HEIGHT*zoom)),
- fill= mylineColor, width=zoom*(self.EACH_GENE_HEIGHT+2))
+ geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
+ fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
if lastGene == 0:
@@ -1670,7 +1670,7 @@ class DisplayMappingResults:
font=ImageFont.truetype(font=VERDANA_FILE,
size=12),
xy=(geneStartPix,
- geneYLocation+17+2*maxind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 17 + 2*maxind*self.EACH_GENE_HEIGHT*zoom),
fill=BLACK, angle=-90)
oldgeneEndPix = geneEndPix;
@@ -1683,9 +1683,9 @@ class DisplayMappingResults:
if _chr.name == self.ChrList[self.selectedChr][0]:
for j, _geno in enumerate(_chr[1].genotype):
- plotbxd=0
+ plotbxd = 0
if samplelist[j] in [item.name for item in smd]:
- plotbxd=1
+ plotbxd = 1
if (plotbxd == 1):
ind = [item.name for item in smd].index(samplelist[j]) - 1
@@ -1695,19 +1695,19 @@ class DisplayMappingResults:
im_drawer.text(
text="%s" % (samplelist[j]),
xy=((xLeftOffset + plotWidth + 10),
- geneYLocation+11+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
font=ImageFont.truetype(font=VERDANA_FILE, size=12),
fill=BLACK)
im_drawer.text(
text="%2.2f" % (expr),
xy=((xLeftOffset + plotWidth + 60),
- geneYLocation+11+2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
font=ImageFont.truetype(font=VERDANA_FILE, size=12),
fill=BLACK)
-## END HaplotypeAnalyst
+# END HaplotypeAnalyst
- def drawClickBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ def drawClickBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1:
return
@@ -1724,12 +1724,12 @@ class DisplayMappingResults:
# but it makes the HTML huge, and takes forever to render the page in the first place)
# Draw the bands that you can click on to go to UCSC / Ensembl
MAX_CLICKABLE_REGION_DIVISIONS = 100
- clickableRegionLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=9)
- pixelStep = max(5, int(float(plotWidth)/MAX_CLICKABLE_REGION_DIVISIONS))
+ clickableRegionLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=9)
+ pixelStep = max(5, int(float(plotWidth) / MAX_CLICKABLE_REGION_DIVISIONS))
# pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome.
- numBasesCurrentlyOnScreen = self.kONE_MILLION*abs(startMb - endMb) # Number of bases on screen now
- flankingWidthInBases = int ( min( (float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION) ) )
+ numBasesCurrentlyOnScreen = self.kONE_MILLION * abs(startMb - endMb) # Number of bases on screen now
+ flankingWidthInBases = int (min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION)))
webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0
# Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing.
@@ -1739,22 +1739,22 @@ class DisplayMappingResults:
paddingTop = yTopOffset
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
phenogenPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING)
- ucscPaddingTop = paddingTop + 2*(self.BAND_HEIGHT + self.BAND_SPACING)
- ensemblPaddingTop = paddingTop + 3*(self.BAND_HEIGHT + self.BAND_SPACING)
+ ucscPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING)
+ ensemblPaddingTop = paddingTop + 3 * (self.BAND_HEIGHT + self.BAND_SPACING)
else:
ucscPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING)
- ensemblPaddingTop = paddingTop + 2*(self.BAND_HEIGHT + self.BAND_SPACING)
+ ensemblPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING)
if zoom == 1:
for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep):
- calBase = self.kONE_MILLION*(startMb + (endMb-startMb)*(pixel-xLeftOffset-0.0)/plotWidth)
+ calBase = self.kONE_MILLION * (startMb + (endMb - startMb) * (pixel - xLeftOffset - 0.0) / plotWidth)
xBrowse1 = pixel
xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
- WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop+self.BAND_HEIGHT))
- WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
+ WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT))
+ WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase - webqtlZoomWidth)) / 1000000.0, (calBase + webqtlZoomWidth) / 1000000.0)
WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
gifmap.append(
@@ -1769,15 +1769,15 @@ class DisplayMappingResults:
outline=self.CLICKABLE_WEBQTL_REGION_COLOR,
fill=self.CLICKABLE_WEBQTL_REGION_COLOR)
im_drawer.line(
- xy=((xBrowse1, paddingTop), ( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
+ xy=((xBrowse1, paddingTop), (xBrowse1, (paddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
- PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))
+ PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT))
if self.dataset.group.species == "mouse":
- PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+ PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
else:
- PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+ PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
gifmap.append(
HtmlGenWrapper.create_area_tag(
@@ -1787,18 +1787,18 @@ class DisplayMappingResults:
title=PHENOGEN_TITLE))
im_drawer.rectangle(
xy=((xBrowse1, phenogenPaddingTop),
- (xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))),
+ (xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT))),
outline=self.CLICKABLE_PHENOGEN_REGION_COLOR,
fill=self.CLICKABLE_PHENOGEN_REGION_COLOR)
im_drawer.line(
- xy=((xBrowse1, phenogenPaddingTop), ( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
+ xy=((xBrowse1, phenogenPaddingTop), (xBrowse1, (phenogenPaddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
- UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))
+ UCSC_COORDS = "%d, %d, %d, %d" % (xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT))
if self.dataset.group.species == "mouse":
- UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr)
+ UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr)
else:
- UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+ UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
gifmap.append(
HtmlGenWrapper.create_area_tag(
@@ -1808,19 +1808,19 @@ class DisplayMappingResults:
title=UCSC_TITLE))
im_drawer.rectangle(
xy=((xBrowse1, ucscPaddingTop),
- (xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))),
+ (xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT))),
outline=self.CLICKABLE_UCSC_REGION_COLOR,
fill=self.CLICKABLE_UCSC_REGION_COLOR)
im_drawer.line(
xy=((xBrowse1, ucscPaddingTop),
- (xBrowse1, (ucscPaddingTop+self.BAND_HEIGHT))),
+ (xBrowse1, (ucscPaddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
- ENSEMBL_COORDS = "%d, %d, %d, %d" %(xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))
+ ENSEMBL_COORDS = "%d, %d, %d, %d" % (xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT))
if self.dataset.group.species == "mouse":
- ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+ ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
else:
- ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
+ ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
gifmap.append(HtmlGenWrapper.create_area_tag(
shape='rect',
@@ -1829,36 +1829,36 @@ class DisplayMappingResults:
title=ENSEMBL_TITLE))
im_drawer.rectangle(
xy=((xBrowse1, ensemblPaddingTop),
- (xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))),
+ (xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT))),
outline=self.CLICKABLE_ENSEMBL_REGION_COLOR,
fill=self.CLICKABLE_ENSEMBL_REGION_COLOR)
im_drawer.line(
xy=((xBrowse1, ensemblPaddingTop),
- (xBrowse1, (ensemblPaddingTop+self.BAND_HEIGHT))),
+ (xBrowse1, (ensemblPaddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_ENSEMBL_REGION_OUTLINE_COLOR)
# end for
im_drawer.text(
text="Click to view the corresponding section of the genome in an 8x expanded WebQTL map",
- xy=((xLeftOffset + 10), paddingTop),# + self.BAND_HEIGHT/2),
+ xy=((xLeftOffset + 10), paddingTop), # + self.BAND_HEIGHT/2),
font=clickableRegionLabelFont,
fill=self.CLICKABLE_WEBQTL_TEXT_COLOR)
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
im_drawer.text(
text="Click to view the corresponding section of the genome in PhenoGen",
- xy=((xLeftOffset + 10), phenogenPaddingTop),# + self.BAND_HEIGHT/2),
+ xy=((xLeftOffset + 10), phenogenPaddingTop), # + self.BAND_HEIGHT/2),
font=clickableRegionLabelFont, fill=self.CLICKABLE_PHENOGEN_TEXT_COLOR)
im_drawer.text(
text="Click to view the corresponding section of the genome in the UCSC Genome Browser",
- xy=((xLeftOffset + 10), ucscPaddingTop),# + self.BAND_HEIGHT/2),
+ xy=((xLeftOffset + 10), ucscPaddingTop), # + self.BAND_HEIGHT/2),
font=clickableRegionLabelFont, fill=self.CLICKABLE_UCSC_TEXT_COLOR)
im_drawer.text(
text="Click to view the corresponding section of the genome in the Ensembl Genome Browser",
- xy=((xLeftOffset+10), ensemblPaddingTop),# + self.BAND_HEIGHT/2),
+ xy=((xLeftOffset + 10), ensemblPaddingTop), # + self.BAND_HEIGHT/2),
font=clickableRegionLabelFont, fill=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
- #draw the gray text
- chrFont = ImageFont.truetype(font=VERDANA_BOLD_FILE, size=26*zoom)
+ # draw the gray text
+ chrFont = ImageFont.truetype(font=VERDANA_BOLD_FILE, size=26 * zoom)
chrX = xLeftOffset + plotWidth - 2 - im_drawer.textsize(
"Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont)[0]
im_drawer.text(
@@ -1866,17 +1866,17 @@ class DisplayMappingResults:
xy=(chrX, phenogenPaddingTop), font=chrFont, fill=GRAY)
# end of drawBrowserClickableRegions
else:
- #draw the gray text
- chrFont = ImageFont.truetype(font=VERDANA_FILE, size=26*zoom)
+ # draw the gray text
+ chrFont = ImageFont.truetype(font=VERDANA_FILE, size=26 * zoom)
chrX = xLeftOffset + (plotWidth - im_drawer.textsize(
- "Chr %s" % currentChromosome, font=chrFont)[0])/2
+ "Chr %s" % currentChromosome, font=chrFont)[0]) / 2
im_drawer.text(
text="Chr %s" % currentChromosome, xy=(chrX, 32), font=chrFont,
fill=GRAY)
# end of drawBrowserClickableRegions
pass
- def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -1886,33 +1886,33 @@ class DisplayMappingResults:
if zoom == 2:
fontZoom = 1.5
- #Parameters
- NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks
+ # Parameters
+ NUM_MINOR_TICKS = 5 # Number of minor ticks between major ticks
X_MAJOR_TICK_THICKNESS = 3
X_MINOR_TICK_THICKNESS = 1
- X_AXIS_THICKNESS = 1*zoom
+ X_AXIS_THICKNESS = 1 * zoom
# ======= Alex: Draw the X-axis labels (megabase location)
- MBLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=15*zoom)
- xMajorTickHeight = 10 * zoom # How high the tick extends below the axis
- xMinorTickHeight = 5*zoom
+ MBLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=15 * zoom)
+ xMajorTickHeight = 10 * zoom # How high the tick extends below the axis
+ xMinorTickHeight = 5 * zoom
xAxisTickMarkColor = BLACK
xAxisLabelColor = BLACK
- fontHeight = 12*fontZoom # How tall the font that we're using is
+ fontHeight = 12 * fontZoom # How tall the font that we're using is
spacingFromLabelToAxis = 10
if self.plotScale == 'physic':
- strYLoc = yZero + MBLabelFont.font.height/2
- ###Physical single chromosome view
+ strYLoc = yZero + MBLabelFont.font.height / 2
+ # Physical single chromosome view
if self.selectedChr > -1:
XScale = Plot.detScale(startMb, endMb)
XStart, XEnd, XStep = XScale
if XStep < 8:
XStep *= 2
- spacingAmtX = spacingAmt = (XEnd-XStart)/XStep
+ spacingAmtX = spacingAmt = (XEnd - XStart) / XStep
j = 0
- while abs(spacingAmtX -int(spacingAmtX)) >= spacingAmtX/100.0 and j < 6:
+ while abs(spacingAmtX - int(spacingAmtX)) >= spacingAmtX / 100.0 and j < 6:
j += 1
spacingAmtX *= 10
@@ -1921,13 +1921,13 @@ class DisplayMappingResults:
for counter, _Mb in enumerate(Plot.frange(XStart, XEnd, spacingAmt / NUM_MINOR_TICKS)):
if _Mb < startMb or _Mb > endMb:
continue
- Xc = xLeftOffset + plotXScale*(_Mb - startMb)
- if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
+ Xc = xLeftOffset + plotXScale * (_Mb - startMb)
+ if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
im_drawer.line(xy=((Xc, yZero),
- (Xc, yZero+xMajorTickHeight)),
+ (Xc, yZero + xMajorTickHeight)),
fill=xAxisTickMarkColor,
- width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
- labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
+ width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
+ labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
strWidth, strHeight = im_drawer.textsize(labelStr, font=MBLabelFont)
drawStringXc = (Xc - (strWidth / 2.0))
im_drawer.text(xy=(drawStringXc, strYLoc),
@@ -1935,16 +1935,16 @@ class DisplayMappingResults:
fill=xAxisLabelColor)
else:
im_drawer.line(xy=((Xc, yZero),
- (Xc, yZero+xMinorTickHeight)),
+ (Xc, yZero + xMinorTickHeight)),
fill=xAxisTickMarkColor,
- width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
+ width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
- ###Physical genome wide view
+ # Physical genome wide view
else:
distScale = 0
startPosX = xLeftOffset
for i, distLen in enumerate(self.ChrLengthDistList):
- if distScale == 0: #universal scale in whole genome mapping
+ if distScale == 0: # universal scale in whole genome mapping
if distLen > 75:
distScale = 25
elif distLen > 30:
@@ -1953,51 +1953,51 @@ class DisplayMappingResults:
distScale = 5
for j, tickdists in enumerate(range(distScale, int(ceil(distLen)), distScale)):
im_drawer.line(
- xy=((startPosX+tickdists*plotXScale, yZero),
- (startPosX+tickdists*plotXScale, yZero + 7)),
- fill=BLACK, width=1*zoom)
+ xy=((startPosX + tickdists * plotXScale, yZero),
+ (startPosX + tickdists * plotXScale, yZero + 7)),
+ fill=BLACK, width=1 * zoom)
if j % 2 == 0:
draw_rotated_text(
canvas, text=str(tickdists), font=MBLabelFont,
- xy=(startPosX+tickdists*plotXScale,
- yZero+10*zoom), fill=BLACK, angle=270)
- startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
+ xy=(startPosX + tickdists * plotXScale,
+ yZero + 10 * zoom), fill=BLACK, angle=270)
+ startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale
- megabaseLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5))
+ megabaseLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5))
im_drawer.text(
text="Megabases",
xy=(
- xLeftOffset+(plotWidth-im_drawer.textsize(
- "Megabases", font=megabaseLabelFont)[0])/2,
- strYLoc+MBLabelFont.font.height+10*(zoom%2)),
+ xLeftOffset + (plotWidth - im_drawer.textsize(
+ "Megabases", font=megabaseLabelFont)[0]) / 2,
+ strYLoc + MBLabelFont.font.height + 10*(zoom%2)),
font=megabaseLabelFont, fill=BLACK)
pass
else:
- strYLoc = yZero + spacingFromLabelToAxis + MBLabelFont.font.height/2
+ strYLoc = yZero + spacingFromLabelToAxis + MBLabelFont.font.height / 2
ChrAInfo = []
preLpos = -1
distinctCount = 0.0
- if self.selectedChr == -1: #ZS: If viewing full genome/all chromosomes
+ if self.selectedChr == -1: # ZS: If viewing full genome/all chromosomes
for i, _chr in enumerate(self.genotype):
thisChr = []
Locus0CM = _chr[0].cM
nLoci = len(_chr)
- if nLoci <= 8:
+ if nLoci <= 8:
for _locus in _chr:
if _locus.name != ' - ':
if _locus.cM != preLpos:
distinctCount += 1
preLpos = _locus.cM
- thisChr.append([_locus.name, _locus.cM-Locus0CM])
+ thisChr.append([_locus.name, _locus.cM - Locus0CM])
else:
- for j in (0, nLoci/4, nLoci/2, nLoci*3/4, -1):
+ for j in (0, nLoci / 4, nLoci / 2, nLoci*3/4, -1):
while _chr[j].name == ' - ':
j += 1
if _chr[j].cM != preLpos:
distinctCount += 1
preLpos = _chr[j].cM
- thisChr.append([_chr[j].name, _chr[j].cM-Locus0CM])
+ thisChr.append([_chr[j].name, _chr[j].cM - Locus0CM])
ChrAInfo.append(thisChr)
else:
for i, _chr in enumerate(self.genotype):
@@ -2009,10 +2009,10 @@ class DisplayMappingResults:
if _locus.cM != preLpos:
distinctCount += 1
preLpos = _locus.cM
- thisChr.append([_locus.name, _locus.cM-Locus0CM])
+ thisChr.append([_locus.name, _locus.cM - Locus0CM])
ChrAInfo.append(thisChr)
- stepA = (plotWidth+0.0)/distinctCount
+ stepA = (plotWidth + 0.0) / distinctCount
LRectWidth = 10
LRectHeight = 3
@@ -2037,28 +2037,28 @@ class DisplayMappingResults:
Zorder = 0
if differ:
im_drawer.line(
- xy=((startPosX+Lpos, yZero), (xLeftOffset+offsetA,\
- yZero+25)),
+ xy=((startPosX + Lpos, yZero), (xLeftOffset + offsetA,\
+ yZero + 25)),
fill=lineColor)
im_drawer.line(
- xy=((xLeftOffset+offsetA, yZero+25), (xLeftOffset+offsetA,\
- yZero+40+Zorder*(LRectWidth+3))),
+ xy=((xLeftOffset + offsetA, yZero + 25), (xLeftOffset+offsetA,\
+ yZero + 40 + Zorder*(LRectWidth+3))),
fill=lineColor)
rectColor = ORANGE
else:
im_drawer.line(
- xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3), (\
- xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3))),
+ xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)-3), (\
+ xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3))),
fill=lineColor)
rectColor = DEEPPINK
im_drawer.rectangle(
- xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)),
- (xLeftOffset+offsetA-LRectHeight,
- yZero+40+Zorder*(LRectWidth+3)+LRectWidth)),
- outline=rectColor, fill=rectColor, width = 0)
- COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
- xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
- HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
+ xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)),
+ (xLeftOffset + offsetA - LRectHeight,
+ yZero + 40 + Zorder*(LRectWidth+3)+LRectWidth)),
+ outline=rectColor, fill=rectColor, width=0)
+ COORDS = "%d,%d,%d,%d" % (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
+ xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth)
+ HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name + "Geno")
#HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
Areas = HtmlGenWrapper.create_area_tag(
shape='rect',
@@ -2067,26 +2067,26 @@ class DisplayMappingResults:
target="_blank",
title="Locus : {}".format(Lname))
gifmap.append(Areas)
- ##piddle bug
+ # piddle bug
if j == 0:
im_drawer.line(
- xy=((startPosX, yZero), (startPosX, yZero+40)),
+ xy=((startPosX, yZero), (startPosX, yZero + 40)),
fill=lineColor)
- startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
+ startPosX += (self.ChrLengthDistList[j] + self.GraphInterval) * plotXScale
- centimorganLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5))
+ centimorganLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5))
im_drawer.text(
text="Centimorgans",
- xy=(xLeftOffset+(plotWidth-im_drawer.textsize(
- "Centimorgans", font=centimorganLabelFont)[0])/2,
- strYLoc + MBLabelFont.font.height+ 10*(zoom%2)),
+ xy=(xLeftOffset + (plotWidth - im_drawer.textsize(
+ "Centimorgans", font=centimorganLabelFont)[0]) / 2,
+ strYLoc + MBLabelFont.font.height + 10 * (zoom %2)),
font=centimorganLabelFont, fill=BLACK)
- im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset+plotWidth, yZero)),
- fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
+ im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset + plotWidth, yZero)),
+ fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
- def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
+ def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -2095,16 +2095,16 @@ class DisplayMappingResults:
if zoom == 2:
fontZoom = 1.5
- INTERCROSS = (self.genotype.type=="intercross")
+ INTERCROSS = (self.genotype.type == "intercross")
- #draw the LRS scale
- #We first determine whether or not we are using a sliding scale.
- #If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRS_LOD_Max.
- #LRSTop is then defined to be above the LRS_LOD_Max by enough to add one additional LRSScale increment.
- #if we are using a set-scale, then we set LRSTop to be the user's value, and LRS_LOD_Max doesn't matter.
+ # draw the LRS scale
+ # We first determine whether or not we are using a sliding scale.
+ # If so, we need to compute the maximum LRS value to determine where the max y-value should be, and call this LRS_LOD_Max.
+ # LRSTop is then defined to be above the LRS_LOD_Max by enough to add one additional LRSScale increment.
+ # if we are using a set-scale, then we set LRSTop to be the user's value, and LRS_LOD_Max doesn't matter.
- #ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD
- if self.lrsMax <= 0: #sliding scale
+ # ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD
+ if self.lrsMax <= 0: # sliding scale
if "lrs_value" in self.qtlresults[0]:
LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults])
if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
@@ -2135,34 +2135,34 @@ class DisplayMappingResults:
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
LRS_LOD_Max = max(self.significant, LRS_LOD_Max)
- #genotype trait will give infinite LRS
+ # genotype trait will give infinite LRS
LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS)
else:
LRS_LOD_Max = self.lrsMax
- #ZS: Needed to pass to genome browser
+ # ZS: Needed to pass to genome browser
js_data = json.loads(self.js_data)
if self.LRS_LOD == "LRS":
- js_data['max_score'] = LRS_LOD_Max/4.61
+ js_data['max_score'] = LRS_LOD_Max / 4.61
else:
js_data['max_score'] = LRS_LOD_Max
self.js_data = json.dumps(js_data)
- LRSScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom)
- LRSLODFont=ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5))
+ LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom)
+ LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5))
yZero = yTopOffset + plotHeight
# LRSHeightThresh = drawAreaHeight
# AdditiveHeightThresh = drawAreaHeight/2
# DominanceHeightThresh = drawAreaHeight/2
if self.selectedChr == 1:
- LRSHeightThresh = drawAreaHeight - yTopOffset + 30*(zoom - 1)
- AdditiveHeightThresh = LRSHeightThresh/2
- DominanceHeightThresh = LRSHeightThresh/2
+ LRSHeightThresh = drawAreaHeight - yTopOffset + 30 * (zoom - 1)
+ AdditiveHeightThresh = LRSHeightThresh / 2
+ DominanceHeightThresh = LRSHeightThresh / 2
else:
LRSHeightThresh = drawAreaHeight
- AdditiveHeightThresh = drawAreaHeight/2
- DominanceHeightThresh = drawAreaHeight/2
+ AdditiveHeightThresh = drawAreaHeight / 2
+ DominanceHeightThresh = drawAreaHeight / 2
# LRSHeightThresh = (yZero - yTopOffset + 30*(zoom - 1))
# AdditiveHeightThresh = LRSHeightThresh/2
# DominanceHeightThresh = LRSHeightThresh/2
@@ -2178,7 +2178,7 @@ class DisplayMappingResults:
LRSAxisList = Plot.frange(LRSScale, LRS_LOD_Max, LRSScale)
- #ZS: Convert to int if all axis values are whole numbers
+ # ZS: Convert to int if all axis values are whole numbers
all_int = True
for item in LRSAxisList:
if isinstance(item, int):
@@ -2192,9 +2192,9 @@ class DisplayMappingResults:
# else:
# max_lrs_width = canvas.stringWidth("%2.1f" % LRS_LOD_Max, font=LRSScaleFont) + 30
- #draw the "LRS" or "LOD" string to the left of the axis
- LRSScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom)
- LRSLODFont=ImageFont.truetype(font=VERDANA_FILE, size=int(18*zoom*1.5))
+ # draw the "LRS" or "LOD" string to the left of the axis
+ LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom)
+ LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5))
yZero = yTopOffset + plotHeight
# TEXT_X_DISPLACEMENT = -20
@@ -2210,64 +2210,64 @@ class DisplayMappingResults:
draw_rotated_text(
canvas, text=self.LRS_LOD, font=LRSLODFont,
xy=(xLeftOffset - im_drawer.textsize(
- "999.99", font=LRSScaleFont)[0] - 15*(zoom-1) + TEXT_X_DISPLACEMENT,
- yZero + TEXT_Y_DISPLACEMENT - 300*(zoom - 1)),
+ "999.99", font=LRSScaleFont)[0] - 15 * (zoom - 1) + TEXT_X_DISPLACEMENT,
+ yZero + TEXT_Y_DISPLACEMENT - 300 * (zoom - 1)),
fill=BLACK, angle=90)
for item in LRSAxisList:
if LRS_LOD_Max == 0.0:
LRS_LOD_Max = 0.000001
- yTopOffset + 30*(zoom - 1)
- yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh
- im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset-4, yLRS)),
- fill=self.LRS_COLOR, width=1*zoom)
+ yTopOffset + 30 * (zoom - 1)
+ yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh
+ im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset - 4, yLRS)),
+ fill=self.LRS_COLOR, width=1 * zoom)
if all_int:
scaleStr = "%d" % item
else:
scaleStr = "%2.1f" % item
- #Draw the LRS/LOD Y axis label
+ # Draw the LRS/LOD Y axis label
TEXT_Y_DISPLACEMENT = -10
im_drawer.text(
text=scaleStr,
- xy=(xLeftOffset-4-im_drawer.textsize(scaleStr, font=LRSScaleFont)[0]-5,
- yLRS+TEXT_Y_DISPLACEMENT),
+ xy=(xLeftOffset - 4 - im_drawer.textsize(scaleStr, font=LRSScaleFont)[0]-5,
+ yLRS + TEXT_Y_DISPLACEMENT),
font=LRSScaleFont, fill=self.LRS_COLOR)
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
- significantY = yZero - self.significant*LRSHeightThresh/LRS_LOD_Max
- suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRS_LOD_Max
+ significantY = yZero - self.significant * LRSHeightThresh / LRS_LOD_Max
+ suggestiveY = yZero - self.suggestive * LRSHeightThresh / LRS_LOD_Max
# significantY = yZero - self.significant*LRSHeightThresh/LRSAxisList[-1]
# suggestiveY = yZero - self.suggestive*LRSHeightThresh/LRSAxisList[-1]
startPosX = xLeftOffset
- #"Significant" and "Suggestive" Drawing Routine
+ # "Significant" and "Suggestive" Drawing Routine
# ======= Draw the thick lines for "Significant" and "Suggestive" ===== (crowell: I tried to make the SNPs draw over these lines, but piddle wouldn't have it...)
- #ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function
+ # ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function
def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist):
- rightEdge = int(start_pos_x + chr_length_dist*plotXScale - self.SUGGESTIVE_WIDTH/1.5)
+ rightEdge = int(start_pos_x + chr_length_dist * plotXScale - self.SUGGESTIVE_WIDTH / 1.5)
im_drawer.line(
- xy=((start_pos_x+self.SUGGESTIVE_WIDTH/1.5, suggestiveY),
+ xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, suggestiveY),
(rightEdge, suggestiveY)),
- fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH*zoom
- #,clipX=(xLeftOffset, xLeftOffset + plotWidth-2)
+ fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH * zoom
+ # ,clipX=(xLeftOffset, xLeftOffset + plotWidth-2)
)
im_drawer.line(
- xy=((start_pos_x+self.SUGGESTIVE_WIDTH/1.5, significantY),
+ xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, significantY),
(rightEdge, significantY)),
fill=self.SIGNIFICANT_COLOR,
- width=self.SIGNIFICANT_WIDTH*zoom
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth-2)
+ width=self.SIGNIFICANT_WIDTH * zoom
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth-2)
)
- sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY-2, rightEdge + 2*zoom, suggestiveY+2)
- sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY-2, rightEdge + 2*zoom, significantY+2)
+ sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY - 2, rightEdge + 2 * zoom, suggestiveY + 2)
+ sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY - 2, rightEdge + 2 * zoom, significantY + 2)
if self.LRS_LOD == 'LRS':
sugg_title = "Suggestive LRS = %0.2f" % self.suggestive
sig_title = "Significant LRS = %0.2f" % self.significant
else:
- sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
- sig_title = "Significant LOD = %0.2f" % (self.significant/4.61)
+ sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive / 4.61)
+ sig_title = "Significant LOD = %0.2f" % (self.significant / 4.61)
Areas1 = HtmlGenWrapper.create_area_tag(
shape='rect',
coords=sugg_coords,
@@ -2279,7 +2279,7 @@ class DisplayMappingResults:
gifmap.append(Areas1)
gifmap.append(Areas2)
- start_pos_x += (chr_length_dist+self.GraphInterval)*plotXScale
+ start_pos_x += (chr_length_dist + self.GraphInterval) * plotXScale
return start_pos_x
for i, _chr in enumerate(self.genotype):
@@ -2306,7 +2306,7 @@ class DisplayMappingResults:
AdditiveCoordXY = []
DominanceCoordXY = []
- symbolFont = ImageFont.truetype(font=FNT_BS_FILE, size=5) #ZS: For Manhattan Plot
+ symbolFont = ImageFont.truetype(font=FNT_BS_FILE, size=5) # ZS: For Manhattan Plot
previous_chr = 1
previous_chr_as_int = 0
@@ -2332,128 +2332,128 @@ class DisplayMappingResults:
minusColor = self.ADDITIVE_COLOR_NEGATIVE
for k, aPoint in enumerate(AdditiveCoordXY):
if k > 0:
- Xc0, Yc0 = AdditiveCoordXY[k-1]
+ Xc0, Yc0 = AdditiveCoordXY[k - 1]
Xc, Yc = aPoint
- if (Yc0-yZero)*(Yc-yZero) < 0:
- if Xc == Xc0: #genotype , locus distance is 0
+ if (Yc0 - yZero) * (Yc-yZero) < 0:
+ if Xc == Xc0: # genotype , locus distance is 0
Xcm = Xc
else:
- Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
+ Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0
if Yc0 < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xcm, yZero)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
im_drawer.line(
- xy=((Xcm, yZero), (Xc, yZero-(Yc-yZero))),
+ xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
im_drawer.line(
- xy=((Xc0, yZero-(Yc0-yZero)),
+ xy=((Xc0, yZero - (Yc0 - yZero)),
(Xcm, yZero)),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
im_drawer.line(
xy=((Xcm, yZero), (Xc, Yc)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
- elif (Yc0-yZero)*(Yc-yZero) > 0:
+ elif (Yc0 - yZero) * (Yc-yZero) > 0:
if Yc < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xc, Yc)),
fill=plusColor,
width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
im_drawer.line(
- xy=((Xc0, yZero - (Yc0-yZero)),
- (Xc, yZero - (Yc-yZero))),
+ xy=((Xc0, yZero - (Yc0 - yZero)),
+ (Xc, yZero - (Yc - yZero))),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
- minYc = min(Yc-yZero, Yc0-yZero)
+ minYc = min(Yc - yZero, Yc0 - yZero)
if minYc < 0:
im_drawer.line(
xy=((Xc0, Yc0), (Xc, Yc)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
im_drawer.line(
- xy=((Xc0, yZero - (Yc0-yZero)),
- (Xc, yZero - (Yc-yZero))),
+ xy=((Xc0, yZero - (Yc0 - yZero)),
+ (Xc, yZero - (Yc - yZero))),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
LRSCoordXY = []
AdditiveCoordXY = []
previous_chr = qtlresult['chr']
previous_chr_as_int += 1
- newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1]+self.GraphInterval)*plotXScale
+ newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1] + self.GraphInterval) * plotXScale
if newStartPosX != oldStartPosX:
startPosX += newStartPosX
oldStartPosX = newStartPosX
- #ZS: This is because the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used
+ # ZS: This is because the chromosome value stored in qtlresult['chr'] can be (for example) either X or 20 depending upon the mapping method/scale used
this_chr = str(self.ChrList[self.selectedChr][0])
if self.plotScale != "physic":
- this_chr = str(self.ChrList[self.selectedChr][1]+1)
+ this_chr = str(self.ChrList[self.selectedChr][1] + 1)
if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
if self.plotScale != "physic" and self.mapping_method == "reaper" and not self.manhattan_plot:
- Xc = startPosX + (qtlresult['cM']-startMb)*plotXScale
+ Xc = startPosX + (qtlresult['cM'] - startMb) * plotXScale
if hasattr(self.genotype, "filler"):
if self.genotype.filler:
if self.selectedChr != -1:
start_cm = self.genotype[self.selectedChr - 1][0].cM
- Xc = startPosX + (qtlresult['Mb'] - start_cm)*plotXScale
+ Xc = startPosX + (qtlresult['Mb'] - start_cm) * plotXScale
else:
start_cm = self.genotype[previous_chr_as_int][0].cM
- Xc = startPosX + ((qtlresult['Mb']-start_cm-startMb)*plotXScale)*(((qtlresult['Mb']-start_cm-startMb)*plotXScale)/((qtlresult['Mb']-start_cm-startMb+self.GraphInterval)*plotXScale))
+ Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * (((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale))
else:
- Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
+ Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale
# updated by NL 06-18-2011:
# fix the over limit LRS graph issue since genotype trait may give infinite LRS;
# for any lrs is over than 460(LRS max in this system), it will be reset to 460
- yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh
+ yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh
if 'lrs_value' in qtlresult:
if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
- if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
+ if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR)
- Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR)
+ Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR)
else:
#Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR)
- Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRS_LOD_Max*self.LODFACTOR)
+ Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR)
else:
- if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
+ if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1]
- Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
+ Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max
else:
#Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1]
- Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
+ Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / LRS_LOD_Max
else:
- if qtlresult['lod_score'] > 100 or qtlresult['lod_score']=='inf':
+ if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf':
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1]
- Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRS_LOD_Max
+ Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max
else:
if self.LRS_LOD == "LRS":
#Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1]
- Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRS_LOD_Max
+ Yc = yZero - qtlresult['lod_score'] * self.LODFACTOR * LRSHeightThresh / LRS_LOD_Max
else:
#Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1]
- Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRS_LOD_Max
+ Yc = yZero - qtlresult['lod_score'] * LRSHeightThresh / LRS_LOD_Max
if self.manhattan_plot == True:
if self.color_scheme == "single":
@@ -2469,8 +2469,8 @@ class DisplayMappingResults:
im_drawer.text(
text="5",
xy=(
- Xc-im_drawer.textsize("5", font=symbolFont)[0]/2+1,
- Yc-4),
+ Xc - im_drawer.textsize("5", font=symbolFont)[0] / 2 + 1,
+ Yc - 4),
fill=point_color, font=symbolFont)
else:
LRSCoordXY.append((Xc, Yc))
@@ -2478,7 +2478,7 @@ class DisplayMappingResults:
if not self.multipleInterval and self.additiveChecked:
if additiveMax == 0.0:
additiveMax = 0.000001
- Yc = yZero - qtlresult['additive']*AdditiveHeightThresh/additiveMax
+ Yc = yZero - qtlresult['additive'] * AdditiveHeightThresh / additiveMax
AdditiveCoordXY.append((Xc, Yc))
m += 1
@@ -2497,64 +2497,64 @@ class DisplayMappingResults:
minusColor = self.ADDITIVE_COLOR_NEGATIVE
for k, aPoint in enumerate(AdditiveCoordXY):
if k > 0:
- Xc0, Yc0 = AdditiveCoordXY[k-1]
+ Xc0, Yc0 = AdditiveCoordXY[k - 1]
Xc, Yc = aPoint
- if (Yc0-yZero)*(Yc-yZero) < 0:
- if Xc == Xc0: #genotype , locus distance is 0
+ if (Yc0 - yZero) * (Yc-yZero) < 0:
+ if Xc == Xc0: # genotype , locus distance is 0
Xcm = Xc
else:
- Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
+ Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0
if Yc0 < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xcm, yZero)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
im_drawer.line(
- xy=((Xcm, yZero), (Xc, yZero-(Yc-yZero))),
+ xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
im_drawer.line(
- xy=((Xc0, yZero - (Yc0-yZero)),
+ xy=((Xc0, yZero - (Yc0 - yZero)),
(Xcm, yZero)),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
im_drawer.line(
xy=((Xcm, yZero), (Xc, Yc)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
- elif (Yc0-yZero)*(Yc-yZero) > 0:
+ elif (Yc0 - yZero) * (Yc-yZero) > 0:
if Yc < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor,
width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
im_drawer.line(
- xy=((Xc0, yZero-(Yc0-yZero)),
- (Xc, yZero-(Yc-yZero))),
+ xy=((Xc0, yZero - (Yc0 - yZero)),
+ (Xc, yZero - (Yc - yZero))),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
- minYc = min(Yc-yZero, Yc0-yZero)
+ minYc = min(Yc - yZero, Yc0 - yZero)
if minYc < 0:
im_drawer.line(
xy=((Xc0, Yc0), (Xc, Yc)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
im_drawer.line(
- xy=((Xc0, yZero - (Yc0-yZero)),
- (Xc, yZero - (Yc-yZero))),
+ xy=((Xc0, yZero - (Yc0 - yZero)),
+ (Xc, yZero - (Yc - yZero))),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
if not self.multipleInterval and INTERCROSS and self.dominanceChecked:
@@ -2562,114 +2562,114 @@ class DisplayMappingResults:
minusColor = self.DOMINANCE_COLOR_NEGATIVE
for k, aPoint in enumerate(DominanceCoordXY):
if k > 0:
- Xc0, Yc0 = DominanceCoordXY[k-1]
+ Xc0, Yc0 = DominanceCoordXY[k - 1]
Xc, Yc = aPoint
- if (Yc0-yZero)*(Yc-yZero) < 0:
- if Xc == Xc0: #genotype , locus distance is 0
+ if (Yc0 - yZero) * (Yc-yZero) < 0:
+ if Xc == Xc0: # genotype , locus distance is 0
Xcm = Xc
else:
- Xcm = (yZero-Yc0)/((Yc-Yc0)/(Xc-Xc0)) +Xc0
+ Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0
if Yc0 < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xcm, yZero)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
im_drawer.line(
- xy=((Xcm, yZero), (Xc, yZero-(Yc-yZero))),
+ xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
im_drawer.line(
- xy=((Xc0, yZero - (Yc0-yZero)), (Xcm, yZero)),
+ xy=((Xc0, yZero - (Yc0 - yZero)), (Xcm, yZero)),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
im_drawer.line(
xy=((Xcm, yZero), (Xc, Yc)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
- elif (Yc0-yZero)*(Yc-yZero) > 0:
+ elif (Yc0 - yZero) * (Yc-yZero) > 0:
if Yc < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xc, Yc)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
im_drawer.line(
- xy=((Xc0, yZero - (Yc0-yZero)),
- (Xc, yZero - (Yc-yZero))),
+ xy=((Xc0, yZero - (Yc0 - yZero)),
+ (Xc, yZero - (Yc - yZero))),
fill=minusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
- minYc = min(Yc-yZero, Yc0-yZero)
+ minYc = min(Yc - yZero, Yc0 - yZero)
if minYc < 0:
im_drawer.line(
xy=((Xc0, Yc0), (Xc, Yc)),
fill=plusColor, width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
else:
im_drawer.line(
- xy=((Xc0, yZero - (Yc0-yZero)),
- (Xc, yZero - (Yc-yZero))), fill=minusColor,
+ xy=((Xc0, yZero - (Yc0 - yZero)),
+ (Xc, yZero - (Yc - yZero))), fill=minusColor,
width=lineWidth
- #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
+ # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
- ###draw additive scale
+ # draw additive scale
if not self.multipleInterval and self.additiveChecked:
- additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom)
+ additiveScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom)
additiveScale = Plot.detScaleOld(0, additiveMax)
- additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
+ additiveStep = (additiveScale[1] - additiveScale[0]) / additiveScale[2]
additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
- addPlotScale = AdditiveHeightThresh/additiveMax
+ addPlotScale = AdditiveHeightThresh / additiveMax
TEXT_Y_DISPLACEMENT = -8
additiveAxisList.append(additiveScale[1])
for item in additiveAxisList:
- additiveY = yZero - item*addPlotScale
+ additiveY = yZero - item * addPlotScale
im_drawer.line(
xy=((xLeftOffset + plotWidth, additiveY),
- (xLeftOffset+4+ plotWidth, additiveY)),
- fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
+ (xLeftOffset + 4 + plotWidth, additiveY)),
+ fill=self.ADDITIVE_COLOR_POSITIVE, width=1 * zoom)
scaleStr = "%2.3f" % item
im_drawer.text(
text=scaleStr,
- xy=(xLeftOffset + plotWidth +6, additiveY+TEXT_Y_DISPLACEMENT),
+ xy= (xLeftOffset + plotWidth + 6, additiveY + TEXT_Y_DISPLACEMENT),
font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE)
im_drawer.line(
- xy=((xLeftOffset+plotWidth, additiveY),
- (xLeftOffset+plotWidth, yZero)),
- fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
+ xy=((xLeftOffset + plotWidth, additiveY),
+ (xLeftOffset + plotWidth, yZero)),
+ fill=self.ADDITIVE_COLOR_POSITIVE, width=1 * zoom)
im_drawer.line(
- xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30*(zoom - 1))),
- fill=self.LRS_COLOR, width=1*zoom) #the blue line running up the y axis
+ xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30 * (zoom - 1))),
+ fill=self.LRS_COLOR, width=1 * zoom) # the blue line running up the y axis
- def drawGraphBackground(self, canvas, gifmap, offset= (80, 120, 80, 50), zoom = 1, startMb = None, endMb = None):
- ##conditions
- ##multiple Chromosome view
- ##single Chromosome Physical
- ##single Chromosome Genetic
+ def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb= None, endMb = None):
+ # conditions
+ # multiple Chromosome view
+ # single Chromosome Physical
+ # single Chromosome Genetic
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
- yBottom = yTopOffset+plotHeight
+ yBottom = yTopOffset + plotHeight
fontZoom = zoom
if zoom == 2:
fontZoom = 1.5
yTopOffset += 30
- #calculate plot scale
+ # calculate plot scale
if self.plotScale != 'physic':
self.ChrLengthDistList = self.ChrLengthCMList
drawRegionDistance = self.ChrLengthCMSum
@@ -2677,10 +2677,10 @@ class DisplayMappingResults:
self.ChrLengthDistList = self.ChrLengthMbList
drawRegionDistance = self.ChrLengthMbSum
- if self.selectedChr > -1: #single chromosome view
- spacingAmt = plotWidth/13.5
+ if self.selectedChr > -1: # single chromosome view
+ spacingAmt = plotWidth / 13.5
i = 0
- for startPix in Plot.frange(xLeftOffset, xLeftOffset+plotWidth, spacingAmt):
+ for startPix in Plot.frange(xLeftOffset, xLeftOffset + plotWidth, spacingAmt):
if (i % 2 == 0):
theBackColor = self.GRAPH_BACK_DARK_COLOR
else:
@@ -2688,25 +2688,25 @@ class DisplayMappingResults:
i += 1
im_drawer.rectangle(
[(startPix, yTopOffset),
- (min(startPix+spacingAmt, xLeftOffset+plotWidth), yBottom)],
+ (min(startPix + spacingAmt, xLeftOffset + plotWidth), yBottom)],
outline=theBackColor, fill=theBackColor)
drawRegionDistance = self.ChrLengthDistList[self.ChrList[self.selectedChr][1]]
self.ChrLengthDistList = [drawRegionDistance]
if self.plotScale == 'physic':
- plotXScale = plotWidth / (endMb-startMb)
+ plotXScale = plotWidth / (endMb - startMb)
else:
plotXScale = plotWidth / drawRegionDistance
- else: #multiple chromosome view
- plotXScale = plotWidth / ((len(self.genotype)-1)*self.GraphInterval + drawRegionDistance)
+ else: # multiple chromosome view
+ plotXScale = plotWidth / ((len(self.genotype) - 1) * self.GraphInterval + drawRegionDistance)
startPosX = xLeftOffset
if fontZoom == 1.5:
chrFontZoom = 2
else:
chrFontZoom = 1
- chrLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=24*chrFontZoom)
+ chrLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=24 * chrFontZoom)
for i, _chr in enumerate(self.genotype):
if (i % 2 == 0):
@@ -2714,23 +2714,23 @@ class DisplayMappingResults:
else:
theBackColor = self.GRAPH_BACK_LIGHT_COLOR
- #draw the shaded boxes and the sig/sug thick lines
+ # draw the shaded boxes and the sig/sug thick lines
im_drawer.rectangle(
((startPosX, yTopOffset),
- (startPosX + self.ChrLengthDistList[i]*plotXScale, yBottom)),
+ (startPosX + self.ChrLengthDistList[i] * plotXScale, yBottom)),
outline=GAINSBORO,
fill=theBackColor)
chrNameWidth, chrNameHeight = im_drawer.textsize(_chr.name, font=chrLabelFont)
- chrStartPix = startPosX + (self.ChrLengthDistList[i]*plotXScale -chrNameWidth)/2
- chrEndPix = startPosX + (self.ChrLengthDistList[i]*plotXScale +chrNameWidth)/2
+ chrStartPix = startPosX + (self.ChrLengthDistList[i] * plotXScale - chrNameWidth) / 2
+ chrEndPix = startPosX + (self.ChrLengthDistList[i] * plotXScale + chrNameWidth) / 2
TEXT_Y_DISPLACEMENT = 0
im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT),
text=_chr.name, font=chrLabelFont, fill=BLACK)
- COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix, yTopOffset +20)
+ COORDS = "%d,%d,%d,%d" % (chrStartPix, yTopOffset, chrEndPix, yTopOffset + 20)
- #add by NL 09-03-2010
+ # add by NL 09-03-2010
HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList)
#HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
Areas = HtmlGenWrapper.create_area_tag(
@@ -2738,7 +2738,7 @@ class DisplayMappingResults:
coords=COORDS,
href=HREF)
gifmap.append(Areas)
- startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
+ startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale
return plotXScale
@@ -2748,15 +2748,15 @@ class DisplayMappingResults:
#########################################
myCanvas = Image.new("RGBA", size=(500, 300))
if 'lod_score' in self.qtlresults[0] and self.LRS_LOD == "LRS":
- perm_output = [value*4.61 for value in self.perm_output]
+ perm_output = [value * 4.61 for value in self.perm_output]
elif 'lod_score' not in self.qtlresults[0] and self.LRS_LOD == "LOD":
- perm_output = [value/4.61 for value in self.perm_output]
+ perm_output = [value / 4.61 for value in self.perm_output]
else:
perm_output = self.perm_output
- filename= webqtlUtil.genRandStr("Reg_")
+ filename = webqtlUtil.genRandStr("Reg_")
Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test')
- myCanvas.save("{}.gif".format(GENERATED_IMAGE_DIR+filename),
+ myCanvas.save("{}.gif".format(GENERATED_IMAGE_DIR + filename),
format='gif')
return filename
@@ -2821,18 +2821,18 @@ class DisplayMappingResults:
tableIterationsCnt = tableIterationsCnt + 1
- this_row = [] #container for the cells of each row
+ this_row = [] # container for the cells of each row
selectCheck = HtmlGenWrapper.create_input_tag(
type_="checkbox",
name="selectCheck",
value=theGO["GeneSymbol"],
Class="checkbox trait_checkbox") # checkbox for each row
- geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0
- tenPercentLength = geneLength*0.0001
+ geneLength = (theGO["TxEnd"] - theGO["TxStart"]) * 1000.0
+ tenPercentLength = geneLength * 0.0001
txStart = theGO["TxStart"]
txEnd = theGO["TxEnd"]
- theGO["snpDensity"] = theGO["snpCount"]/geneLength
+ theGO["snpDensity"] = theGO["snpCount"] / geneLength
if self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST:
geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"]
@@ -2844,16 +2844,16 @@ class DisplayMappingResults:
f"end={theGO['TxEnd']}&"
f"geneName={theGO['GeneSymbol']}&"
f"s1={self.diffCol[0]}&s2=%d"),
- str(theGO["snpCount"]) # The text to display
+ str(theGO["snpCount"]) # The text to display
)
snpString.set_blank_target()
snpString.set_attribute("class", "normalsize")
else:
snpString = 0
- mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"]*1000000.0)) +"&pix=620&Submit=submit"
+ mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit"
- #the chromosomes for human 1 are 1qXX.XX
+ # the chromosomes for human 1 are 1qXX.XX
if theGO['humanGene']:
if theGO['humanGene']["TxStart"] == '':
humanStartDisplay = ""
@@ -2863,20 +2863,20 @@ class DisplayMappingResults:
humanChr = theGO['humanGene']["Chromosome"]
humanTxStart = theGO['humanGene']["TxStart"]
- humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000*theGO['humanGene']["TxStart"]), int(1000000*theGO['humanGene']["TxEnd"]))
+ humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000 * theGO['humanGene']["TxStart"]), int(1000000 * theGO['humanGene']["TxEnd"]))
else:
humanStartString = humanChr = humanStartDisplay = "--"
geneDescription = theGO["GeneDescription"]
if len(geneDescription) > 70:
- geneDescription = geneDescription[:70]+"..."
+ geneDescription = geneDescription[:70] + "..."
if theGO["snpDensity"] < 0.000001:
snpDensityStr = "0"
else:
snpDensityStr = "%0.6f" % theGO["snpDensity"]
- avgExpr = [] #theGO["avgExprVal"]
+ avgExpr = [] # theGO["avgExprVal"]
if avgExpr in ([], None):
avgExpr = "--"
else:
@@ -2905,8 +2905,8 @@ class DisplayMappingResults:
str(HtmlGenWrapper.create_link_tag(
"javascript:rangeView('{}', {:f}, {:f})".format(
str(chr_as_int),
- txStart-tenPercentLength,
- txEnd+tenPercentLength),
+ txStart - tenPercentLength,
+ txEnd + tenPercentLength),
"{:.3f}".format(geneLength))),
snpString,
snpDensityStr,
@@ -2931,8 +2931,8 @@ class DisplayMappingResults:
str(HtmlGenWrapper.create_link_tag(
"javascript:rangeView('{}', {:f}, {:f})".format(
str(chr_as_int),
- txStart-tenPercentLength,
- txEnd+tenPercentLength),
+ txStart - tenPercentLength,
+ txEnd + tenPercentLength),
"{:.3f}".format(geneLength))),
snpString,
snpDensityStr,
@@ -2969,7 +2969,7 @@ class DisplayMappingResults:
chr_as_int = int(theGO["Chromosome"]) - 1
geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
- geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"])-(geneLength*0.1), float(theGO["TxEnd"])+(geneLength*0.1))
+ geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1))
avgExprVal = []
if avgExprVal != "" and avgExprVal:
@@ -2977,14 +2977,14 @@ class DisplayMappingResults:
else:
avgExprVal = ""
- #Mouse Gene
+ # Mouse Gene
if theGO['mouseGene']:
mouseChr = theGO['mouseGene']["Chromosome"]
mouseTxStart = "%0.6f" % theGO['mouseGene']["TxStart"]
else:
mouseChr = mouseTxStart = ""
- #the chromosomes for human 1 are 1qXX.XX
+ # the chromosomes for human 1 are 1qXX.XX
if theGO['humanGene']:
humanChr = theGO['humanGene']["Chromosome"]
humanTxStart = "%0.6f" % theGO['humanGene']["TxStart"]
@@ -2996,12 +2996,12 @@ class DisplayMappingResults:
geneDesc = ""
this_row = [selectCheck.__str__(),
- str(gIndex+1),
+ str(gIndex + 1),
geneSymbolNCBI,
"%0.6f" % theGO["TxStart"],
str(HtmlGenWrapper.create_link_tag(
geneLengthURL,
- "{:.3f}".format(geneLength*1000.0))),
+ "{:.3f}".format(geneLength * 1000.0))),
avgExprVal,
mouseChr,
mouseTxStart,
@@ -3013,7 +3013,7 @@ class DisplayMappingResults:
return gene_table_body
- def getLiteratureCorrelation(cursor,geneId1=None,geneId2=None):
+ def getLiteratureCorrelation(cursor, geneId1=None, geneId2=None):
if not geneId1 or not geneId2:
return None
if geneId1 == geneId2:
@@ -3025,9 +3025,9 @@ class DisplayMappingResults:
query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s'
for x, y in [(geneId1, geneId2), (geneId2, geneId1)]:
cursor.execute(query, (x, y))
- lCorr = cursor.fetchone()
+ lCorr = cursor.fetchone()
if lCorr:
lCorr = lCorr[0]
break
- except: raise #lCorr = None
+ except: raise # lCorr = None
return lCorr
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 06c9300a..68689104 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -149,7 +149,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
dataset_name = covariate.split(":")[1]
if dataset_name == "Temp":
temp_group = trait_name.split("_")[2]
- dataset_ob = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+ dataset_ob = create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = temp_group)
else:
dataset_ob = create_dataset(covariate.split(":")[1])
trait_ob = create_trait(dataset=dataset_ob,
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 5d675c38..e6c78536 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -6,7 +6,7 @@ from utility import webqtlUtil
from utility.tools import flat_files, PLINK_COMMAND
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
def run_plink(this_trait, dataset, species, vals, maf):
plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_")
@@ -34,7 +34,7 @@ def gen_pheno_txt_file(this_dataset, vals):
split_line = line.split()
current_file_data.append(split_line)
- with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam","w") as outfile:
+ with open(f"{flat_files('mapping')}/{this_dataset.group.name}.fam", "w") as outfile:
for i, line in enumerate(current_file_data):
if vals[i] == "x":
this_val = -9
@@ -42,7 +42,7 @@ def gen_pheno_txt_file(this_dataset, vals):
this_val = vals[i]
outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
-def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
+def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''):
ped_sample_list = get_samples_from_ped_file(dataset)
output_file = open(f"{TMPDIR}{pheno_filename}.txt", "wb")
header = f"FID\tIID\t{this_trait.name}\n"
@@ -50,7 +50,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
new_value_list = []
- #if valueDict does not include some strain, value will be set to -9999 as missing value
+ # if valueDict does not include some strain, value will be set to -9999 as missing value
for i, sample in enumerate(ped_sample_list):
try:
value = vals[i]
@@ -63,11 +63,11 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
new_line = ''
for i, sample in enumerate(ped_sample_list):
- j = i+1
+ j = i + 1
value = new_value_list[i]
new_line += f"{sample}\t{sample}\t{value}\n"
- if j%1000 == 0:
+ if j % 1000 == 0:
output_file.write(newLine)
new_line = ''
@@ -78,9 +78,9 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
# get strain name from ped file in order
def get_samples_from_ped_file(dataset):
- ped_file= open(f"{flat_files('mapping')}{dataset.group.name}.ped","r")
+ ped_file = open(f"{flat_files('mapping')}{dataset.group.name}.ped", "r")
line = ped_file.readline()
- sample_list=[]
+ sample_list = []
while line:
lineList = line.strip().split('\t')
@@ -94,24 +94,24 @@ def get_samples_from_ped_file(dataset):
return sample_list
def parse_plink_output(output_filename, species):
- plink_results={}
+ plink_results = {}
threshold_p_value = 1
- result_fp = open(f"{TMPDIR}{output_filename}.qassoc","rb")
+ result_fp = open(f"{TMPDIR}{output_filename}.qassoc", "rb")
line = result_fp.readline()
- value_list = [] # initialize value list, this list will include snp, bp and pvalue info
+ value_list = [] # initialize value list, this list will include snp, bp and pvalue info
p_value_dict = {}
count = 0
while line:
- #convert line from str to list
+ # convert line from str to list
line_list = build_line_list(line=line)
# only keep the records whose chromosome name is in db
- if int(line_list[0]) in species.chromosomes.chromosomes and line_list[-1] and line_list[-1].strip()!='NA':
+ if int(line_list[0]) in species.chromosomes.chromosomes and line_list[-1] and line_list[-1].strip() != 'NA':
chr_name = species.chromosomes.chromosomes[int(line_list[0])]
snp = line_list[1]
@@ -125,7 +125,7 @@ def parse_plink_output(output_filename, species):
value_list = plink_results[chr_name]
# pvalue range is [0,1]
- if threshold_p_value >=0 and threshold_p_value <= 1:
+ if threshold_p_value >= 0 and threshold_p_value <= 1:
if p_value < threshold_p_value:
value_list.append((snp, BP, p_value))
count += 1
@@ -141,7 +141,7 @@ def parse_plink_output(output_filename, species):
if value_list:
plink_results[chr_name] = value_list
- value_list=[]
+ value_list = []
line = result_fp.readline()
else:
@@ -155,8 +155,8 @@ def parse_plink_output(output_filename, species):
# output: lineList list
#######################################################
def build_line_list(line=""):
- line_list = line.strip().split(' ')# irregular number of whitespaces between columns
- line_list = [item for item in line_list if item !='']
+ line_list = line.strip().split(' ') # irregular number of whitespaces between columns
+ line_list = [item for item in line_list if item != '']
line_list = [item.strip() for item in line_list]
return line_list
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 8341ee55..dd044cb0 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -6,7 +6,7 @@ from base.data_set import create_dataset
from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None):
"""Generates p-values for each marker using qtlreaper"""
@@ -17,10 +17,10 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
else:
genofile_name = this_dataset.group.name
- trait_filename =f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno"
+ trait_filename = f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno"
gen_pheno_txt_file(samples, vals, trait_filename)
- output_filename = (f"{this_dataset.group.name}_GWA_"+
+ output_filename = (f"{this_dataset.group.name}_GWA_" +
''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
)
bootstrap_filename = None
@@ -36,7 +36,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list.append(f"--n_bootstrap {str(num_bootstrap)}")
opt_list.append(f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
if num_perm > 0:
- permu_filename =("{this_dataset.group.name}_PERM_" +
+ permu_filename = ("{this_dataset.group.name}_PERM_" +
''.join(random.choice(string.ascii_uppercase +
string.digits) for _ in range(6))
)
@@ -67,8 +67,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
suggestive = 0
significant = 0
if len(permu_vals) > 0:
- suggestive = permu_vals[int(num_perm*0.37-1)]
- significant = permu_vals[int(num_perm*0.95-1)]
+ suggestive = permu_vals[int(num_perm * 0.37 - 1)]
+ significant = permu_vals[int(num_perm * 0.95 - 1)]
return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals,
[output_filename, permu_filename, bootstrap_filename])
@@ -76,7 +76,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
def gen_pheno_txt_file(samples, vals, trait_filename):
"""Generates phenotype file for GEMMA"""
- with open(f"{TEMPDIR}/gn2/{trait_filename}.txt","w") as outfile:
+ with open(f"{TEMPDIR}/gn2/{trait_filename}.txt", "w") as outfile:
outfile.write("Trait\t")
filtered_sample_list = []
@@ -121,7 +121,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
marker['cM'] = float(line.split("\t")[3])
else:
if float(line.split("\t")[3]) > 1000:
- marker['Mb'] = float(line.split("\t")[3])/1000000
+ marker['Mb'] = float(line.split("\t")[3]) / 1000000
else:
marker['Mb'] = float(line.split("\t")[3])
if float(line.split("\t")[6]) != 1:
@@ -132,7 +132,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
else:
marker['cM'] = float(line.split("\t")[3])
if float(line.split("\t")[4]) > 1000:
- marker['Mb'] = float(line.split("\t")[4])/1000000
+ marker['Mb'] = float(line.split("\t")[4]) / 1000000
else:
marker['Mb'] = float(line.split("\t")[4])
if float(line.split("\t")[7]) != 1:
@@ -142,7 +142,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
marker['additive'] = float(line.split("\t")[6])
marker_obs.append(marker)
- #ZS: Results have to be reordered because the new reaper returns results sorted alphabetically by chr for some reason, resulting in chr 1 being followed by 10, etc
+ # ZS: Results have to be reordered because the new reaper returns results sorted alphabetically by chr for some reason, resulting in chr 1 being followed by 10, etc
sorted_indices = natural_sort(marker_obs)
permu_vals = []
@@ -185,18 +185,18 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
suggestive = 0
significant = 0
else:
- perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=num_perm)
- suggestive = perm_output[int(num_perm*0.37-1)]
- significant = perm_output[int(num_perm*0.95-1)]
- #highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case
+ perm_output = genotype.permutation(strains=trimmed_samples, trait=trimmed_values, nperm=num_perm)
+ suggestive = perm_output[int(num_perm * 0.37 - 1)]
+ significant = perm_output[int(num_perm * 0.95 - 1)]
+ # highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case
json_data['suggestive'] = suggestive
json_data['significant'] = significant
if control_marker != "" and do_control == "true":
- reaper_results = genotype.regression(strains = trimmed_samples,
- trait = trimmed_values,
- control = str(control_marker))
+ reaper_results = genotype.regression(strains=trimmed_samples,
+ trait=trimmed_values,
+ control=str(control_marker))
if bootCheck:
control_geno = []
control_geno2 = []
@@ -215,31 +215,31 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
_idx = _prgy.index(_strain)
control_geno.append(control_geno2[_idx])
- bootstrap_results = genotype.bootstrap(strains = trimmed_samples,
- trait = trimmed_values,
- control = control_geno,
- nboot = num_bootstrap)
+ bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
+ trait=trimmed_values,
+ control=control_geno,
+ nboot=num_bootstrap)
else:
- reaper_results = genotype.regression(strains = trimmed_samples,
- trait = trimmed_values)
+ reaper_results = genotype.regression(strains=trimmed_samples,
+ trait=trimmed_values)
if bootCheck:
- bootstrap_results = genotype.bootstrap(strains = trimmed_samples,
- trait = trimmed_values,
- nboot = num_bootstrap)
+ bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
+ trait=trimmed_values,
+ nboot=num_bootstrap)
json_data['chr'] = []
json_data['pos'] = []
json_data['lod.hk'] = []
json_data['markernames'] = []
- #if self.additive:
+ # if self.additive:
# self.json_data['additive'] = []
- #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+ # Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
qtl_results = []
for qtl in reaper_results:
reaper_locus = qtl.locus
- #ZS: Convert chr to int
+ # ZS: Convert chr to int
converted_chr = reaper_locus.chr
if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y":
converted_chr = int(reaper_locus.chr)
@@ -247,11 +247,11 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
json_data['pos'].append(reaper_locus.Mb)
json_data['lod.hk'].append(qtl.lrs)
json_data['markernames'].append(reaper_locus.name)
- #if self.additive:
+ # if self.additive:
# self.json_data['additive'].append(qtl.additive)
- locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb}
- qtl = {"lrs_value": qtl.lrs, "chr":converted_chr, "Mb":reaper_locus.Mb,
- "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive, "dominance":qtl.dominance}
+ locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, "cM": reaper_locus.cM, "Mb": reaper_locus.Mb}
+ qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb,
+ "cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance}
qtl_results.append(qtl)
return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results
@@ -261,5 +261,5 @@ def natural_sort(marker_list):
Changed to return indices instead of values, though, since the same reordering needs to be applied to bootstrap results
"""
convert = lambda text: int(text) if text.isdigit() else text.lower()
- alphanum_key = lambda key: [ convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr'])) ]
- return sorted(list(range(len(marker_list))), key = alphanum_key)
\ No newline at end of file
+ alphanum_key = lambda key: [convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr']))]
+ return sorted(list(range(len(marker_list))), key=alphanum_key)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 4117a0e5..2bd94512 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -13,7 +13,7 @@ from utility.tools import locate, TEMPDIR
from flask import g
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
# Get a trait's type (numeric, categorical, etc) from the DB
def get_trait_data_type(trait_db_string):
@@ -35,29 +35,29 @@ def get_trait_data_type(trait_db_string):
# Run qtl mapping using R/qtl
def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permCheck, num_perm, perm_strata_list, do_control, control_marker, manhattan_plot, pair_scan, cofactors):
logger.info("Start run_rqtl_geno");
- ## Get pointers to some common R functions
- r_library = ro.r["library"] # Map the library function
- r_c = ro.r["c"] # Map the c function
- plot = ro.r["plot"] # Map the plot function
- png = ro.r["png"] # Map the png function
- dev_off = ro.r["dev.off"] # Map the device off function
+ # Get pointers to some common R functions
+ r_library = ro.r["library"] # Map the library function
+ r_c = ro.r["c"] # Map the c function
+ plot = ro.r["plot"] # Map the plot function
+ png = ro.r["png"] # Map the png function
+ dev_off = ro.r["dev.off"] # Map the device off function
print((r_library("qtl"))) # Load R/qtl
logger.info("QTL library loaded");
- ## Get pointers to some R/qtl functions
- scanone = ro.r["scanone"] # Map the scanone function
- scantwo = ro.r["scantwo"] # Map the scantwo function
- calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function
+ # Get pointers to some R/qtl functions
+ scanone = ro.r["scanone"] # Map the scanone function
+ scantwo = ro.r["scantwo"] # Map the scantwo function
+ calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function
crossname = dataset.group.name
- #try:
+ # try:
# generate_cross_from_rdata(dataset)
# read_cross_from_rdata = ro.r["generate_cross_from_rdata"] # Map the local read_cross_from_rdata function
# genofilelocation = locate(crossname + ".RData", "genotype/rdata")
# cross_object = read_cross_from_rdata(genofilelocation) # Map the local GENOtoCSVR function
- #except:
+ # except:
if mapping_scale == "morgan":
scale_units = "cM"
@@ -65,10 +65,10 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
scale_units = "Mb"
generate_cross_from_geno(dataset, scale_units)
- GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
+ GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
crossfilelocation = TMPDIR + crossname + ".cross"
if dataset.group.genofile:
- genofilelocation = locate(dataset.group.genofile, "genotype")
+ genofilelocation = locate(dataset.group.genofile, "genotype")
else:
genofilelocation = locate(dataset.group.name + ".geno", "genotype")
logger.info("Going to create a cross from geno");
@@ -95,38 +95,38 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
else:
ro.r('all_covars <- marker_covars')
covars = ro.r['all_covars']
- #DEBUG to save the session object to file
+ # DEBUG to save the session object to file
if pair_scan:
if do_control == "true":
- logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method, n_cluster = 16)
+ logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16)
else:
- logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=model, method=method, n_cluster = 16)
+ logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno="the_pheno", model=model, method=method, n_cluster=16)
pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
- png(file=TEMPDIR+pair_scan_filename)
+ png(file=TEMPDIR + pair_scan_filename)
plot(result_data_frame)
dev_off()
return process_pair_scan_results(result_data_frame)
else:
if do_control == "true" or cofactors != "":
- logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covars, model=model, method=method)
+ logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method)
ro.r('save.image(file = "/home/zas1024/gn2-zach/itp_cofactor_test.RData")')
else:
- logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=model, method=method)
+ logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno="the_pheno", model=model, method=method)
if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user)
- if len(perm_strata_list) > 0: #ZS: The strata list would only be populated if "Stratified" was checked on before mapping
+ if len(perm_strata_list) > 0: # ZS: The strata list would only be populated if "Stratified" was checked on before mapping
cross_object, strata_ob = add_perm_strata(cross_object, perm_strata_list)
if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method)
+ perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method)
else:
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, perm_strata = strata_ob, model=model, method=method)
+ perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method)
else:
if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covars, n_perm = int(num_perm), model=model, method=method)
+ perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), model=model, method=method)
else:
- perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
+ perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, model=model, method=method)
perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species)
@@ -134,7 +134,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
return process_rqtl_results(result_data_frame, dataset.group.species)
def generate_cross_from_rdata(dataset):
- rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
+ rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
ro.r("""
generate_cross_from_rdata <- function(filename = '%s') {
load(file=filename)
@@ -206,7 +206,7 @@ def sanitize_rqtl_phenotype(vals):
for i, val in enumerate(vals):
if val == "x":
if i < (len(vals) - 1):
- pheno_as_string += "NA,"
+ pheno_as_string += "NA,"
else:
pheno_as_string += "NA"
else:
@@ -223,7 +223,7 @@ def sanitize_rqtl_names(vals):
for i, val in enumerate(vals):
if val == "x":
if i < (len(vals) - 1):
- pheno_as_string += "NA,"
+ pheno_as_string += "NA,"
else:
pheno_as_string += "NA"
else:
@@ -238,7 +238,7 @@ def sanitize_rqtl_names(vals):
def add_phenotype(cross, pheno_as_string, col_name):
ro.globalenv["the_cross"] = cross
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
- ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric('+ pheno_as_string +'))')
+ ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric(' + pheno_as_string + '))')
return ro.r["the_cross"]
def add_categorical_covar(cross, covar_as_string, i):
@@ -256,8 +256,8 @@ def add_categorical_covar(cross, covar_as_string, i):
nCol = int(nCol[0])
logger.info("nCol python int:" + str(nCol));
col_names = []
- #logger.info("loop")
- for x in range(1, (nCol+1)):
+ # logger.info("loop")
+ for x in range(1, (nCol + 1)):
#logger.info("loop" + str(x));
col_name = "covar_" + str(i) + "_" + str(x)
#logger.info("col_name" + col_name);
@@ -272,12 +272,12 @@ def add_categorical_covar(cross, covar_as_string, i):
def add_names(cross, names_as_string, col_name):
ro.globalenv["the_cross"] = cross
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
- ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = '+ names_as_string +')')
+ ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = ' + names_as_string + ')')
return ro.r["the_cross"]
def pull_var(var_name, cross, var_string):
ro.globalenv["the_cross"] = cross
- ro.r(var_name +' <- pull.pheno(the_cross, ' + var_string + ')')
+ ro.r(var_name + ' <- pull.pheno(the_cross, ' + var_string + ')')
return ro.r[var_name]
@@ -317,15 +317,15 @@ def add_cofactors(cross, this_dataset, covariates, samples):
datatype = get_trait_data_type(covariate)
logger.info("Covariate: " + covariate + " is of type: " + datatype);
- if(datatype == "categorical"): # Cat variable
+ if(datatype == "categorical"): # Cat variable
logger.info("call of add_categorical_covar");
- cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross
+ cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross
logger.info("add_categorical_covar returned");
- for z, col_name in enumerate(col_names): # Go through the additional covar names
+ for z, col_name in enumerate(col_names): # Go through the additional covar names
if i < (len(covariate_list) - 1):
covar_name_string += '"' + col_name + '", '
else:
- if(z < (len(col_names) -1)):
+ if(z < (len(col_names) - 1)):
covar_name_string += '"' + col_name + '", '
else:
covar_name_string += '"' + col_name + '"'
@@ -376,7 +376,7 @@ def process_pair_scan_results(result):
def process_rqtl_perm_results(num_perm, results):
perm_vals = []
- for line in str(results).split("\n")[1:(num_perm+1)]:
+ for line in str(results).split("\n")[1:(num_perm + 1)]:
#print("R/qtl permutation line:", line.split())
perm_vals.append(float(line.split()[1]))
@@ -393,7 +393,7 @@ def process_rqtl_results(result, species_name): # TODO: how to make this
for i, line in enumerate(result.iter_row()):
marker = {}
marker['name'] = result.rownames[i]
- if species_name == "mouse" and output[i][0] == 20: #ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file
+ if species_name == "mouse" and output[i][0] == 20: # ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file
marker['chr'] = "X"
else:
marker['chr'] = output[i][0]
@@ -402,4 +402,4 @@ def process_rqtl_results(result, species_name): # TODO: how to make this
marker['lod_score'] = output[i][2]
qtl_results.append(marker)
- return qtl_results
\ No newline at end of file
+ return qtl_results
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 7dd0bcb6..f1665570 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -1,5 +1,5 @@
from base.trait import GeneralTrait
-from base import data_set #import create_dataset
+from base import data_set # import create_dataset
from pprint import pformat as pf
@@ -43,16 +43,16 @@ from utility.external import shell
from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
class RunMapping:
def __init__(self, start_vars, temp_uuid):
helper_functions.get_species_dataset_trait(self, start_vars)
- self.temp_uuid = temp_uuid #needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py)
+ self.temp_uuid = temp_uuid # needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py)
- #ZS: Needed to zoom in or remap temp traits like PCA traits
+ # ZS: Needed to zoom in or remap temp traits like PCA traits
if "temp_trait" in start_vars and start_vars['temp_trait'] != "False":
self.temp_trait = "True"
self.group = self.dataset.group.name
@@ -60,7 +60,7 @@ class RunMapping:
self.json_data = {}
self.json_data['lodnames'] = ['lod.hk']
- #ZS: Sometimes a group may have a genofile that only includes a subset of samples
+ # ZS: Sometimes a group may have a genofile that only includes a subset of samples
genofile_samplelist = []
if 'genofile' in start_vars:
if start_vars['genofile'] != "":
@@ -93,7 +93,7 @@ class RunMapping:
else:
self.n_samples = len([val for val in self.vals if val != "x"])
- #ZS: Check if genotypes exist in the DB in order to create links for markers
+ # ZS: Check if genotypes exist in the DB in order to create links for markers
self.geno_db_exists = geno_db_exists(self.dataset)
@@ -114,19 +114,19 @@ class RunMapping:
self.manhattan_single_color = start_vars['manhattan_single_color']
self.manhattan_plot = True
- self.maf = start_vars['maf'] # Minor allele frequency
+ self.maf = start_vars['maf'] # Minor allele frequency
if "use_loco" in start_vars:
self.use_loco = start_vars['use_loco']
else:
self.use_loco = None
self.suggestive = ""
self.significant = ""
- self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
+ self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
if 'transform' in start_vars:
self.transform = start_vars['transform']
else:
self.transform = ""
- self.score_type = "LRS" #ZS: LRS or LOD
+ self.score_type = "LRS" # ZS: LRS or LOD
self.mapping_scale = "physic"
if "mapping_scale" in start_vars:
self.mapping_scale = start_vars['mapping_scale']
@@ -136,10 +136,10 @@ class RunMapping:
self.covariates = start_vars['covariates'] if "covariates" in start_vars else ""
self.categorical_vars = []
- #ZS: This is passed to GN1 code for single chr mapping
+ # ZS: This is passed to GN1 code for single chr mapping
self.selected_chr = -1
if "selected_chr" in start_vars:
- if int(start_vars['selected_chr']) != -1: #ZS: Needs to be -1 if showing full map; there's probably a better way to fix this
+ if int(start_vars['selected_chr']) != -1: # ZS: Needs to be -1 if showing full map; there's probably a better way to fix this
self.selected_chr = int(start_vars['selected_chr']) + 1
else:
self.selected_chr = int(start_vars['selected_chr'])
@@ -153,7 +153,7 @@ class RunMapping:
self.lrsMax = start_vars['lrsMax']
if "haplotypeAnalystCheck" in start_vars:
self.haplotypeAnalystCheck = start_vars['haplotypeAnalystCheck']
- if "startMb" in start_vars: #ZS: This is to ensure showGenes, Legend, etc are checked the first time you open the mapping page, since startMb will only not be set during the first load
+ if "startMb" in start_vars: # ZS: This is to ensure showGenes, Legend, etc are checked the first time you open the mapping page, since startMb will only not be set during the first load
if "permCheck" in start_vars:
self.permCheck = "ON"
else:
@@ -191,13 +191,13 @@ class RunMapping:
self.showGenes = "ON"
self.viewLegend = "ON"
- #self.dataset.group.get_markers()
+ # self.dataset.group.get_markers()
if self.mapping_method == "gemma":
self.first_run = True
self.output_files = None
if 'output_files' in start_vars:
self.output_files = start_vars['output_files']
- if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
+ if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
self.first_run = False
self.score_type = "-logP"
self.manhattan_plot = True
@@ -214,9 +214,9 @@ class RunMapping:
if "perm_strata" in start_vars and "categorical_vars" in start_vars:
self.categorical_vars = start_vars["categorical_vars"].split(",")
if len(self.categorical_vars) and start_vars["perm_strata"] == "True":
- primary_samples = SampleList(dataset = self.dataset,
- sample_names = self.samples,
- this_trait = self.this_trait)
+ primary_samples = SampleList(dataset=self.dataset,
+ sample_names=self.samples,
+ this_trait=self.this_trait)
perm_strata = get_perm_strata(self.this_trait, primary_samples, self.categorical_vars, self.samples)
self.score_type = "LOD"
@@ -227,14 +227,14 @@ class RunMapping:
else:
self.method = "em"
self.model = start_vars['mapmodel_rqtl_geno']
- #if start_vars['pair_scan'] == "true":
+ # if start_vars['pair_scan'] == "true":
# self.pair_scan = True
if self.permCheck and self.num_perm > 0:
- self.perm_output, self.suggestive, self.significant, results= rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
else:
results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
elif self.mapping_method == "reaper":
- if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
+ if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON
if "additiveCheck" in start_vars:
self.additiveCheck = start_vars['additiveCheck']
else:
@@ -267,7 +267,7 @@ class RunMapping:
if self.reaper_version == "new":
self.first_run = True
self.output_files = None
- if 'first_run' in start_vars: #ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
+ if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
self.first_run = False
if 'output_files' in start_vars:
self.output_files = start_vars['output_files'].split(",")
@@ -311,7 +311,7 @@ class RunMapping:
else:
if self.pair_scan == True:
self.qtl_results = []
- highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
+ highest_chr = 1 # This is needed in order to convert the highest chr to X/Y
for marker in results:
if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
@@ -328,51 +328,51 @@ class RunMapping:
self.json_data['markernames'].append(qtl['name'])
self.js_data = dict(
- json_data = self.json_data,
- this_trait = self.this_trait.name,
- data_set = self.dataset.name,
- maf = self.maf,
- manhattan_plot = self.manhattan_plot,
- mapping_scale = self.mapping_scale,
- qtl_results = self.qtl_results
+ json_data=self.json_data,
+ this_trait=self.this_trait.name,
+ data_set=self.dataset.name,
+ maf=self.maf,
+ manhattan_plot=self.manhattan_plot,
+ mapping_scale=self.mapping_scale,
+ qtl_results=self.qtl_results
)
else:
self.qtl_results = []
self.results_for_browser = []
self.annotations_for_browser = []
- highest_chr = 1 #This is needed in order to convert the highest chr to X/Y
+ highest_chr = 1 # This is needed in order to convert the highest chr to X/Y
for marker in results:
if 'Mb' in marker:
- this_ps = marker['Mb']*1000000
+ this_ps = marker['Mb'] * 1000000
else:
- this_ps = marker['cM']*1000000
+ this_ps = marker['cM'] * 1000000
browser_marker = dict(
- chr = str(marker['chr']),
- rs = marker['name'],
- ps = this_ps,
- url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno"
+ chr=str(marker['chr']),
+ rs=marker['name'],
+ ps=this_ps,
+ url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno"
)
if self.geno_db_exists == "True":
annot_marker = dict(
- name = str(marker['name']),
- chr = str(marker['chr']),
- rs = marker['name'],
- pos = this_ps,
- url = "/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno"
+ name=str(marker['name']),
+ chr=str(marker['chr']),
+ rs=marker['name'],
+ pos=this_ps,
+ url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno"
)
else:
annot_marker = dict(
- name = str(marker['name']),
- chr = str(marker['chr']),
- rs = marker['name'],
- pos = this_ps
+ name=str(marker['name']),
+ chr=str(marker['chr']),
+ rs=marker['name'],
+ pos=this_ps
)
if 'lrs_value' in marker and marker['lrs_value'] > 0:
- browser_marker['p_wald'] = 10**-(marker['lrs_value']/4.61)
+ browser_marker['p_wald'] = 10**-(marker['lrs_value'] / 4.61)
elif 'lod_score' in marker and marker['lod_score'] > 0:
browser_marker['p_wald'] = 10**-(marker['lod_score'])
else:
@@ -417,7 +417,7 @@ class RunMapping:
chr_lengths = get_chr_lengths(self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results)
- #ZS: For zooming into genome browser, need to pass chromosome name instead of number
+ # ZS: For zooming into genome browser, need to pass chromosome name instead of number
if self.dataset.group.species == "mouse":
if self.selected_chr == 20:
this_chr = "X"
@@ -451,29 +451,29 @@ class RunMapping:
#mapping_scale = self.mapping_scale,
#chromosomes = chromosome_mb_lengths,
#qtl_results = self.qtl_results,
- categorical_vars = self.categorical_vars,
- chr_lengths = chr_lengths,
- num_perm = self.num_perm,
- perm_results = self.perm_output,
- significant = significant_for_browser,
- browser_files = browser_files,
- selected_chr = this_chr,
- total_markers = total_markers
+ categorical_vars=self.categorical_vars,
+ chr_lengths=chr_lengths,
+ num_perm=self.num_perm,
+ perm_results=self.perm_output,
+ significant=significant_for_browser,
+ browser_files=browser_files,
+ selected_chr=this_chr,
+ total_markers=total_markers
)
else:
self.js_data = dict(
- chr_lengths = chr_lengths,
- browser_files = browser_files,
- selected_chr = this_chr,
- total_markers = total_markers
+ chr_lengths=chr_lengths,
+ browser_files=browser_files,
+ selected_chr=this_chr,
+ total_markers=total_markers
)
def run_rqtl_plink(self):
# os.chdir("") never do this inside a webserver!!
- output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))
+ output_filename = webqtlUtil.genRandStr("%s_%s_" % (self.dataset.group.name, self.this_trait.name))
- plink_mapping.gen_pheno_txt_file_plink(self.this_trait, self.dataset, self.vals, pheno_filename = output_filename)
+ plink_mapping.gen_pheno_txt_file_plink(self.this_trait, self.dataset, self.vals, pheno_filename=output_filename)
rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename)
@@ -612,11 +612,11 @@ def trim_markers_for_figure(markers):
if low_counter % 20 == 0:
filtered_markers.append(marker)
low_counter += 1
- elif 4.61 <= marker[score_type] < (2*4.61):
+ elif 4.61 <= marker[score_type] < (2 * 4.61):
if med_counter % 10 == 0:
filtered_markers.append(marker)
med_counter += 1
- elif (2*4.61) <= marker[score_type] <= (3*4.61):
+ elif (2 * 4.61) <= marker[score_type] <= (3 * 4.61):
if high_counter % 2 == 0:
filtered_markers.append(marker)
high_counter += 1
@@ -630,7 +630,7 @@ def trim_markers_for_table(markers):
else:
sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True)
- #ZS: So we end up with a list of just 2000 markers
+ # ZS: So we end up with a list of just 2000 markers
if len(sorted_markers) >= 2000:
trimmed_sorted_markers = sorted_markers[:2000]
return trimmed_sorted_markers
@@ -682,9 +682,9 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
highest_pos = float(result['cM']) * 1000000
else:
highest_pos = float(result['Mb']) * 1000000
- chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)})
+ chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)})
else:
- chr_lengths.append({ "chr": str(this_chr), "size": str(highest_pos)})
+ chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)})
this_chr = chr_as_num
else:
if mapping_method == "reaper":
@@ -721,7 +721,7 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
perm_strata_strings.append(combined_string)
- d = dict([(y, x+1) for x, y in enumerate(sorted(set(perm_strata_strings)))])
+ d = dict([(y, x + 1) for x, y in enumerate(sorted(set(perm_strata_strings)))])
list_to_numbers = [d[x] for x in perm_strata_strings]
perm_strata = list_to_numbers
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 772f74e4..8abd6516 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -29,14 +29,14 @@ class User(Base):
registration_info = Column(Text) # json detailing when they were registered, etc.
- confirmed = Column(Text) # json detailing when they confirmed, etc.
+ confirmed = Column(Text) # json detailing when they confirmed, etc.
- superuser = Column(Text) # json detailing when they became a superuser, otherwise empty
+ superuser = Column(Text) # json detailing when they became a superuser, otherwise empty
# if not superuser
logins = relationship("Login",
order_by="desc(Login.timestamp)",
- lazy='dynamic', # Necessary for filter in login_count
+ lazy='dynamic', # Necessary for filter in login_count
foreign_keys="Login.user",
)
@@ -67,7 +67,7 @@ class User(Base):
def get_collection_by_name(self, collection_name):
try:
collect = self.user_collections.filter_by(name=collection_name).first()
- except sqlalchemy.orm.exc.NoResultFound:
+ except sqlalchemy.orm.exc.NoResultFound:
collect = None
return collect
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index dcd328c9..dfd374e2 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -22,7 +22,7 @@ import re
from pprint import pformat as pf
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
def parse(pstring):
"""
@@ -52,7 +52,7 @@ def parse(pstring):
if '(' in value or '[' in value:
assert value.startswith(("(", "[")), "Invalid token"
assert value.endswith((")", "]")), "Invalid token"
- value = value[1:-1] # Get rid of the parenthesis
+ value = value[1:-1] # Get rid of the parenthesis
values = re.split(r"""\s+|,""", value)
value = [value.strip() for value in values if value.strip()]
else:
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 7d51a83d..a1fe0f8f 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -26,7 +26,7 @@ def manage_resource():
owner_display_name = None
if owner_id != "none":
- try: #ZS: User IDs are sometimes stored in Redis as bytes and sometimes as strings, so this is just to avoid any errors for the time being
+ try: # ZS: User IDs are sometimes stored in Redis as bytes and sometimes as strings, so this is just to avoid any errors for the time being
owner_id = str.encode(owner_id)
except:
pass
@@ -38,7 +38,7 @@ def manage_resource():
elif 'email_address' in owner_info:
owner_display_name = owner_info['email_address']
- return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status)
+ return render_template("admin/manage_resource.html", owner_name=owner_display_name, resource_id=resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status)
@app.route("/search_for_users", methods=('POST',))
def search_for_user():
@@ -79,7 +79,7 @@ def change_owner():
flash("You lack the permissions to make this change.", "error")
return redirect(url_for("manage_resource", resource_id=resource_id))
else:
- return render_template("admin/change_resource_owner.html", resource_id = resource_id)
+ return render_template("admin/change_resource_owner.html", resource_id=resource_id)
@app.route("/resources/change_default_privileges", methods=('POST',))
def change_default_privileges():
@@ -108,7 +108,7 @@ def add_group_to_resource():
group_id = request.form['selected_group']
resource_info = get_resource_info(resource_id)
default_privileges = resource_info['default_mask']
- return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id, default_privileges = default_privileges)
+ return render_template("admin/set_group_privileges.html", resource_id=resource_id, group_id=group_id, default_privileges = default_privileges)
elif all(key in request.form for key in ('data_privilege', 'metadata_privilege', 'admin_privilege')):
group_id = request.form['group_id']
group_name = get_group_info(group_id)['name']
@@ -121,7 +121,7 @@ def add_group_to_resource():
flash("Privileges have been added for group {}.".format(group_name), "alert-info")
return redirect(url_for("manage_resource", resource_id=resource_id))
else:
- return render_template("admin/search_for_groups.html", resource_id = resource_id)
+ return render_template("admin/search_for_groups.html", resource_id=resource_id)
else:
return redirect(url_for("no_access_page"))
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index fd7c132b..16eb1864 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -22,7 +22,7 @@ from utility.tools import GN2_BASE_URL
from utility.type_checking import is_str
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
class SearchResultPage:
#maxReturn = 3000
@@ -39,7 +39,7 @@ class SearchResultPage:
self.uc_id = uuid.uuid4()
self.go_term = None
- logger.debug("uc_id:", self.uc_id) # contains a unique id
+ logger.debug("uc_id:", self.uc_id) # contains a unique id
logger.debug("kw is:", kw) # dict containing search terms
if kw['search_terms_or']:
@@ -72,7 +72,7 @@ class SearchResultPage:
self.dataset = create_dataset(kw['dataset'], dataset_type)
logger.debug("search_terms:", self.search_terms)
- #ZS: I don't like using try/except, but it seems like the easiest way to account for all possible bad searches here
+ # ZS: I don't like using try/except, but it seems like the easiest way to account for all possible bad searches here
try:
self.search()
except:
@@ -183,7 +183,7 @@ class SearchResultPage:
combined_from_clause = ""
combined_where_clause = ""
- previous_from_clauses = [] #The same table can't be referenced twice in the from clause
+ previous_from_clauses = [] # The same table can't be referenced twice in the from clause
logger.debug("len(search_terms)>1")
symbol_list = []
@@ -231,7 +231,7 @@ class SearchResultPage:
combined_from_clause += from_clause
where_clause = the_search.get_where_clause()
combined_where_clause += "(" + where_clause + ")"
- if (i+1) < len(self.search_terms):
+ if (i + 1) < len(self.search_terms):
if self.and_or == "and":
combined_where_clause += "AND"
else:
@@ -291,7 +291,7 @@ def insert_newlines(string, every=64):
""" This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """
lines = []
for i in range(0, len(string), every):
- lines.append(string[i:i+every])
+ lines.append(string[i:i + every])
return '\n'.join(lines)
def get_aliases(symbol_list, species):
@@ -322,9 +322,9 @@ def get_aliases(symbol_list, species):
search_terms = []
for alias in filtered_aliases:
- the_search_term = {'key': None,
+ the_search_term = {'key': None,
'search_term': [alias],
- 'separator' : None}
+ 'separator': None}
search_terms.append(the_search_term)
return search_terms
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index f955f632..388f831f 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -36,16 +36,16 @@ class SampleList:
if isinstance(self.this_trait, list):
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
if counter <= len(self.this_trait):
- if isinstance(self.this_trait[counter-1], (bytes, bytearray)):
- if (self.this_trait[counter-1].decode("utf-8").lower() != 'x'):
+ if isinstance(self.this_trait[counter - 1], (bytes, bytearray)):
+ if (self.this_trait[counter - 1].decode("utf-8").lower() != 'x'):
sample = webqtlCaseData.webqtlCaseData(
name=sample_name,
- value=float(self.this_trait[counter-1]))
+ value=float(self.this_trait[counter - 1]))
else:
- if (self.this_trait[counter-1].lower() != 'x'):
+ if (self.this_trait[counter - 1].lower() != 'x'):
sample = webqtlCaseData.webqtlCaseData(
name=sample_name,
- value=float(self.this_trait[counter-1]))
+ value=float(self.this_trait[counter - 1]))
else:
# ZS - If there's no value for the sample/strain,
# create the sample object (so samples with no value
@@ -69,7 +69,7 @@ class SampleList:
sample.extra_attributes = self.sample_attribute_values.get(
sample_name, {})
- #ZS: Add a url so RRID case attributes can be displayed as links
+ # ZS: Add a url so RRID case attributes can be displayed as links
if 'rrid' in sample.extra_attributes:
if self.dataset.group.species == "mouse":
if len(sample.extra_attributes['rrid'].split(":")) > 1:
@@ -129,7 +129,7 @@ class SampleList:
self.attributes[key].name = name
self.attributes[key].distinct_values = [
item.Value for item in values]
- self.attributes[key].distinct_values=natural_sort(self.attributes[key].distinct_values)
+ self.attributes[key].distinct_values = natural_sort(self.attributes[key].distinct_values)
all_numbers = True
for value in self.attributes[key].distinct_values:
try:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index f9c5fbe6..18cadea4 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -46,7 +46,7 @@ class ShowTrait:
resource_id=self.resource_id)
elif 'group' in kw:
self.temp_trait = True
- self.trait_id = "Temp_"+kw['species'] + "_" + kw['group'] + \
+ self.trait_id = "Temp_" + kw['species'] + "_" + kw['group'] + \
"_" + datetime.datetime.now().strftime("%m%d%H%M%S")
self.temp_species = kw['species']
self.temp_group = kw['group']
@@ -368,8 +368,8 @@ class ShowTrait:
chr = transcript_start = transcript_end = None
if chr and transcript_start and transcript_end and self.this_trait.refseq_transcriptid:
- transcript_start = int(transcript_start*1000000)
- transcript_end = int(transcript_end*1000000)
+ transcript_start = int(transcript_start * 1000000)
+ transcript_end = int(transcript_end * 1000000)
self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % (
'mm10', self.this_trait.refseq_transcriptid, chr, transcript_start, transcript_end)
@@ -393,8 +393,8 @@ class ShowTrait:
if chr and transcript_start and transcript_end and kgId:
# Convert to bases from megabases
- transcript_start = int(transcript_start*1000000)
- transcript_end = int(transcript_end*1000000)
+ transcript_start = int(transcript_start * 1000000)
+ transcript_end = int(transcript_end * 1000000)
self.ucsc_blat_link = webqtlConfig.UCSC_REFSEQ % (
'rn6', kgId, chr, transcript_start, transcript_end)
@@ -515,13 +515,13 @@ def quantile_normalize_vals(sample_groups):
ranked_vals = ss.rankdata(trait_vals)
p_list = []
for i, val in enumerate(trait_vals):
- p_list.append(((i+1) - 0.5)/len(trait_vals))
+ p_list.append(((i + 1) - 0.5) / len(trait_vals))
z = ss.norm.ppf(p_list)
normed_vals = []
for rank in ranked_vals:
- normed_vals.append("%0.3f" % z[int(rank)-1])
+ normed_vals.append("%0.3f" % z[int(rank) - 1])
return normed_vals
@@ -585,7 +585,7 @@ def get_nearest_marker(this_trait, this_db):
GenoXRef.GenoId = Geno.Id AND
GenoFreeze.Id = GenoXRef.GenoFreezeId AND
GenoFreeze.Name = '{}'
- ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb)
+ ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name + "Geno", this_mb)
logger.sql(query)
result = g.db.execute(query).fetchall()
@@ -605,7 +605,7 @@ def get_table_widths(sample_groups, sample_column_width, has_num_cases=False):
trait_table_width += 80
if has_num_cases:
trait_table_width += 80
- trait_table_width += len(sample_groups[0].attributes)*88
+ trait_table_width += len(sample_groups[0].attributes) * 88
trait_table_width = str(trait_table_width) + "px"
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 8658abf8..7a0df94b 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -26,9 +26,9 @@ class SnpBrowser:
self.table_rows = []
if self.limit_strains == "true":
- self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
+ self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns)
else:
- self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
+ self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
def initialize_parameters(self, start_vars):
if 'first_run' in start_vars:
@@ -249,7 +249,7 @@ class SnpBrowser:
def filter_results(self, results):
filtered_results = []
- strain_index_list = [] #ZS: List of positions of selected strains in strain list
+ strain_index_list = [] # ZS: List of positions of selected strains in strain list
last_mb = -1
if self.limit_strains == "true" and len(self.chosen_strains) > 0:
@@ -272,9 +272,9 @@ class SnpBrowser:
if self.limit_strains == "true" and len(self.chosen_strains) > 0:
for index in strain_index_list:
if self.species_id == 1:
- display_strains.append(result[29+index])
+ display_strains.append(result[29 + index])
elif self.species_id == 2:
- display_strains.append(result[31+index])
+ display_strains.append(result[31 + index])
self.allele_list = display_strains
effect_info_dict = get_effect_info(effect_list)
@@ -300,7 +300,7 @@ class SnpBrowser:
else:
gene = check_if_in_gene(species_id, chr, mb)
transcript = exon = function = function_details = ''
- if self.redundant == "false" or last_mb != mb: # filter redundant
+ if self.redundant == "false" or last_mb != mb: # filter redundant
if self.include_record(domain, function, snp_source, conservation_score):
info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id]
info_list.extend(self.allele_list)
@@ -366,7 +366,7 @@ class SnpBrowser:
if len(gene_name_list) > 0:
gene_id_name_dict = get_gene_id_name_dict(self.species_id, gene_name_list)
- #ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc)
+ # ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc)
self.empty_columns = {
"snp_source": "false",
"conservation_score": "false",
@@ -389,8 +389,8 @@ class SnpBrowser:
snp_name = rs
else:
rs = ""
- start_bp = int(mb*1000000 - 100)
- end_bp = int(mb*1000000 + 100)
+ start_bp = int(mb * 1000000 - 100)
+ end_bp = int(mb * 1000000 + 100)
position_info = "chr%s:%d-%d" % (chr, start_bp, end_bp)
if self.species_id == 2:
snp_url = webqtlConfig.GENOMEBROWSER_URL % ("rn6", position_info)
@@ -434,7 +434,7 @@ class SnpBrowser:
transcript_link = ""
if exon:
- exon = exon[1] # exon[0] is exon_id, exon[1] is exon_rank
+ exon = exon[1] # exon[0] is exon_id, exon[1] is exon_rank
self.empty_columns['exon'] = "true"
else:
exon = ""
@@ -575,7 +575,7 @@ class SnpBrowser:
if conservation_score:
score_as_float = float(conservation_score)
try:
- input_score_float = float(self.score) # the user-input score
+ input_score_float = float(self.score) # the user-input score
except:
input_score_float = 0.0
@@ -628,17 +628,17 @@ class SnpBrowser:
left_offset, right_offset, top_offset, bottom_offset = (30, 30, 40, 50)
plot_width = canvas_width - left_offset - right_offset
plot_height = canvas_height - top_offset - bottom_offset
- y_zero = top_offset + plot_height/2
+ y_zero = top_offset + plot_height / 2
- x_scale = plot_width/(self.end_mb - self.start_mb)
+ x_scale = plot_width / (self.end_mb - self.start_mb)
- #draw clickable image map at some point
+ # draw clickable image map at some point
n_click = 80.0
- click_step = plot_width/n_click
- click_mb_step = (self.end_mb - self.start_mb)/n_click
+ click_step = plot_width / n_click
+ click_mb_step = (self.end_mb - self.start_mb) / n_click
- #for i in range(n_click):
+ # for i in range(n_click):
# href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles)
def get_browser_sample_lists(species_id=1):
@@ -660,7 +660,7 @@ def get_browser_sample_lists(species_id=1):
return strain_lists
-def get_header_list(variant_type, strains, species = None, empty_columns = None):
+def get_header_list(variant_type, strains, species=None, empty_columns=None):
if species == "Mouse":
strain_list = strains['mouse']
elif species == "Rat":
@@ -668,7 +668,7 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
else:
strain_list = strains
- empty_field_count = 0 #ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this
+ empty_field_count = 0 # ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this
header_fields = []
header_data_names = []
@@ -715,7 +715,7 @@ def get_header_list(variant_type, strains, species = None, empty_columns = None)
return header_fields, empty_field_count, header_data_names
-def get_effect_details_by_category(effect_name = None, effect_value = None):
+def get_effect_details_by_category(effect_name=None, effect_value=None):
gene_list = []
transcript_list = []
exon_list = []
@@ -878,7 +878,7 @@ def get_gene_id_name_dict(species_id, gene_name_list):
return gene_id_name_dict
def check_if_in_gene(species_id, chr, mb):
- if species_id != 0: #ZS: Check if this is necessary
+ if species_id != 0: # ZS: Check if this is necessary
query = """SELECT geneId, geneSymbol
FROM GeneList
WHERE SpeciesId = {0} AND chromosome = '{1}' AND
diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py
index a0e84c8c..4ad6f9e3 100644
--- a/wqflask/wqflask/submit_bnw.py
+++ b/wqflask/wqflask/submit_bnw.py
@@ -3,7 +3,7 @@ from base import data_set
from utility import helper_functions
import utility.logger
-logger = utility.logger.getLogger(__name__ )
+logger = utility.logger.getLogger(__name__)
def get_bnw_input(start_vars):
logger.debug("BNW VARS:", start_vars)
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 22a46ef2..08b4f9f5 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -53,7 +53,7 @@ class GSearch:
for line in re:
dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
trait_id = line[4]
- #with Bench("Building trait object"):
+ # with Bench("Building trait object"):
this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
self.trait_list.append(this_trait)
@@ -108,8 +108,8 @@ class GSearch:
json_dict['data'] = []
for i, trait in enumerate(self.trait_list):
- trait_row = { "checkbox": "Hello There! "
+
if __name__ == "__main__":
app.run(host='0.0.0.0')
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
index 8e8ba482..cebd41ce 100644
--- a/wqflask/tests/unit/base/test_webqtl_case_data.py
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
@@ -4,6 +4,7 @@ import unittest
from wqflask import app # Required because of utility.tools in webqtlCaseData.py
from base.webqtlCaseData import webqtlCaseData
+
class TestWebqtlCaseData(unittest.TestCase):
"""Tests for WebqtlCaseData class"""
diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py
index 42dcae88..024ab43f 100644
--- a/wqflask/tests/unit/utility/test_authentication_tools.py
+++ b/wqflask/tests/unit/utility/test_authentication_tools.py
@@ -5,6 +5,7 @@ from unittest import mock
from utility.authentication_tools import check_resource_availability
from utility.authentication_tools import add_new_resource
+
class TestResponse:
"""Mock Test Response after a request"""
@property
diff --git a/wqflask/tests/unit/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py
index 8d90a1ec..1d349193 100644
--- a/wqflask/tests/unit/utility/test_chunks.py
+++ b/wqflask/tests/unit/utility/test_chunks.py
@@ -7,6 +7,7 @@ from utility.chunks import divide_into_chunks
class TestChunks(unittest.TestCase):
"Test Utility method for chunking"
+
def test_divide_into_chunks(self):
"Check that a list is chunked correctly"
self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3),
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index 8ae0f09f..219a6a29 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -9,6 +9,7 @@ from wqflask.marker_regression.display_mapping_results import (
class TestDisplayMappingResults(unittest.TestCase):
"""Basic Methods to test Mapping Results"""
+
def test_pil_colors(self):
"""Test that colors use PILLOW color format"""
self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR,
@@ -17,6 +18,7 @@ class TestDisplayMappingResults(unittest.TestCase):
class TestHtmlGenWrapper(unittest.TestCase):
"""Test Wrapper around HTMLGen"""
+
def test_create_image(self):
"""Test HT.Image method"""
self.assertEqual(
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
index 5eec93f1..fd21a825 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -12,9 +12,10 @@ class AttributeSetter:
def __init__(self, obj):
for key, val in obj.items():
setattr(self, key, val)
-class TestPlinkMapping(unittest.TestCase):
+class TestPlinkMapping(unittest.TestCase):
+
def test_build_line_list(self):
"""test for building line list"""
line_1 = "this is line one test"
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index bbb79f98..5cc8fd0f 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -4,6 +4,8 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
# issues some methods in genofile object are not defined
# modify samples should equal to vals
+
+
class TestQtlReaperMapping(unittest.TestCase):
@mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
def test_gen_pheno_txt_file(self):
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 0e617e93..6267ce9a 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -5,6 +5,7 @@ from wqflask.marker_regression.rqtl_mapping import get_trait_data_type
from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype
from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names
+
class TestRqtlMapping(unittest.TestCase):
def setUp(self):
@@ -14,7 +15,6 @@ class TestRqtlMapping(unittest.TestCase):
def tearDown(self):
self.app_context.pop()
-
@mock.patch("wqflask.marker_regression.rqtl_mapping.g")
@mock.patch("wqflask.marker_regression.rqtl_mapping.logger")
def test_get_trait_data(self, mock_logger, mock_db):
diff --git a/wqflask/tests/unit/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py
index 9a36132d..2a914fb2 100644
--- a/wqflask/tests/unit/wqflask/test_collect.py
+++ b/wqflask/tests/unit/wqflask/test_collect.py
@@ -11,6 +11,7 @@ app = Flask(__name__)
class MockSession:
"""Helper class for mocking wqflask.collect.g.user_session.logged_in"""
+
def __init__(self, is_logged_in=False):
self.is_logged_in = is_logged_in
@@ -21,6 +22,7 @@ class MockSession:
class MockFlaskG:
"""Helper class for mocking wqflask.collect.g.user_session"""
+
def __init__(self, is_logged_in=False):
self.is_logged_in = is_logged_in
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 8c866874..24c3923e 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -242,7 +242,6 @@ class TestTraits(unittest.TestCase):
self.assertEqual(get_genotype_scales(file_location), expected_results)
mock_get_scales.assert_called_once_with(file_location)
-
@mock.patch("wqflask.show_trait.show_trait.locate_ignore_error")
def test_get_scales_from_genofile_found(self, mock_ignore_location):
""""add test for get scales from genofile where file is found"""
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 68c2cb72..d35b2089 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -47,6 +47,7 @@ COUR_FILE = "./wqflask/static/fonts/courbd.ttf"
TAHOMA_FILE = "./wqflask/static/fonts/tahoma.ttf"
# ---- END: FONT FILES ---- #
+
def cformat(d, rank=0):
'custom string format'
strD = "%2.6f" % d
@@ -68,6 +69,7 @@ def cformat(d, rank=0):
strD = '0.0'
return strD
+
def frange(start, end=None, inc=1.0):
"A faster range-like function that does accept float increments..."
if end == None:
@@ -84,6 +86,7 @@ def frange(start, end=None, inc=1.0):
L[i] = start + i * inc
return L
+
def find_outliers(vals):
"""Calculates the upper and lower bounds of a set of sample/case values
@@ -119,6 +122,8 @@ def find_outliers(vals):
# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)
+
+
def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset=(60, 20, 40, 40), zoom=1):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -230,6 +235,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
font=labelFont, fill=labelColor)
# This function determines the scale of the plot
+
+
def detScaleOld(min, max):
if min >= max:
return None
@@ -246,6 +253,7 @@ def detScaleOld(min, max):
high = c * ceil(max / c)
return [low, high, round((high - low) / c)]
+
def detScale(min=0, max=0):
if min >= max:
@@ -283,15 +291,19 @@ def detScale(min=0, max=0):
return [low, high, n]
+
def bluefunc(x):
return 1.0 / (1.0 + exp(-10 * (x - 0.6)))
+
def redfunc(x):
return 1.0 / (1.0 + exp(10 * (x - 0.5)))
+
def greenfunc(x):
return 1 - pow(redfunc(x + 0.2), 2) - bluefunc(x - 0.3)
+
def colorSpectrum(n=100):
multiple = 10
if n == 1:
@@ -319,6 +331,7 @@ def colorSpectrum(n=100):
out2.append(out[-1])
return out2
+
def _test():
import doctest
doctest.testmod()
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index ec7e72d0..d540c96e 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -2,8 +2,10 @@ from pprint import pformat as pf
# Todo: Move these out of __init__
+
class Bunch:
"""Like a dictionary but using object notation"""
+
def __init__(self, **kw):
self.__dict__ = kw
diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py
index 06091ecb..2b560e48 100644
--- a/wqflask/utility/after.py
+++ b/wqflask/utility/after.py
@@ -7,6 +7,7 @@ from flask import g
from wqflask import app
+
def after_this_request(f):
if not hasattr(g, 'after_request_callbacks'):
g.after_request_callbacks = []
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 672b36d5..57dbf8ba 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -11,6 +11,7 @@ from utility.redis_tools import (get_redis_conn,
add_resource)
Redis = get_redis_conn()
+
def check_resource_availability(dataset, trait_id=None):
# At least for now assume temporary entered traits are accessible
if type(dataset) == str or dataset.type == "Temp":
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 3d40a3b8..48ab1dc0 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -6,6 +6,7 @@ from utility.tools import LOG_BENCH
from utility.logger import getLogger
logger = getLogger(__name__)
+
class Bench:
entries = collections.OrderedDict()
diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py
index 15d1cb8d..523280a1 100644
--- a/wqflask/utility/corestats.py
+++ b/wqflask/utility/corestats.py
@@ -16,6 +16,8 @@
import sys
# ZS: Should switch to using some third party library for this; maybe scipy has an equivalent
+
+
class Stats:
def __init__(self, sequence):
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index ae1181e4..9415cef0 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -47,11 +47,13 @@ logger = getLogger(__name__)
from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
+
def test_elasticsearch_connection():
es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True)
if not es.ping():
logger.warning("Elasticsearch is DOWN")
+
def get_elasticsearch_connection(for_user=True):
"""Return a connection to ES. Returns None on failure"""
logger.info("get_elasticsearch_connection")
@@ -77,6 +79,7 @@ def get_elasticsearch_connection(for_user=True):
return es
+
def setup_users_index(es_connection):
if es_connection:
index_settings = {
@@ -87,12 +90,15 @@ def setup_users_index(es_connection):
es_connection.indices.create(index='users', ignore=400)
es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local")
+
def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type)
+
def save_user(es, user, user_id):
es_save_data(es, "users", "local", user, user_id)
+
def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
item_details = None
try:
@@ -106,6 +112,7 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
pass
return item_details
+
def es_save_data(es, index, doc_type, data_item, data_id,):
from time import sleep
es.create(index, doc_type, body=data_item, id=data_id)
diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py
index c1bf4043..805d2ffe 100644
--- a/wqflask/utility/external.py
+++ b/wqflask/utility/external.py
@@ -4,6 +4,7 @@ import os
import sys
import subprocess
+
def shell(command):
if subprocess.call(command, shell=True) != 0:
raise Exception("ERROR: failed on " + command)
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 9cfa39f9..24604e58 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,6 +1,7 @@
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class genotype:
"""
Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
@@ -119,6 +120,7 @@ class genotype:
self.chromosomes.append(chr_ob)
+
class Chr:
def __init__(self, name, geno_ob):
self.name = name
@@ -140,6 +142,7 @@ class Chr:
def add_marker(self, marker_row):
self.loci.append(Locus(self.geno_ob, marker_row))
+
class Locus:
def __init__(self, geno_ob, marker_row=None):
self.chr = None
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index f8e96d19..94a08c17 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -12,6 +12,7 @@ import simplejson as json
from pprint import pformat as pf
+
class Marker:
def __init__(self):
self.name = None
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 16912e58..47079818 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -35,6 +35,7 @@ import datetime
from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL
+
class GNLogger:
"""A logger class with some additional functionality, such as
multiple parameter logging, SQL logging, timing, colors, and lazy
@@ -139,6 +140,8 @@ LOG_LEVEL_DEBUG (NYI).
# Get the module logger. You can override log levels at the
# module level
+
+
def getLogger(name, level=None):
gnlogger = GNLogger(name)
logger = gnlogger.logger
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index 6e95beb0..5713e155 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -9,6 +9,8 @@ BLACK = ImageColor.getrgb("black")
WHITE = ImageColor.getrgb("white")
# def draw_rotated_text(canvas: Image, text: str, font: ImageFont, xy: tuple, fill: ImageColor=BLACK, angle: int=-90):
+
+
def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
# type: (Image, str, ImageFont, tuple, ImageColor, int)
"""Utility function draw rotated text"""
@@ -20,6 +22,8 @@ def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy]))
# def draw_open_polygon(canvas: Image, xy: tuple, fill: ImageColor=WHITE, outline: ImageColor=BLACK):
+
+
def draw_open_polygon(canvas, xy, fill=None, outline=BLACK, width=0):
# type: (Image, tuple, ImageColor, ImageColor)
draw_ctx = ImageDraw.Draw(canvas)
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index f22f4b14..92f944bc 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -10,6 +10,7 @@ GREEN = '\033[92m'
BOLD = '\033[1m'
ENDC = '\033[0m'
+
def app_config():
app.config['SESSION_TYPE'] = 'filesystem'
if not app.config.get('SECRET_KEY'):
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 4c478c36..f5ef81e1 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -459,11 +459,13 @@ class rect(SVGelement):
if stroke_width != None:
self.attributes['stroke-width'] = stroke_width
+
class ellipse(SVGelement):
"""e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
an ellipse is defined as a center and a x and y radius.
"""
+
def __init__(self, cx=None, cy=None, rx=None, ry=None,fill=None,stroke=None,stroke_width=None,**args):
if rx == None or ry == None:
raise ValueError('both rx and ry are required')
@@ -486,6 +488,7 @@ class circle(SVGelement):
The circle creates an element using a x, y and radius values eg
"""
+
def __init__(self, cx=None, cy=None, r=None, fill=None,stroke=None,stroke_width=None,**args):
if r == None:
raise ValueError('r is required')
@@ -501,20 +504,24 @@ class circle(SVGelement):
if stroke_width != None:
self.attributes['stroke-width'] = stroke_width
+
class point(circle):
"""p=point(x,y,color)
A point is defined as a circle with a size 1 radius. It may be more efficient to use a
very small rectangle if you use many points because a circle is difficult to render.
"""
+
def __init__(self, x, y, fill='black', **args):
circle.__init__(self, x, y, 1, fill, **args)
+
class line(SVGelement):
"""l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
A line is defined by a begin x,y pair and an end x,y pair
"""
+
def __init__(self, x1=None, y1=None, x2=None, y2=None,stroke=None,stroke_width=None,**args):
SVGelement.__init__(self, 'line', **args)
if x1 != None:
@@ -530,11 +537,13 @@ class line(SVGelement):
if stroke != None:
self.attributes['stroke'] = stroke
+
class polyline(SVGelement):
"""pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
a polyline is defined by a list of xy pairs
"""
+
def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
SVGelement.__init__(self, 'polyline', {'points': _xypointlist(points)}, **args)
if fill != None:
@@ -544,11 +553,13 @@ class polyline(SVGelement):
if stroke != None:
self.attributes['stroke'] = stroke
+
class polygon(SVGelement):
"""pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
a polygon is defined by a list of xy pairs
"""
+
def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
SVGelement.__init__(self, 'polygon', {'points': _xypointlist(points)}, **args)
if fill != None:
@@ -558,11 +569,13 @@ class polygon(SVGelement):
if stroke != None:
self.attributes['stroke'] = stroke
+
class path(SVGelement):
"""p=path(path,fill,stroke,stroke_width,**args)
a path is defined by a path object and optional width, stroke and fillcolor
"""
+
def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None,id=None,**args):
SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args)
if stroke != None:
@@ -580,6 +593,7 @@ class text(SVGelement):
a text element can bge used for displaying text on the screen
"""
+
def __init__(self, x=None, y=None, text=None, font_size=None,font_family=None,text_anchor=None,**args):
SVGelement.__init__(self, 'text', **args)
if x != None:
@@ -601,11 +615,13 @@ class textpath(SVGelement):
a textpath places a text on a path which is referenced by a link.
"""
+
def __init__(self, link, text=None, **args):
SVGelement.__init__(self, 'textPath', {'xlink:href': link}, **args)
if text != None:
self.text = text
+
class pattern(SVGelement):
"""p=pattern(x,y,width,height,patternUnits,**args)
@@ -613,6 +629,7 @@ class pattern(SVGelement):
graphic object which can be replicated ("tiled") at fixed intervals
in x and y to cover the areas to be painted.
"""
+
def __init__(self, x=None, y=None, width=None, height=None,patternUnits=None,**args):
SVGelement.__init__(self, 'pattern', **args)
if x != None:
@@ -626,34 +643,40 @@ class pattern(SVGelement):
if patternUnits != None:
self.attributes['patternUnits'] = patternUnits
+
class title(SVGelement):
"""t=title(text,**args)
a title is a text element. The text is displayed in the title bar
add at least one to the root svg element
"""
+
def __init__(self, text=None, **args):
SVGelement.__init__(self, 'title', **args)
if text != None:
self.text = text
+
class description(SVGelement):
"""d=description(text,**args)
a description can be added to any element and is used for a tooltip
Add this element before adding other elements.
"""
+
def __init__(self, text=None, **args):
SVGelement.__init__(self, 'desc', **args)
if text != None:
self.text = text
+
class lineargradient(SVGelement):
"""lg=lineargradient(x1,y1,x2,y2,id,**args)
defines a lineargradient using two xy pairs.
stop elements van be added to define the gradient colors.
"""
+
def __init__(self, x1=None, y1=None, x2=None, y2=None,id=None,**args):
SVGelement.__init__(self, 'linearGradient', **args)
if x1 != None:
@@ -667,12 +690,14 @@ class lineargradient(SVGelement):
if id != None:
self.attributes['id'] = id
+
class radialgradient(SVGelement):
"""rg=radialgradient(cx,cy,r,fx,fy,id,**args)
defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint.
stop elements van be added to define the gradient colors.
"""
+
def __init__(self, cx=None, cy=None, r=None, fx=None,fy=None,id=None,**args):
SVGelement.__init__(self, 'radialGradient', **args)
if cx != None:
@@ -688,21 +713,25 @@ class radialgradient(SVGelement):
if id != None:
self.attributes['id'] = id
+
class stop(SVGelement):
"""st=stop(offset,stop_color,**args)
Puts a stop color at the specified radius
"""
+
def __init__(self, offset, stop_color=None, **args):
SVGelement.__init__(self, 'stop', {'offset': offset}, **args)
if stop_color != None:
self.attributes['stop-color'] = stop_color
+
class style(SVGelement):
"""st=style(type,cdata=None,**args)
Add a CDATA element to this element for defing in line stylesheets etc..
"""
+
def __init__(self, type, cdata=None, **args):
SVGelement.__init__(self, 'style', {'type': type}, cdata=cdata, **args)
@@ -712,6 +741,7 @@ class image(SVGelement):
adds an image to the drawing. Supported formats are .png, .jpg and .svg.
"""
+
def __init__(self, url, x=None, y=None, width=None,height=None,**args):
if width == None or height == None:
raise ValueError('both height and width are required')
@@ -721,11 +751,13 @@ class image(SVGelement):
if y != None:
self.attributes['y'] = y
+
class cursor(SVGelement):
"""c=cursor(url,**args)
defines a custom cursor for a element or a drawing
"""
+
def __init__(self, url, **args):
SVGelement.__init__(self, 'cursor', {'xlink:href': url}, **args)
@@ -736,6 +768,7 @@ class marker(SVGelement):
defines a marker which can be used as an endpoint for a line or other pathtypes
add an element to it which should be used as a marker.
"""
+
def __init__(self, id=None, viewBox=None, refx=None, refy=None,markerWidth=None,markerHeight=None,**args):
SVGelement.__init__(self, 'marker', **args)
if id != None:
@@ -751,17 +784,20 @@ class marker(SVGelement):
if markerHeight != None:
self.attributes['markerHeight'] = markerHeight
+
class group(SVGelement):
"""g=group(id,**args)
a group is defined by an id and is used to contain elements
g.addElement(SVGelement)
"""
+
def __init__(self, id=None, **args):
SVGelement.__init__(self, 'g', **args)
if id != None:
self.attributes['id'] = id
+
class symbol(SVGelement):
"""sy=symbol(id,viewbox,**args)
@@ -778,14 +814,17 @@ class symbol(SVGelement):
if viewBox != None:
self.attributes['viewBox'] = _viewboxlist(viewBox)
+
class defs(SVGelement):
"""d=defs(**args)
container for defining elements
"""
+
def __init__(self, **args):
SVGelement.__init__(self, 'defs', **args)
+
class switch(SVGelement):
"""sw=switch(**args)
@@ -793,6 +832,7 @@ class switch(SVGelement):
requiredFeatures, requiredExtensions and systemLanguage.
Refer to the SVG specification for details.
"""
+
def __init__(self, **args):
SVGelement.__init__(self, 'switch', **args)
@@ -802,6 +842,7 @@ class use(SVGelement):
references a symbol by linking to its id and its position, height and width
"""
+
def __init__(self, link, x=None, y=None, width=None,height=None,**args):
SVGelement.__init__(self, 'use', {'xlink:href': link}, **args)
if x != None:
@@ -821,32 +862,39 @@ class link(SVGelement):
a link is defined by a hyperlink. add elements which have to be linked
a.addElement(SVGelement)
"""
+
def __init__(self, link='', **args):
SVGelement.__init__(self, 'a', {'xlink:href': link}, **args)
+
class view(SVGelement):
"""v=view(id,**args)
a view can be used to create a view with different attributes"""
+
def __init__(self, id=None, **args):
SVGelement.__init__(self, 'view', **args)
if id != None:
self.attributes['id'] = id
+
class script(SVGelement):
"""sc=script(type,type,cdata,**args)
adds a script element which contains CDATA to the SVG drawing
"""
+
def __init__(self, type, cdata=None, **args):
SVGelement.__init__(self, 'script', {'type': type}, cdata=cdata, **args)
+
class animate(SVGelement):
"""an=animate(attribute,from,to,during,**args)
animates an attribute.
"""
+
def __init__(self, attribute, fr=None, to=None, dur=None,**args):
SVGelement.__init__(self, 'animate', {'attributeName': attribute}, **args)
if fr != None:
@@ -856,11 +904,13 @@ class animate(SVGelement):
if dur != None:
self.attributes['dur'] = dur
+
class animateMotion(SVGelement):
"""an=animateMotion(pathdata,dur,**args)
animates a SVGelement over the given path in dur seconds
"""
+
def __init__(self, pathdata, dur, **args):
SVGelement.__init__(self, 'animateMotion', **args)
if pathdata != None:
@@ -868,11 +918,13 @@ class animateMotion(SVGelement):
if dur != None:
self.attributes['dur'] = dur
+
class animateTransform(SVGelement):
"""antr=animateTransform(type,from,to,dur,**args)
transform an element from and to a value.
"""
+
def __init__(self, type=None, fr=None, to=None, dur=None,**args):
SVGelement.__init__(self, 'animateTransform', {'attributeName': 'transform'}, **args)
# As far as I know the attributeName is always transform
@@ -884,11 +936,14 @@ class animateTransform(SVGelement):
self.attributes['to'] = to
if dur != None:
self.attributes['dur'] = dur
+
+
class animateColor(SVGelement):
"""ac=animateColor(attribute,type,from,to,dur,**args)
Animates the color of a element
"""
+
def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args):
SVGelement.__init__(self, 'animateColor', {'attributeName': attribute}, **args)
if type != None:
@@ -899,11 +954,14 @@ class animateColor(SVGelement):
self.attributes['to'] = to
if dur != None:
self.attributes['dur'] = dur
+
+
class set(SVGelement):
"""st=set(attribute,to,during,**args)
sets an attribute to a value for a
"""
+
def __init__(self, attribute, to=None, dur=None, **args):
SVGelement.__init__(self, 'set', {'attributeName': attribute}, **args)
if to != None:
@@ -912,7 +970,6 @@ class set(SVGelement):
self.attributes['dur'] = dur
-
class svg(SVGelement):
"""s=svg(viewbox,width,height,**args)
@@ -928,6 +985,7 @@ class svg(SVGelement):
d.setSVG(s)
d.toXml()
"""
+
def __init__(self, viewBox=None, width=None, height=None, **args):
SVGelement.__init__(self, 'svg', **args)
if viewBox != None:
@@ -938,6 +996,7 @@ class svg(SVGelement):
self.attributes['height'] = height
self.namespace = "http://www.w3.org/2000/svg"
+
class drawing:
"""d=drawing()
@@ -952,6 +1011,7 @@ class drawing:
def __init__(self, entity={}):
self.svg = None
self.entity = entity
+
def setSVG(self, svg):
self.svg = svg
# Voeg een element toe aan de grafiek toe.
@@ -1005,6 +1065,7 @@ class drawing:
root = implementation.createDocument(None, None, doctype)
# Create the xml document.
global appender
+
def appender(element, elementroot):
"""This recursive function appends elements to an element and sets the attributes
and type. It stops when alle elements have been appended"""
@@ -1053,6 +1114,7 @@ class drawing:
f.close()
except:
print(("Cannot write SVG file: " + filename))
+
def validate(self):
try:
import xml.parsers.xmlproc.xmlval
@@ -1066,9 +1128,10 @@ class drawing:
raise Exception("SVG is not well formed, see messages above")
else:
print("SVG well formed")
-if __name__ == '__main__':
+if __name__ == '__main__':
+
d = drawing()
s = svg((0, 0, 100, 100))
r = rect(-100, -100, 300, 300, 'cyan')
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 2088ba9a..07c5a318 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -2,6 +2,7 @@ from redis import Redis
import simplejson as json
+
class TempData:
def __init__(self, temp_uuid):
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 9b751344..4fe4db08 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -13,11 +13,13 @@ logger = logging.getLogger(__name__)
OVERRIDES = {}
+
def app_set(command_id, value):
"""Set application wide value"""
app.config.setdefault(command_id, value)
return value
+
def get_setting(command_id, guess=None):
"""Resolve a setting from the environment or the global settings in
app.config, with valid_path is a function checking whether the
@@ -66,12 +68,14 @@ def get_setting(command_id, guess=None):
# print("Set "+command_id+"="+str(command))
return command
+
def get_setting_bool(id):
v = get_setting(id)
if v not in [0, False, 'False', 'FALSE', None]:
return True
return False
+
def get_setting_int(id):
v = get_setting(id)
if isinstance(v, str):
@@ -80,21 +84,25 @@ def get_setting_int(id):
return 0
return v
+
def valid_bin(bin):
if os.path.islink(bin) or valid_file(bin):
return bin
return None
+
def valid_file(fn):
if os.path.isfile(fn):
return fn
return None
+
def valid_path(dir):
if os.path.isdir(dir):
return dir
return None
+
def js_path(module=None):
"""
Find the JS module in the two paths
@@ -107,38 +115,47 @@ def js_path(module=None):
return try_guix
raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)"
+
def reaper_command(guess=None):
return get_setting("REAPER_COMMAND", guess)
+
def gemma_command(guess=None):
return assert_bin(get_setting("GEMMA_COMMAND", guess))
+
def gemma_wrapper_command(guess=None):
return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess))
+
def plink_command(guess=None):
return assert_bin(get_setting("PLINK_COMMAND", guess))
+
def flat_file_exists(subdir):
base = get_setting("GENENETWORK_FILES")
return valid_path(base + "/" + subdir)
+
def flat_files(subdir=None):
base = get_setting("GENENETWORK_FILES")
if subdir:
return assert_dir(base + "/" + subdir)
return assert_dir(base)
+
def assert_bin(fn):
if not valid_bin(fn):
raise Exception("ERROR: can not find binary " + fn)
return fn
+
def assert_dir(dir):
if not valid_path(dir):
raise Exception("ERROR: can not find directory " + dir)
return dir
+
def assert_writable_dir(dir):
try:
fn = dir + "/test.txt"
@@ -150,16 +167,19 @@ def assert_writable_dir(dir):
raise Exception('Unable to write test.txt to directory ' + dir)
return dir
+
def assert_file(fn):
if not valid_file(fn):
raise Exception('Unable to find file ' + fn)
return fn
+
def mk_dir(dir):
if not valid_path(dir):
os.makedirs(dir)
return assert_dir(dir)
+
def locate(name, subdir=None):
"""
Locate a static flat file in the GENENETWORK_FILES environment.
@@ -179,9 +199,11 @@ def locate(name, subdir=None):
if subdir: sys.stderr.write(subdir)
raise Exception("Can not locate " + name + " in " + base)
+
def locate_phewas(name, subdir=None):
return locate(name, '/phewas/' + subdir)
+
def locate_ignore_error(name, subdir=None):
"""
Locate a static flat file in the GENENETWORK_FILES environment.
@@ -200,17 +222,20 @@ def locate_ignore_error(name, subdir=None):
logger.info("WARNING: file " + name + " not found\n")
return None
+
def tempdir():
"""
Get UNIX TMPDIR by default
"""
return valid_path(get_setting("TMPDIR", "/tmp"))
+
BLUE = '\033[94m'
GREEN = '\033[92m'
BOLD = '\033[1m'
ENDC = '\033[0m'
+
def show_settings():
from utility.tools import LOG_LEVEL
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
index 662bf794..00f14ba9 100644
--- a/wqflask/utility/type_checking.py
+++ b/wqflask/utility/type_checking.py
@@ -7,6 +7,7 @@ def is_float(value):
except:
return False
+
def is_int(value):
try:
int(value)
@@ -14,6 +15,7 @@ def is_int(value):
except:
return False
+
def is_str(value):
if value is None:
return False
@@ -23,18 +25,21 @@ def is_str(value):
except:
return False
+
def get_float(vars_obj, name, default=None):
if name in vars_obj:
if is_float(vars_obj[name]):
return float(vars_obj[name])
return default
+
def get_int(vars_obj, name, default=None):
if name in vars_obj:
if is_int(vars_obj[name]):
return float(vars_obj[name])
return default
+
def get_string(vars_obj, name, default=None):
if name in vars_obj:
if not vars_obj[name] is None:
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index ed59b0eb..f355a865 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -64,6 +64,7 @@ ParInfo = {
# Accessory Functions
#########################################
+
def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits):
from random import choice
_str = prefix[:]
@@ -71,6 +72,7 @@ def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits):
_str += choice(chars)
return _str
+
def ListNotNull(lst):
'''Obsolete - Use built in function any (or all or whatever)
@@ -83,6 +85,7 @@ def ListNotNull(lst):
return 1
return None
+
def readLineCSV(line): # dcrowell July 2008
"""Parses a CSV string of text and returns a list containing each element as a string.
Used by correlationPage"""
@@ -91,6 +94,7 @@ def readLineCSV(line): # dcrowell July 2008
returnList[0] = returnList[0][1:]
return returnList
+
def cmpEigenValue(A, B):
try:
if A[0] > B[0]:
@@ -102,6 +106,7 @@ def cmpEigenValue(A, B):
except:
return 0
+
def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
access_to_confidential_phenotype_trait = 0
if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index bab87115..712517a3 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -30,6 +30,7 @@ app.register_blueprint(policies_blueprint, url_prefix="/policies")
app.register_blueprint(environments_blueprint, url_prefix="/environments")
app.register_blueprint(facilities_blueprint, url_prefix="/facilities")
+
@app.before_request
def before_request():
g.request_start_time = time.time()
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index e0b7fea0..f1dd148f 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -18,6 +18,7 @@ from utility.benchmark import Bench
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def do_correlation(start_vars):
assert('db' in start_vars)
assert('target_db' in start_vars)
@@ -66,6 +67,7 @@ def do_correlation(start_vars):
return final_results
+
def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
corr_results = {}
@@ -91,6 +93,7 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
return sorted_results
+
def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1):
# Gets tissue expression values for the primary trait
primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=[this_trait.symbol])
@@ -113,6 +116,7 @@ def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_par
return tissue_corr_data
+
def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params):
input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid)
@@ -145,6 +149,7 @@ def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_g
return lit_corr_data
+
def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, type):
"""
Calculates the sample r (or rho) and p-value
@@ -176,6 +181,7 @@ def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_data
else:
return [sample_r, sample_p, num_overlap]
+
def convert_to_mouse_gene_id(species=None, gene_id=None):
"""If the species is rat or human, translate the gene_id to the mouse geneid
@@ -212,6 +218,7 @@ def convert_to_mouse_gene_id(species=None, gene_id=None):
return mouse_gene_id
+
def init_corr_params(start_vars):
method = "pearson"
if 'method' in start_vars:
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index fbfbc879..662090d5 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -10,6 +10,7 @@ from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_map
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def do_mapping_for_api(start_vars):
assert('db' in start_vars)
assert('trait_id' in start_vars)
@@ -74,7 +75,6 @@ def do_mapping_for_api(start_vars):
return result_markers, None
-
def initialize_parameters(start_vars, dataset, this_trait):
mapping_params = {}
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index b0559a07..4f9cc6e5 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -27,10 +27,12 @@ logger = utility.logger.getLogger(__name__)
version = "pre1"
+
@app.route("/api/v_{}/".format(version))
def hello_world():
return flask.jsonify({"hello": "world"})
+
@app.route("/api/v_{}/species".format(version))
def get_species_list():
results = g.db.execute("SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;")
@@ -47,6 +49,7 @@ def get_species_list():
return flask.jsonify(species_list)
+
@app.route("/api/v_{}/species/".format(version))
@app.route("/api/v_{}/species/.".format(version))
def get_species_info(species_name, file_format="json"):
@@ -64,6 +67,7 @@ def get_species_info(species_name, file_format="json"):
return flask.jsonify(species_dict)
+
@app.route("/api/v_{}/groups".format(version))
@app.route("/api/v_{}/groups/".format(version))
def get_groups_list(species_name=None):
@@ -102,6 +106,7 @@ def get_groups_list(species_name=None):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/group/".format(version))
@app.route("/api/v_{}/group/.".format(version))
@app.route("/api/v_{}/group//".format(version))
@@ -145,6 +150,7 @@ def get_group_info(group_name, species_name=None, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/datasets/".format(version))
@app.route("/api/v_{}/datasets//".format(version))
def get_datasets_for_group(group_name, species_name=None):
@@ -197,6 +203,7 @@ def get_datasets_for_group(group_name, species_name=None):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/dataset/".format(version))
@app.route("/api/v_{}/dataset/.".format(version))
@app.route("/api/v_{}/dataset//".format(version))
@@ -302,6 +309,7 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/traits/".format(version), methods=("GET",))
@app.route("/api/v_{}/traits/.".format(version), methods=("GET",))
def fetch_traits(dataset_name, file_format="json"):
@@ -430,6 +438,7 @@ def fetch_traits(dataset_name, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/sample_data/".format(version))
@app.route("/api/v_{}/sample_data/.".format(version))
def all_sample_data(dataset_name, file_format="csv"):
@@ -536,6 +545,7 @@ def all_sample_data(dataset_name, file_format="csv"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/sample_data//".format(version))
@app.route("/api/v_{}/sample_data//.".format(version))
def trait_sample_data(dataset_name, trait_name, file_format="json"):
@@ -625,6 +635,7 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/trait//".format(version))
@app.route("/api/v_{}/trait//.".format(version))
@app.route("/api/v_{}/trait_info//".format(version))
@@ -694,6 +705,7 @@ def get_trait_info(dataset_name, trait_name, file_format="json"):
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/correlation".format(version), methods=("GET",))
def get_corr_results():
results = correlation.do_correlation(request.args)
@@ -703,6 +715,7 @@ def get_corr_results():
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/mapping".format(version), methods=("GET",))
def get_mapping_results():
results, format = mapping.do_mapping_for_api(request.args)
@@ -726,6 +739,7 @@ def get_mapping_results():
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+
@app.route("/api/v_{}/genotypes///.zip".format(version))
@app.route("/api/v_{}/genotypes///".format(version))
@app.route("/api/v_{}/genotypes//.zip".format(version))
@@ -813,6 +827,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
return output
+
@app.route("/api/v_{}/gen_dropdown".format(version), methods=("GET",))
def gen_dropdown_menu():
results = gen_menu.gen_dropdown_json()
@@ -822,6 +837,7 @@ def gen_dropdown_menu():
else:
return return_error(code=500, source=request.url_rule.rule, title="Some error occurred", details="")
+
def return_error(code, source, title, details):
json_ob = {"errors": [
{
@@ -834,6 +850,7 @@ def return_error(code, source, title, details):
return flask.jsonify(json_ob)
+
def get_dataset_trait_ids(dataset_name, start_vars):
if 'limit_to' in start_vars:
@@ -906,6 +923,7 @@ def get_dataset_trait_ids(dataset_name, start_vars):
dataset_id = results[0][2]
return trait_ids, trait_names, data_type, dataset_id
+
def get_samplelist(dataset_name):
group_id = get_group_id_from_dataset(dataset_name)
@@ -922,6 +940,7 @@ def get_samplelist(dataset_name):
return samplelist
+
def get_group_id_from_dataset(dataset_name):
if "Publish" in dataset_name:
query = """
@@ -962,6 +981,7 @@ def get_group_id_from_dataset(dataset_name):
else:
return None
+
def get_group_id(group_name):
query = """
SELECT InbredSet.Id
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 6a1b88ca..61f73106 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -40,6 +40,7 @@ def process_traits(unprocessed_traits):
return traits
+
def report_change(len_before, len_now):
new_length = len_now - len_before
if new_length:
@@ -48,6 +49,7 @@ def report_change(len_before, len_now):
else:
logger.debug("No new traits were added.")
+
@app.route("/collections/store_trait_list", methods=('POST',))
def store_traits_list():
params = request.form
@@ -59,6 +61,7 @@ def store_traits_list():
return hash
+
@app.route("/collections/add")
def collections_add():
@@ -82,6 +85,7 @@ def collections_add():
collections=collections,
)
+
@app.route("/collections/new")
def collections_new():
params = request.args
@@ -118,6 +122,7 @@ def collections_new():
# CauseAnError
pass
+
def create_new(collection_name):
params = request.args
@@ -133,6 +138,7 @@ def create_new(collection_name):
return redirect(url_for('view_collection', uc_id=uc_id))
+
@app.route("/collections/list")
def list_collections():
params = request.args
@@ -143,6 +149,7 @@ def list_collections():
collections=user_collections,
)
+
@app.route("/collections/remove", methods=('POST',))
def remove_traits():
params = request.form
@@ -216,6 +223,7 @@ def view_collection():
**collection_info
)
+
@app.route("/collections/change_name", methods=('POST',))
def change_collection_name():
params = request.form
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 22941ad5..6afea715 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -11,6 +11,7 @@ import numpy as np
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class CorrScatterPlot:
"""Page that displays a correlation scatterplot with a line fitted to it"""
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 051ac1cb..e2fe1ff4 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -172,7 +172,6 @@ class CorrelationResults:
self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
key=lambda t: -abs(t[1][0])))
-
# ZS: Convert min/max chromosome to an int for the location range option
range_chr_as_int = None
for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
@@ -348,7 +347,6 @@ class CorrelationResults:
else:
trait.lit_corr = 0
-
def do_lit_correlation_for_all_traits(self):
input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
@@ -484,6 +482,7 @@ def do_bicor(this_trait_vals, target_trait_vals):
return the_r, the_p
+
def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False):
results_list = []
for i, trait in enumerate(corr_results):
@@ -574,6 +573,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
return json.dumps(results_list)
+
def get_header_fields(data_type, corr_method):
if data_type == "ProbeSet":
if corr_method == "spearman":
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 94c8931f..331cb1dc 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -233,6 +233,7 @@ class CorrelationMatrix:
loadings_array.append(loadings_row)
return loadings_array
+
def export_corr_matrix(corr_results):
corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename)
@@ -263,6 +264,7 @@ def export_corr_matrix(corr_results):
return corr_matrix_filename, matrix_export_path
+
def zScore(trait_data_array):
NN = len(trait_data_array[0])
if NN < 10:
@@ -283,6 +285,7 @@ def zScore(trait_data_array):
i += 1
return trait_data_array
+
def sortEigenVectors(vector):
try:
eigenValues = vector[0].tolist()
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 2fa90a93..ec66e59f 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -39,6 +39,7 @@ r_write_table = ro.r["write.table"] # Map the write.table function
r_data_frame = ro.r["data.frame"] # Map the write.table function
r_as_numeric = ro.r["as.numeric"] # Map the write.table function
+
class CTL:
def __init__(self):
logger.info("Initialization of CTL")
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index b6e85494..e743c4b3 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -17,6 +17,7 @@ db_session = scoped_session(sessionmaker(autocommit=False,
Base = declarative_base()
Base.query = db_session.query_property()
+
def init_db():
# import all modules here that might define models so that
# they will be registered properly on the metadata. Otherwise
@@ -27,4 +28,5 @@ def init_db():
Base.metadata.create_all(bind=engine)
logger.info("Done creating all model metadata")
+
init_db()
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index 25e624ef..c7558ed8 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -90,6 +90,7 @@ class InfoPage:
except Exception as e:
pass
+
def process_query_results(results):
info_ob = {
'info_page_name': results[0],
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 115182e4..7442dc72 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -73,6 +73,7 @@ class DoSearch:
else:
return None
+
class MrnaAssaySearch(DoSearch):
"""A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites"""
@@ -296,6 +297,7 @@ class PhenotypeSearch(DoSearch):
return self.execute(query)
+
class GenotypeSearch(DoSearch):
"""A search within a genotype dataset"""
@@ -339,7 +341,6 @@ class GenotypeSearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
-
if self.search_term[0] == "*":
query = (self.base_query +
"""WHERE Geno.Id = GenoXRef.GenoId
@@ -367,6 +368,7 @@ class GenotypeSearch(DoSearch):
return self.execute(self.query)
+
class RifSearch(MrnaAssaySearch):
"""Searches for traits with a Gene RIF entry including the search term."""
@@ -390,6 +392,7 @@ class RifSearch(MrnaAssaySearch):
return self.execute(query)
+
class WikiSearch(MrnaAssaySearch):
"""Searches GeneWiki for traits other people have annotated"""
@@ -415,6 +418,7 @@ class WikiSearch(MrnaAssaySearch):
return self.execute(query)
+
class GoSearch(MrnaAssaySearch):
"""Searches for synapse-associated genes listed in the Gene Ontology."""
@@ -449,6 +453,8 @@ class GoSearch(MrnaAssaySearch):
return self.execute(query)
# ZS: Not sure what the best way to deal with LRS searches is
+
+
class LrsSearch(DoSearch):
"""Searches for genes with a QTL within the given LRS values
@@ -526,7 +532,6 @@ class LrsSearch(DoSearch):
return where_clause
-
def run(self):
self.from_clause = self.get_from_clause()
@@ -550,6 +555,7 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):
return self.execute(self.query)
+
class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):
for search_key in ('LRS', 'LOD'):
@@ -649,6 +655,7 @@ class CisTransLrsSearch(DoSearch):
return where_clause
+
class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""
Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
@@ -680,6 +687,7 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
return self.execute(self.query)
+
class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
"""Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
@@ -744,6 +752,7 @@ class MeanSearch(MrnaAssaySearch):
return self.execute(self.query)
+
class RangeSearch(MrnaAssaySearch):
"""Searches for genes with a range of expression varying between two values"""
@@ -779,6 +788,7 @@ class RangeSearch(MrnaAssaySearch):
return self.execute(self.query)
+
class PositionSearch(DoSearch):
"""Searches for genes/markers located within a specified range on a specified chromosome"""
@@ -800,7 +810,6 @@ class PositionSearch(DoSearch):
self.dataset.type,
max(self.mb_min, self.mb_max))
-
return where_clause
def get_chr(self):
@@ -819,6 +828,7 @@ class PositionSearch(DoSearch):
return self.execute(self.query)
+
class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
"""Searches for genes located within a specified range on a specified chromosome"""
@@ -832,6 +842,7 @@ class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
return self.execute(self.query)
+
class GenotypePositionSearch(PositionSearch, GenotypeSearch):
"""Searches for genes located within a specified range on a specified chromosome"""
@@ -845,6 +856,7 @@ class GenotypePositionSearch(PositionSearch, GenotypeSearch):
return self.execute(self.query)
+
class PvalueSearch(MrnaAssaySearch):
"""Searches for traits with a permutationed p-value between low and high"""
@@ -878,6 +890,7 @@ class PvalueSearch(MrnaAssaySearch):
logger.sql(self.query)
return self.execute(self.query)
+
class AuthorSearch(PhenotypeSearch):
"""Searches for phenotype traits with specified author(s)"""
@@ -900,6 +913,7 @@ def is_number(s):
except ValueError:
return False
+
def get_aliases(symbol, species):
if species == "mouse":
symbol_string = symbol.capitalize()
@@ -923,6 +937,7 @@ def get_aliases(symbol, species):
return filtered_aliases
+
if __name__ == "__main__":
# Usually this will be used as a library, but call it from the command line for testing
# And it runs the code below
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 207767c4..81424b9c 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -5,6 +5,7 @@ from flask import g
from utility.logger import getLogger
logger = getLogger(__name__)
+
class Docs:
def __init__(self, entry, start_vars={}):
@@ -23,7 +24,6 @@ class Docs:
self.title = result[0]
self.content = result[1].decode("utf-8")
-
self.editable = "false"
# ZS: Removing option to edit to see if text still gets vandalized
try:
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 95c20673..d0745ef7 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -15,6 +15,7 @@ from pprint import pformat as pf
from utility.logger import getLogger
logger = getLogger(__name__)
+
def export_search_results_csv(targs):
table_data = json.loads(targs['export_data'])
@@ -132,6 +133,7 @@ def export_search_results_csv(targs):
return file_list
+
def sort_traits_by_group(trait_list=[]):
traits_by_group = {}
for trait in trait_list:
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index 9836eb9c..1556c6a0 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -24,6 +24,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class SendToBNW:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 36f1b8e5..c55c43e6 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -29,6 +29,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class SendToGeneWeaver:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -58,6 +59,7 @@ class SendToGeneWeaver:
'list': ",".join(trait_name_list),
}
+
def get_trait_name_list(trait_list):
name_list = []
for trait_db in trait_list:
@@ -65,6 +67,7 @@ def get_trait_name_list(trait_list):
return name_list
+
def test_chip(trait_list):
final_chip_name = ""
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index f50eeb8b..6b78725c 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -29,6 +29,7 @@ from utility import helper_functions, corr_result_helpers
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class SendToWebGestalt:
def __init__(self, start_vars):
trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -69,6 +70,7 @@ class SendToWebGestalt:
else:
self.hidden_vars['organism'] = "others"
+
def test_chip(trait_list):
final_chip_name = ""
@@ -113,6 +115,7 @@ def test_chip(trait_list):
return chip_name
+
def gen_gene_id_list(trait_list):
trait_name_list = []
gene_id_list = []
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index f29c0e4d..92a65112 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -12,6 +12,7 @@ from utility.redis_tools import get_user_groups, get_group_info, save_user, crea
from utility.logger import getLogger
logger = getLogger(__name__)
+
@app.route("/groups/manage", methods=('GET', 'POST'))
def manage_groups():
params = request.form if request.form else request.args
@@ -21,6 +22,7 @@ def manage_groups():
admin_groups, member_groups = get_user_groups(g.user_session.user_id)
return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups)
+
@app.route("/groups/view", methods=('GET', 'POST'))
def view_group():
params = request.form if request.form else request.args
@@ -58,6 +60,7 @@ def view_group():
return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info)
+
@app.route("/groups/remove", methods=('POST',))
def remove_groups():
group_ids_to_remove = request.form['selected_group_ids']
@@ -66,6 +69,7 @@ def remove_groups():
return redirect(url_for('manage_groups'))
+
@app.route("/groups/remove_users", methods=('POST',))
def remove_users():
group_id = request.form['group_id']
@@ -77,6 +81,7 @@ def remove_users():
return redirect(url_for('view_group', id=group_id))
+
@app.route("/groups/add_", methods=('POST',))
def add_users(user_type='members'):
group_id = request.form['group_id']
@@ -89,6 +94,7 @@ def add_users(user_type='members'):
return redirect(url_for('view_group', id=group_id))
+
@app.route("/groups/change_name", methods=('POST',))
def change_name():
group_id = request.form['group_id']
@@ -97,6 +103,7 @@ def change_name():
return new_name
+
@app.route("/groups/create", methods=('GET', 'POST'))
def add_or_edit_group():
params = request.form if request.form else request.args
@@ -125,6 +132,8 @@ def add_or_edit_group():
return render_template("admin/create_group.html")
# ZS: Will integrate this later, for now just letting users be added directly
+
+
def send_group_invites(group_id, user_email_list=[], user_type="members"):
for user_email in user_email_list:
user_details = get_user_by_unique_column("email_address", user_email)
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 8cb81dcc..a21dae84 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -18,6 +18,7 @@ from utility.type_checking import is_float, is_int, is_str, get_float, get_int,
from utility.logger import getLogger
logger = getLogger(__name__)
+
class GSearch:
def __init__(self, kw):
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index f8ef7028..0b477446 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -14,6 +14,7 @@ Redis = Redis()
logger = getLogger(__name__)
+
class Heatmap:
def __init__(self, start_vars, temp_uuid):
@@ -132,6 +133,7 @@ class Heatmap:
else:
self.trait_results[this_trait.name].append(float(qtl['lrs_value']))
+
def gen_pheno_txt_file(samples, vals, filename):
"""Generates phenotype file for GEMMA"""
@@ -151,6 +153,7 @@ def gen_pheno_txt_file(samples, vals, filename):
values_string = "\t".join(filtered_vals_list)
outfile.write(values_string)
+
def parse_reaper_output(gwa_filename):
included_markers = []
p_values = []
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 9779878e..8dd1c7c0 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -4,6 +4,8 @@ from flask import Flask, g
# Just return a list of dictionaries
# each dictionary contains sub-dictionary
+
+
def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 3753d1ce..5c7b81dd 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -509,9 +509,6 @@ class DisplayMappingResults:
self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT
# END HaplotypeAnalyst
-
-
-
#########################
# Get the sorting column
#########################
@@ -1640,7 +1637,6 @@ class DisplayMappingResults:
geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)),
outline=outlineColor, fill=fillColor)
-
COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT))
TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
HREF = ''
@@ -1663,7 +1659,6 @@ class DisplayMappingResults:
geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
-
if lastGene == 0:
draw_rotated_text(
canvas, text="%s" % (_chr[j].name),
@@ -2085,7 +2080,6 @@ class DisplayMappingResults:
im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset + plotWidth, yZero)),
fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
-
def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -2427,7 +2421,6 @@ class DisplayMappingResults:
yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh
-
if 'lrs_value' in qtlresult:
if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
@@ -2621,7 +2614,6 @@ class DisplayMappingResults:
# , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
-
# draw additive scale
if not self.multipleInterval and self.additiveChecked:
additiveScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom)
@@ -2653,7 +2645,6 @@ class DisplayMappingResults:
xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30 * (zoom - 1))),
fill=self.LRS_COLOR, width=1 * zoom) # the blue line running up the y axis
-
def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb= None, endMb = None):
# conditions
# multiple Chromosome view
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index e6c78536..22a50bb8 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -8,11 +8,11 @@ from utility.tools import flat_files, PLINK_COMMAND
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def run_plink(this_trait, dataset, species, vals, maf):
plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_")
gen_pheno_txt_file(dataset, vals)
-
plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc "
logger.debug("plink_command:", plink_command)
@@ -25,6 +25,7 @@ def run_plink(this_trait, dataset, species, vals, maf):
return dataset.group.markers.markers
+
def gen_pheno_txt_file(this_dataset, vals):
"""Generates phenotype file for GEMMA/PLINK"""
@@ -42,6 +43,7 @@ def gen_pheno_txt_file(this_dataset, vals):
this_val = vals[i]
outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
+
def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''):
ped_sample_list = get_samples_from_ped_file(dataset)
output_file = open(f"{TMPDIR}{pheno_filename}.txt", "wb")
@@ -77,6 +79,8 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''):
output_file.close()
# get strain name from ped file in order
+
+
def get_samples_from_ped_file(dataset):
ped_file = open(f"{flat_files('mapping')}{dataset.group.name}.ped", "r")
line = ped_file.readline()
@@ -93,6 +97,7 @@ def get_samples_from_ped_file(dataset):
return sample_list
+
def parse_plink_output(output_filename, species):
plink_results = {}
@@ -154,6 +159,8 @@ def parse_plink_output(output_filename, species):
# function: convert line from str to list;
# output: lineList list
#######################################################
+
+
def build_line_list(line=""):
line_list = line.strip().split(' ') # irregular number of whitespaces between columns
line_list = [item for item in line_list if item != '']
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index dd044cb0..313c40ca 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -8,6 +8,7 @@ from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None):
"""Generates p-values for each marker using qtlreaper"""
@@ -73,6 +74,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals,
[output_filename, permu_filename, bootstrap_filename])
+
def gen_pheno_txt_file(samples, vals, trait_filename):
"""Generates phenotype file for GEMMA"""
@@ -92,6 +94,7 @@ def gen_pheno_txt_file(samples, vals, trait_filename):
values_string = "\t".join(filtered_vals_list)
outfile.write(values_string)
+
def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
included_markers = []
p_values = []
@@ -163,6 +166,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
return marker_obs, permu_vals, bootstrap_vals
+
def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
genotype = dataset.group.read_genotype_file(use_reaper=True)
@@ -255,6 +259,7 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
qtl_results.append(qtl)
return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results
+
def natural_sort(marker_list):
"""
Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 2bd94512..588600f5 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -16,6 +16,8 @@ import utility.logger
logger = utility.logger.getLogger(__name__)
# Get a trait's type (numeric, categorical, etc) from the DB
+
+
def get_trait_data_type(trait_db_string):
logger.info("get_trait_data_type");
the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'"
@@ -133,6 +135,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
else:
return process_rqtl_results(result_data_frame, dataset.group.species)
+
def generate_cross_from_rdata(dataset):
rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
ro.r("""
@@ -143,6 +146,7 @@ def generate_cross_from_rdata(dataset):
}
""" % (rdata_location))
+
def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
ro.r("""
@@ -187,6 +191,7 @@ def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figur
}
""" % (dataset.group.genofile, scale_units))
+
def add_perm_strata(cross, perm_strata):
col_string = 'c("the_strata")'
perm_strata_string = "c("
@@ -201,6 +206,7 @@ def add_perm_strata(cross, perm_strata):
return cross, strata_ob
+
def sanitize_rqtl_phenotype(vals):
pheno_as_string = "c("
for i, val in enumerate(vals):
@@ -218,6 +224,7 @@ def sanitize_rqtl_phenotype(vals):
return pheno_as_string
+
def sanitize_rqtl_names(vals):
pheno_as_string = "c("
for i, val in enumerate(vals):
@@ -235,12 +242,14 @@ def sanitize_rqtl_names(vals):
return pheno_as_string
+
def add_phenotype(cross, pheno_as_string, col_name):
ro.globalenv["the_cross"] = cross
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric(' + pheno_as_string + '))')
return ro.r["the_cross"]
+
def add_categorical_covar(cross, covar_as_string, i):
ro.globalenv["the_cross"] = cross
logger.info("cross set");
@@ -275,12 +284,14 @@ def add_names(cross, names_as_string, col_name):
ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = ' + names_as_string + ')')
return ro.r["the_cross"]
+
def pull_var(var_name, cross, var_string):
ro.globalenv["the_cross"] = cross
ro.r(var_name + ' <- pull.pheno(the_cross, ' + var_string + ')')
return ro.r[var_name]
+
def add_cofactors(cross, this_dataset, covariates, samples):
ro.numpy2ri.activate()
@@ -341,6 +352,7 @@ def add_cofactors(cross, this_dataset, covariates, samples):
covars_ob = pull_var("trait_covars", cross, covar_name_string)
return cross, covars_ob
+
def create_marker_covariates(control_marker, cross):
ro.globalenv["the_cross"] = cross
ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
@@ -358,6 +370,7 @@ def create_marker_covariates(control_marker, cross):
# TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc
return ro.r["marker_covars"]
+
def process_pair_scan_results(result):
pair_scan_results = []
@@ -374,6 +387,7 @@ def process_pair_scan_results(result):
return pair_scan_results
+
def process_rqtl_perm_results(num_perm, results):
perm_vals = []
for line in str(results).split("\n")[1:(num_perm + 1)]:
@@ -386,6 +400,7 @@ def process_rqtl_perm_results(num_perm, results):
return perm_output, suggestive, significant
+
def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop
qtl_results = []
output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index f1665570..31c58083 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -45,6 +45,7 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
import utility.logger
logger = utility.logger.getLogger(__name__)
+
class RunMapping:
def __init__(self, start_vars, temp_uuid):
@@ -504,6 +505,7 @@ class RunMapping:
trimmed_genotype_data.append(new_genotypes)
return trimmed_genotype_data
+
def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples):
with open(results_path, "w+") as output_file:
output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
@@ -564,6 +566,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
if i < (len(markers) - 1):
output_file.write("\n")
+
def trim_markers_for_figure(markers):
if 'p_wald' in list(markers[0].keys()):
score_type = 'p_wald'
@@ -624,6 +627,7 @@ def trim_markers_for_figure(markers):
filtered_markers.append(marker)
return filtered_markers
+
def trim_markers_for_table(markers):
if 'lod_score' in list(markers[0].keys()):
sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
@@ -637,6 +641,7 @@ def trim_markers_for_table(markers):
else:
return sorted_markers
+
def write_input_for_browser(this_dataset, gwas_results, annotations):
file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
gwas_filename = file_base + "_GWAS"
@@ -650,6 +655,7 @@ def write_input_for_browser(this_dataset, gwas_results, annotations):
return [gwas_filename, annot_filename]
+
def geno_db_exists(this_dataset):
geno_db_name = this_dataset.group.name + "Geno"
try:
@@ -658,6 +664,7 @@ def geno_db_exists(this_dataset):
except:
return "False"
+
def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
chr_lengths = []
if mapping_scale == "physic":
@@ -696,6 +703,7 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
return chr_lengths
+
def get_genofile_samplelist(dataset):
genofile_samplelist = []
@@ -706,6 +714,7 @@ def get_genofile_samplelist(dataset):
return genofile_samplelist
+
def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
perm_strata_strings = []
for sample in used_samples:
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 8abd6516..d7c9ef95 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -14,6 +14,7 @@ from sqlalchemy.orm import relationship
from wqflask.database import Base, init_db
+
class User(Base):
__tablename__ = "user"
id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
@@ -63,7 +64,6 @@ class User(Base):
print("Couldn't display_num_collections:", why)
return ""
-
def get_collection_by_name(self, collection_name):
try:
collect = self.user_collections.filter_by(name=collection_name).first()
@@ -83,7 +83,6 @@ class User(Base):
def login_count(self):
return self.logins.filter_by(successful=True).count()
-
@property
def confirmed_at(self):
if self.confirmed:
@@ -116,6 +115,7 @@ class User(Base):
except IndexError:
return None
+
class Login(Base):
__tablename__ = "login"
id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
@@ -134,6 +134,7 @@ class Login(Base):
##################################################################################################
+
class UserCollection(Base):
__tablename__ = "user_collection"
id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
@@ -158,12 +159,14 @@ class UserCollection(Base):
def members_as_set(self):
return set(json.loads(self.members))
+
def display_collapsible(number):
if number:
return number
else:
return ""
+
def user_uuid():
"""Unique cookie for a user"""
user_uuid = request.cookies.get('user_uuid')
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 93785a3a..e089643e 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -27,6 +27,7 @@ from utility import helper_functions
from utility import corr_result_helpers
from utility.tools import GN2_BRANCH_URL
+
class NetworkGraph:
def __init__(self, start_vars):
diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py
index 861a93f2..e262dd51 100644
--- a/wqflask/wqflask/news.py
+++ b/wqflask/wqflask/news.py
@@ -1,5 +1,6 @@
from flask import g
+
class News:
def __init__(self):
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index dfd374e2..6b836e20 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -24,6 +24,7 @@ from pprint import pformat as pf
from utility.logger import getLogger
logger = getLogger(__name__)
+
def parse(pstring):
"""
diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py
index 6346df03..1a965fc5 100644
--- a/wqflask/wqflask/pbkdf2.py
+++ b/wqflask/wqflask/pbkdf2.py
@@ -4,6 +4,8 @@ from werkzeug.security import safe_str_cmp as ssc
# Replace this because it just wraps around Python3's internal
# functions. Added this during migration.
+
+
def pbkdf2_hex(data, salt, iterations=1000, keylen=24, hashfunc="sha1"):
"""Wrapper function of python's hashlib.pbkdf2_hmac.
"""
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index a1fe0f8f..4591710c 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -11,6 +11,7 @@ from utility.redis_tools import get_resource_info, get_group_info, get_groups_li
from utility.logger import getLogger
logger = getLogger(__name__)
+
@app.route("/resources/manage", methods=('GET', 'POST'))
def manage_resource():
params = request.form if request.form else request.args
@@ -40,6 +41,7 @@ def manage_resource():
return render_template("admin/manage_resource.html", owner_name=owner_display_name, resource_id=resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status)
+
@app.route("/search_for_users", methods=('POST',))
def search_for_user():
params = request.form
@@ -49,6 +51,7 @@ def search_for_user():
return json.dumps(user_list)
+
@app.route("/search_for_groups", methods=('POST',))
def search_for_groups():
params = request.form
@@ -65,6 +68,7 @@ def search_for_groups():
return json.dumps(group_list)
+
@app.route("/resources/change_owner", methods=('POST',))
def change_owner():
resource_id = request.form['resource_id']
@@ -81,6 +85,7 @@ def change_owner():
else:
return render_template("admin/change_resource_owner.html", resource_id=resource_id)
+
@app.route("/resources/change_default_privileges", methods=('POST',))
def change_default_privileges():
resource_id = request.form['resource_id']
@@ -99,6 +104,7 @@ def change_default_privileges():
else:
return redirect(url_for("no_access_page"))
+
@app.route("/resources/add_group", methods=('POST',))
def add_group_to_resource():
resource_id = request.form['resource_id']
@@ -125,6 +131,7 @@ def add_group_to_resource():
else:
return redirect(url_for("no_access_page"))
+
def get_group_names(group_masks):
group_masks_with_names = {}
for group_id, group_mask in list(group_masks.items()):
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 16eb1864..ed5f9bad 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -24,6 +24,7 @@ from utility.type_checking import is_str
from utility.logger import getLogger
logger = getLogger(__name__)
+
class SearchResultPage:
#maxReturn = 3000
@@ -270,6 +271,7 @@ class SearchResultPage:
else:
return None
+
def get_GO_symbols(a_search):
query = """SELECT genes
FROM GORef
@@ -287,6 +289,7 @@ def get_GO_symbols(a_search):
return new_terms
+
def insert_newlines(string, every=64):
""" This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """
lines = []
@@ -294,6 +297,7 @@ def insert_newlines(string, every=64):
lines.append(string[i:i + every])
return '\n'.join(lines)
+
def get_aliases(symbol_list, species):
updated_symbols = []
diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py
index 86e8a558..299c866a 100644
--- a/wqflask/wqflask/send_mail.py
+++ b/wqflask/wqflask/send_mail.py
@@ -8,10 +8,12 @@ Redis = StrictRedis()
import mailer
+
def timestamp():
ts = datetime.datetime.utcnow()
return ts.isoformat()
+
def main():
while True:
print("I'm alive!")
@@ -31,7 +33,6 @@ def main():
process_message(msg)
-
def process_message(msg):
msg = json.loads(msg)
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 48761fa0..8b3a4faa 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -1,7 +1,6 @@
# handles server side table processing
-
class ServerSideTable:
"""
This class is used to do server-side processing
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 388f831f..496dee57 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -8,6 +8,7 @@ from pprint import pformat as pf
from utility import Plot
from utility import Bunch
+
class SampleList:
def __init__(self,
dataset,
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 379b746c..f0fcd27d 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -5,6 +5,7 @@ from functools import cmp_to_key
from base.trait import create_trait
from base import data_set
+
def export_sample_table(targs):
sample_data = json.loads(targs['export_data'])
@@ -28,6 +29,7 @@ def export_sample_table(targs):
return trait_name, final_sample_data
+
def get_export_metadata(trait_id, dataset_name):
dataset = data_set.create_dataset(dataset_name)
this_trait = create_trait(dataset=dataset,
@@ -64,6 +66,7 @@ def dict_to_sorted_list(dictionary):
sorted_values = [item[1] for item in sorted_list]
return sorted_values
+
def cmp_samples(a, b):
if b[0] == 'name':
return 1
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 7a0df94b..e5c67165 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -9,6 +9,7 @@ logger = getLogger(__name__)
from base import species
from base import webqtlConfig
+
class SnpBrowser:
def __init__(self, start_vars):
@@ -472,7 +473,6 @@ class SnpBrowser:
base_color_dict = {"A": "#C33232", "C": "#1569C7", "T": "#CFCF32", "G": "#32C332",
"t": "#FF6", "c": "#5CB3FF", "a": "#F66", "g": "#CF9", ":": "#FFFFFF", "-": "#FFFFFF", "?": "#FFFFFF"}
-
the_bases = []
for j, item in enumerate(allele_value_list):
if item and isinstance(item, str):
@@ -641,6 +641,7 @@ class SnpBrowser:
# for i in range(n_click):
# href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles)
+
def get_browser_sample_lists(species_id=1):
strain_lists = {}
mouse_strain_list = []
@@ -660,6 +661,7 @@ def get_browser_sample_lists(species_id=1):
return strain_lists
+
def get_header_list(variant_type, strains, species=None, empty_columns=None):
if species == "Mouse":
strain_list = strains['mouse']
@@ -715,6 +717,7 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None):
return header_fields, empty_field_count, header_data_names
+
def get_effect_details_by_category(effect_name=None, effect_value=None):
gene_list = []
transcript_list = []
@@ -764,6 +767,7 @@ def get_effect_details_by_category(effect_name=None, effect_value=None):
return [gene_list, transcript_list, exon_list, function_list, function_detail_list]
+
def get_effect_info(effect_list):
domain = ""
effect_detail_list = []
@@ -836,6 +840,7 @@ def get_effect_info(effect_list):
return effect_info_dict
+
def get_gene_id(species_id, gene_name):
query = """
SELECT
@@ -853,6 +858,7 @@ def get_gene_id(species_id, gene_name):
else:
return ""
+
def get_gene_id_name_dict(species_id, gene_name_list):
gene_id_name_dict = {}
if len(gene_name_list) == 0:
@@ -877,6 +883,7 @@ def get_gene_id_name_dict(species_id, gene_name_list):
return gene_id_name_dict
+
def check_if_in_gene(species_id, chr, mb):
if species_id != 0: # ZS: Check if this is necessary
query = """SELECT geneId, geneSymbol
diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py
index 4ad6f9e3..b21a88cc 100644
--- a/wqflask/wqflask/submit_bnw.py
+++ b/wqflask/wqflask/submit_bnw.py
@@ -5,5 +5,6 @@ from utility import helper_functions
import utility.logger
logger = utility.logger.getLogger(__name__)
+
def get_bnw_input(start_vars):
logger.debug("BNW VARS:", start_vars)
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 08b4f9f5..07073d6a 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -10,6 +10,7 @@ from utility.benchmark import Bench
from utility.logger import getLogger
logger = getLogger(__name__)
+
class GSearch:
def __init__(self, kw):
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 3f5b43ee..2a2f8484 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -29,9 +29,11 @@ from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_AL
THREE_DAYS = 60 * 60 * 24 * 3
+
def timestamp():
return datetime.datetime.utcnow().isoformat()
+
def basic_info():
return dict(timestamp=timestamp(),
ip_address=request.remote_addr,
@@ -54,6 +56,7 @@ def encode_password(pass_gen_fields, unencrypted_password):
return pass_gen_fields
+
def set_password(password):
pass_gen_fields = {
"unencrypted_password": password,
@@ -71,6 +74,7 @@ def set_password(password):
return encoded_password
+
def get_signed_session_id(user):
session_id = str(uuid.uuid4())
@@ -109,6 +113,7 @@ def get_signed_session_id(user):
return session_id_signed
+
def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
"""Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
'UNKNOWN' TLS is used
@@ -125,6 +130,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
server.quit()
logger.info("Successfully sent email to " + toaddr)
+
def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject = "GeneNetwork e-mail verification"):
verification_code = str(uuid.uuid4())
key = key_prefix + ":" + verification_code
@@ -139,12 +145,14 @@ def send_verification_email(user_details, template_name="email/user_verification
send_email(recipient, subject, body)
return {"recipient": recipient, "subject": subject, "body": body}
+
def send_invitation_email(user_email, temp_password, template_name="email/user_invitation.txt", subject= "You've been added to a GeneNetwork user group"):
recipient = user_email
body = render_template(template_name, temp_password)
send_email(recipient, subject, body)
return {"recipient": recipient, "subject": subject, "body": body}
+
@app.route("/manage/verify_email")
def verify_email():
if 'code' in request.args:
@@ -160,6 +168,7 @@ def verify_email():
else:
flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+
@app.route("/n/login", methods=('GET', 'POST'))
def login():
params = request.form if request.form else request.args
@@ -232,6 +241,7 @@ def login():
return response
+
@app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
def github_oauth2():
from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET, GITHUB_AUTH_URL
@@ -264,12 +274,14 @@ def github_oauth2():
url = "/n/login?type=github&uid=" + user_details["user_id"]
return redirect(url)
+
def get_github_user_details(access_token):
from utility.tools import GITHUB_API_URL
result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
return json.loads(result)
+
@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
def orcid_oauth2():
from uuid import uuid4
@@ -308,6 +320,7 @@ def orcid_oauth2():
flash("There was an error getting code from ORCID")
return redirect(url)
+
def get_github_user_details(access_token):
from utility.tools import GITHUB_API_URL
result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
@@ -325,6 +338,7 @@ def logout():
response.set_cookie(UserSession.user_cookie_name, '', expires=0)
return response
+
@app.route("/n/forgot_password", methods=['GET'])
def forgot_password():
"""Entry point for forgotten password"""
@@ -333,6 +347,7 @@ def forgot_password():
print("ERRORS: ", errors)
return render_template("new_security/forgot_password.html", errors=errors)
+
def send_forgot_password_email(verification_email):
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
@@ -365,6 +380,7 @@ def send_forgot_password_email(verification_email):
return subject
+
@app.route("/n/forgot_password_submit", methods=('POST',))
def forgot_password_submit():
"""When a forgotten password form is submitted we get here"""
@@ -386,6 +402,7 @@ def forgot_password_submit():
flash("You MUST provide an email", "alert-danger")
return redirect(url_for("forgot_password"))
+
@app.route("/n/password_reset", methods=['GET'])
def password_reset():
"""Entry point after user clicks link in E-mail"""
@@ -405,6 +422,7 @@ def password_reset():
else:
return redirect(url_for("login"))
+
@app.route("/n/password_reset_step2", methods=('POST',))
def password_reset_step2():
"""Handle confirmation E-mail for password reset"""
@@ -422,6 +440,7 @@ def password_reset_step2():
flash("Password changed successfully. You can now sign in.", "alert-info")
return redirect(url_for('login'))
+
def register_user(params):
thank_you_mode = False
errors = []
@@ -461,6 +480,7 @@ def register_user(params):
return errors
+
@app.route("/n/register", methods=('GET', 'POST'))
def register():
errors = []
@@ -478,6 +498,7 @@ def register():
return render_template("new_security/register_user.html", values=params, errors=errors)
+
@app.errorhandler(401)
def unauthorized(error):
return redirect(url_for('login'))
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 013920f9..a9bd65e6 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -151,6 +151,7 @@ def verify_cookie(cookie):
assert the_signature == actual_hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?"
return the_uuid
+
def create_signed_cookie():
the_uuid = str(uuid.uuid4())
signature = actual_hmac_creation(the_uuid)
@@ -158,6 +159,7 @@ def create_signed_cookie():
logger.debug("uuid_signed:", uuid_signed)
return the_uuid, uuid_signed
+
class UserSession:
"""Logged in user handling"""
@@ -341,6 +343,7 @@ class UserSession:
Redis.delete(self.cookie_name)
logger.debug("At end of delete_session")
+
@app.before_request
def get_cookie():
logger.info("@app.before_request get cookie")
@@ -348,16 +351,20 @@ def get_cookie():
g.cookie_session = AnonUser()
# @app.after_request
+
+
def set_cookie(response):
if not request.cookies.get(g.cookie_session.cookie_name):
response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie)
return response
+
class UsersManager:
def __init__(self):
self.users = model.User.query.all()
logger.debug("Users are:", self.users)
+
class UserManager:
def __init__(self, kw):
self.user_id = kw['user_id']
@@ -419,6 +426,7 @@ class RegisterUser:
self.user.registration_info = json.dumps(basic_info(), sort_keys=True)
save_user(self.user.__dict__, self.user.user_id)
+
def set_password(password, user):
pwfields = Bunch()
@@ -476,6 +484,7 @@ class VerificationEmail:
verification_code=verification_code)
send_email(to, subject, body)
+
class ForgotPasswordEmail(VerificationEmail):
template_name = "email/forgot_password.txt"
key_prefix = "forgot_password_code"
@@ -496,7 +505,6 @@ class ForgotPasswordEmail(VerificationEmail):
save_verification_code(toaddr, verification_code)
-
subject = self.subject
body = render_template(
self.template_name,
@@ -530,6 +538,8 @@ def basic_info():
user_agent=request.headers.get('User-Agent'))
# @app.route("/manage/verify_email")
+
+
def verify_email():
user = DecodeUser(VerificationEmail.key_prefix).user
user.confirmed = json.dumps(basic_info(), sort_keys=True)
@@ -544,6 +554,8 @@ def verify_email():
return response
# @app.route("/n/password_reset", methods=['GET'])
+
+
def password_reset():
"""Entry point after user clicks link in E-mail"""
logger.debug("in password_reset request.url is:", request.url)
@@ -568,6 +580,8 @@ def password_reset():
return redirect(url_for("login"))
# @app.route("/n/password_reset_step2", methods=('POST',))
+
+
def password_reset_step2():
"""Handle confirmation E-mail for password reset"""
logger.debug("in password_reset request.url is:", request.url)
@@ -577,7 +591,6 @@ def password_reset_step2():
logger.debug("locals are:", locals())
-
user = Bunch()
password = request.form['password']
set_password(password, user)
@@ -589,6 +602,7 @@ def password_reset_step2():
return response
+
class DecodeUser:
def __init__(self, code_prefix):
@@ -612,6 +626,8 @@ class DecodeUser:
return model.User.query.get(data['id'])
# @app.route("/n/login", methods=('GET', 'POST'))
+
+
def login():
lu = LoginUser()
login_type = request.args.get("type")
@@ -622,6 +638,8 @@ def login():
return lu.standard_login()
# @app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
+
+
def github_oauth2():
from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET
code = request.args.get("code")
@@ -646,6 +664,8 @@ def github_oauth2():
return redirect(url)
# @app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
+
+
def orcid_oauth2():
from uuid import uuid4
from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL
@@ -673,11 +693,13 @@ def orcid_oauth2():
flash("There was an error getting code from ORCID")
return redirect(url)
+
def get_github_user_details(access_token):
from utility.tools import GITHUB_API_URL
result = requests.get(GITHUB_API_URL, params={"access_token": access_token})
return result.json()
+
class LoginUser:
remember_time = 60 * 60 * 24 * 30 # One month in seconds
@@ -814,6 +836,8 @@ class LoginUser:
db_session.commit()
# @app.route("/n/logout")
+
+
def logout():
logger.debug("Logging out...")
UserSession().delete_session()
@@ -833,6 +857,8 @@ def forgot_password():
return render_template("new_security/forgot_password.html", errors=errors)
# @app.route("/n/forgot_password_submit", methods=('POST',))
+
+
def forgot_password_submit():
"""When a forgotten password form is submitted we get here"""
params = request.form
@@ -853,10 +879,12 @@ def forgot_password_submit():
flash("You MUST provide an email", "alert-danger")
return redirect(url_for("forgot_password"))
+
@app.errorhandler(401)
def unauthorized(error):
return redirect(url_for('login'))
+
def is_redis_available():
try:
Redis.ping()
@@ -922,7 +950,6 @@ def register():
params = None
errors = None
-
params = request.form if request.form else request.args
params = params.to_dict(flat=True)
@@ -952,6 +979,7 @@ def url_for_hmac(endpoint, **values):
combiner = "?"
return url + combiner + "hm=" + hm
+
def data_hmac(stringy):
"""Takes arbitray data string and appends :hmac so we know data hasn't been tampered with"""
return stringy + ":" + actual_hmac_creation(stringy)
@@ -974,6 +1002,7 @@ def verify_url_hmac(url):
assert hm == hmac, "Unexpected url (stage 3)"
+
def actual_hmac_creation(stringy):
"""Helper function to create the actual hmac"""
@@ -986,6 +1015,7 @@ def actual_hmac_creation(stringy):
hm = hm[:20]
return hm
+
app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
data_hmac=data_hmac)
@@ -998,6 +1028,7 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
# Body=body))
# Redis.rpush("mail_queue", msg)
+
def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
"""Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
'UNKNOWN' TLS is used
@@ -1020,6 +1051,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
server.quit()
logger.info("Successfully sent email to " + toaddr)
+
class GroupsManager:
def __init__(self, kw):
self.datasets = create_datasets_list()
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 78db7bd2..f0f0d60c 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -20,6 +20,7 @@ logger = getLogger(__name__)
THREE_DAYS = 60 * 60 * 24 * 3
THIRTY_DAYS = 60 * 60 * 24 * 30
+
@app.before_request
def get_user_session():
logger.info("@app.before_request get_session")
@@ -30,6 +31,7 @@ def get_user_session():
response.set_cookie('session_id_v2', '', expires=0)
return response
+
@app.after_request
def set_user_session(response):
if hasattr(g, 'user_session'):
@@ -37,6 +39,7 @@ def set_user_session(response):
response.set_cookie(g.user_session.cookie_name, g.user_session.cookie)
return response
+
def verify_cookie(cookie):
the_uuid, separator, the_signature = cookie.partition(':')
assert len(the_uuid) == 36, "Is session_id a uuid?"
@@ -44,6 +47,7 @@ def verify_cookie(cookie):
assert the_signature == hmac.hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?"
return the_uuid
+
def create_signed_cookie():
the_uuid = str(uuid.uuid4())
signature = hmac.hmac_creation(the_uuid)
@@ -51,6 +55,7 @@ def create_signed_cookie():
logger.debug("uuid_signed:", uuid_signed)
return the_uuid, uuid_signed
+
@app.route("/user/manage", methods=('GET', 'POST'))
def manage_user():
params = request.form if request.form else request.args
@@ -63,6 +68,7 @@ def manage_user():
return render_template("admin/manage_user.html", user_details=user_details)
+
class UserSession:
"""Logged in user handling"""
--
cgit v1.2.3
From 03b6bcee689c1910bd850c6109cc37adc509cf5a Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 30 Apr 2021 12:45:59 +0300
Subject: autopep8: Fix E501
---
wqflask/base/data_set.py | 6 +-
wqflask/base/mrna_assay_tissue_data.py | 3 +-
wqflask/base/species.py | 3 +-
wqflask/base/webqtlCaseData.py | 6 +-
wqflask/db/webqtlDatabaseFunction.py | 6 +-
wqflask/maintenance/convert_geno_to_bimbam.py | 21 +-
wqflask/maintenance/gen_select_dataset.py | 6 +-
.../maintenance/generate_kinship_from_bimbam.py | 13 +-
wqflask/maintenance/geno_to_json.py | 3 +-
wqflask/maintenance/quantile_normalize.py | 3 +-
.../test_display_mapping_results.py | 3 +-
.../marker_regression/test_gemma_mapping.py | 15 +-
.../marker_regression/test_qtlreaper_mapping.py | 6 +-
.../wqflask/marker_regression/test_rqtl_mapping.py | 3 +-
.../wqflask/marker_regression/test_run_mapping.py | 3 +-
wqflask/tests/unit/wqflask/test_server_side.py | 9 +-
wqflask/tests/wqflask/show_trait/testSampleList.py | 3 +-
.../tests/wqflask/show_trait/test_show_trait.py | 3 +-
wqflask/utility/Plot.py | 9 +-
wqflask/utility/benchmark.py | 9 +-
wqflask/utility/corestats.py | 3 +-
wqflask/utility/elasticsearch_tools.py | 6 +-
wqflask/utility/gen_geno_ob.py | 12 +-
wqflask/utility/genofile_parser.py | 3 +-
wqflask/utility/logger.py | 3 +-
wqflask/utility/redis_tools.py | 9 +-
wqflask/utility/startup_config.py | 6 +-
wqflask/utility/svg.py | 60 ++-
wqflask/utility/tools.py | 12 +-
wqflask/wqflask/api/correlation.py | 54 +-
wqflask/wqflask/api/mapping.py | 15 +-
wqflask/wqflask/api/router.py | 48 +-
wqflask/wqflask/collect.py | 15 +-
.../comparison_bar_chart/comparison_bar_chart.py | 6 +-
wqflask/wqflask/correlation/corr_scatter_plot.py | 33 +-
wqflask/wqflask/correlation/show_corr_results.py | 75 ++-
.../wqflask/correlation_matrix/show_corr_matrix.py | 64 ++-
wqflask/wqflask/ctl/ctl_analysis.py | 72 ++-
wqflask/wqflask/do_search.py | 69 ++-
wqflask/wqflask/docs.py | 6 +-
wqflask/wqflask/export_traits.py | 24 +-
wqflask/wqflask/external_tools/send_to_bnw.py | 6 +-
.../wqflask/external_tools/send_to_geneweaver.py | 3 +-
.../wqflask/external_tools/send_to_webgestalt.py | 3 +-
wqflask/wqflask/group_manager.py | 24 +-
wqflask/wqflask/gsearch.py | 41 +-
wqflask/wqflask/heatmap/heatmap.py | 19 +-
wqflask/wqflask/interval_analyst/GeneUtil.py | 9 +-
.../marker_regression/display_mapping_results.py | 548 ++++++++++++++-------
wqflask/wqflask/marker_regression/gemma_mapping.py | 3 +-
wqflask/wqflask/marker_regression/plink_mapping.py | 9 +-
.../wqflask/marker_regression/qtlreaper_mapping.py | 27 +-
wqflask/wqflask/marker_regression/rqtl_mapping.py | 103 ++--
wqflask/wqflask/marker_regression/run_mapping.py | 126 +++--
wqflask/wqflask/model.py | 30 +-
wqflask/wqflask/resource_manager.py | 9 +-
wqflask/wqflask/search_results.py | 33 +-
wqflask/wqflask/show_trait/SampleList.py | 24 +-
wqflask/wqflask/show_trait/export_trait_data.py | 21 +-
wqflask/wqflask/snp_browser/snp_browser.py | 150 ++++--
wqflask/wqflask/update_search_results.py | 9 +-
wqflask/wqflask/user_login.py | 87 ++--
wqflask/wqflask/user_manager.py | 96 ++--
wqflask/wqflask/user_session.py | 28 +-
64 files changed, 1431 insertions(+), 705 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index c14808d6..8ec0aaad 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -168,7 +168,8 @@ class DatasetType:
results = g.db.execute(sql_query_mapping[t] % group_name).fetchone()
if results:
self.datasets[name] = dataset_name_mapping[t]
- self.redis_instance.set("dataset_structure", json.dumps(self.datasets))
+ self.redis_instance.set(
+ "dataset_structure", json.dumps(self.datasets))
return True
return None
@@ -239,7 +240,8 @@ class Markers:
for line in bimbam_fh:
marker = {}
marker['name'] = line.split(delimiter)[0].rstrip()
- marker['Mb'] = float(line.split(delimiter)[1].rstrip()) / 1000000
+ marker['Mb'] = float(line.split(delimiter)[
+ 1].rstrip()) / 1000000
marker['chr'] = line.split(delimiter)[2].rstrip()
markers.append(marker)
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index cbc05738..9bb29664 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -88,6 +88,7 @@ class MrnaAssayTissueData:
if result.Symbol.lower() not in symbol_values_dict:
symbol_values_dict[result.Symbol.lower()] = [result.value]
else:
- symbol_values_dict[result.Symbol.lower()].append(result.value)
+ symbol_values_dict[result.Symbol.lower()].append(
+ result.value)
return symbol_values_dict
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 44f133b5..e3c29916 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -55,4 +55,5 @@ class Chromosomes:
results = g.db.execute(query).fetchall()
for item in results:
- self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
+ self.chromosomes[item.OrderId] = IndChromosome(
+ item.Name, item.Length)
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 2d07ab9d..25b6cb8a 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -34,12 +34,14 @@ class webqtlCaseData:
def __init__(self, name, value=None, variance=None, num_cases=None, name2=None):
self.name = name
- self.name2 = name2 # Other name (for traits like BXD65a)
+ # Other name (for traits like BXD65a)
+ self.name2 = name2
self.value = value # Trait Value
self.variance = variance # Trait Variance
self.num_cases = num_cases # Number of individuals/cases
self.extra_attributes = None
- self.this_id = None # Set a sane default (can't be just "id" cause that's a reserved word)
+ # Set a sane default (can't be just "id" cause that's a reserved word)
+ self.this_id = None
self.outlier = None # Not set to True/False until later
def __repr__(self):
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 50ac06fd..29112949 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -36,13 +36,15 @@ def retrieve_species(group):
"""Get the species of a group (e.g. returns string "mouse" on "BXD"
"""
- result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/" + group + ".json", lambda r: (r["species"],))[0]
+ result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (
+ group), "/cross/" + group + ".json", lambda r: (r["species"],))[0]
logger.debug("retrieve_species result:", result)
return result
def retrieve_species_id(group):
- result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0]
+ result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (
+ group), "/cross/" + group + ".json", lambda r: (r["species_id"],))[0]
logger.debug("retrieve_species_id result:", result)
return result
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 5b2369c9..a1712500 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -83,7 +83,8 @@ class ConvertGenoFile:
genotypes = row_items[2:]
for item_count, genotype in enumerate(genotypes):
if genotype.upper().strip() in self.configurations:
- this_marker.genotypes.append(self.configurations[genotype.upper().strip()])
+ this_marker.genotypes.append(
+ self.configurations[genotype.upper().strip()])
else:
this_marker.genotypes.append("NA")
@@ -106,9 +107,11 @@ class ConvertGenoFile:
with open(self.output_files[2], "w") as snp_fh:
for marker in self.markers:
if self.mb_exists:
- snp_fh.write(marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n")
+ snp_fh.write(
+ marker['name'] + ", " + str(int(float(marker['Mb']) * 1000000)) + ", " + marker['chr'] + "\n")
else:
- snp_fh.write(marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n")
+ snp_fh.write(
+ marker['name'] + ", " + str(int(float(marker['cM']) * 1000000)) + ", " + marker['chr'] + "\n")
def get_sample_list(self, row_contents):
self.sample_list = []
@@ -160,10 +163,14 @@ class ConvertGenoFile:
group_name = ".".join(input_file.split('.')[:-1])
if group_name == "HSNIH-Palmer":
continue
- geno_output_file = os.path.join(new_directory, group_name + "_geno.txt")
- pheno_output_file = os.path.join(new_directory, group_name + "_pheno.txt")
- snp_output_file = os.path.join(new_directory, group_name + "_snps.txt")
- output_files = [geno_output_file, pheno_output_file, snp_output_file]
+ geno_output_file = os.path.join(
+ new_directory, group_name + "_geno.txt")
+ pheno_output_file = os.path.join(
+ new_directory, group_name + "_pheno.txt")
+ snp_output_file = os.path.join(
+ new_directory, group_name + "_snps.txt")
+ output_files = [geno_output_file,
+ pheno_output_file, snp_output_file]
print("%s -> %s" % (
os.path.join(old_directory, input_file), geno_output_file))
convertob = ConvertGenoFile(input_file, output_files)
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 583a06e1..484336a6 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -120,14 +120,16 @@ def get_types(groups):
else:
if not phenotypes_exist(group_name) and not genotypes_exist(group_name):
types[species].pop(group_name, None)
- groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
+ groups[species] = tuple(
+ group for group in groups[species] if group[0] != group_name)
else: # ZS: This whole else statement might be unnecessary, need to check
types_list = build_types(species, group_name)
if len(types_list) > 0:
types[species][group_name] = types_list
else:
types[species].pop(group_name, None)
- groups[species] = tuple(group for group in groups[species] if group[0] != group_name)
+ groups[species] = tuple(
+ group for group in groups[species] if group[0] != group_name)
return types
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 7cc60c9e..bed634fa 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -21,7 +21,9 @@ class GenerateKinshipMatrices:
self.pheno_file = pheno_file
def generate_kinship(self):
- gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + " -p " + self.pheno_file + " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
+ gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \
+ " -p " + self.pheno_file + \
+ " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
print("command:", gemma_command)
os.system(gemma_command)
@@ -34,9 +36,12 @@ class GenerateKinshipMatrices:
group_name = ".".join(input_file.split('.')[:-1])
if group_name == "HSNIH-Palmer":
continue
- geno_input_file = os.path.join(bimbam_dir, group_name + "_geno.txt")
- pheno_input_file = os.path.join(bimbam_dir, group_name + "_pheno.txt")
- convertob = GenerateKinshipMatrices(group_name, geno_input_file, pheno_input_file)
+ geno_input_file = os.path.join(
+ bimbam_dir, group_name + "_geno.txt")
+ pheno_input_file = os.path.join(
+ bimbam_dir, group_name + "_pheno.txt")
+ convertob = GenerateKinshipMatrices(
+ group_name, geno_input_file, pheno_input_file)
try:
convertob.generate_kinship()
except EmptyConfigurations as why:
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index ad3f2b72..7bdf2b53 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -100,7 +100,8 @@ class ConvertGenoFile:
genotypes = row_items[2:]
for item_count, genotype in enumerate(genotypes):
if genotype.upper() in self.configurations:
- this_marker.genotypes.append(self.configurations[genotype.upper()])
+ this_marker.genotypes.append(
+ self.configurations[genotype.upper()])
else:
this_marker.genotypes.append("NA")
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 1896bc52..ac7689f5 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -34,7 +34,8 @@ def create_dataframe(input_file):
with open(input_file) as f:
ncols = len(f.readline().split("\t"))
- input_array = np.loadtxt(open(input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols)))
+ input_array = np.loadtxt(open(
+ input_file, "rb"), delimiter="\t", skiprows=1, usecols=list(range(1, ncols)))
return pd.DataFrame(input_array)
# This function taken from https://github.com/ShawnLYU/Quantile_Normalize
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index 219a6a29..f4869c45 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -39,7 +39,8 @@ class TestHtmlGenWrapper(unittest.TestCase):
cgi="/testing/",
enctype='multipart/form-data',
name="formName",
- submit=HtmlGenWrapper.create_input_tag(type_='hidden', name='Default_Name')
+ submit=HtmlGenWrapper.create_input_tag(
+ type_='hidden', name='Default_Name')
)
test_image = HtmlGenWrapper.create_image_tag(
src="test.png",
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index f194c6c9..5cbaf0e0 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -70,7 +70,8 @@ class TestGemmaMapping(unittest.TestCase):
], vals=[], covariates="", use_loco=True)
self.assertEqual(mock_os.system.call_count, 2)
mock_gen_pheno_txt.assert_called_once()
- mock_parse_loco.assert_called_once_with(dataset, "GP1_GWA_RRRRRR", True)
+ mock_parse_loco.assert_called_once_with(
+ dataset, "GP1_GWA_RRRRRR", True)
mock_os.path.isfile.assert_called_once_with(
('/home/user/imgfile_output.assoc.txt'))
self.assertEqual(mock_flat_files.call_count, 4)
@@ -102,7 +103,8 @@ class TestGemmaMapping(unittest.TestCase):
create_trait_side_effect = []
for i in range(4):
- create_dataset_side_effect.append(AttributeSetter({"name": f'name_{i}'}))
+ create_dataset_side_effect.append(
+ AttributeSetter({"name": f'name_{i}'}))
create_trait_side_effect.append(
AttributeSetter({"data": [f'data_{i}']}))
@@ -160,9 +162,12 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
results = parse_loco_output(
this_dataset={}, gwa_output_filename=".xw/")
expected_results = [
- {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727},
- {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812},
- {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432},
+ {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85,
+ 'additive': 23.3, 'lod_score': 0.07058107428570727},
+ {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5,
+ 'additive': 24.0, 'lod_score': 0.3010299956639812},
+ {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7,
+ 'additive': 11.6, 'lod_score': 0.1549019599857432},
{'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
self.assertEqual(expected_results, results)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index 5cc8fd0f..c762982b 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -13,10 +13,12 @@ class TestQtlReaperMapping(unittest.TestCase):
samples = ["S1", "S2", "S3", "S4","S5"]
trait_filename = "trait_file"
with mock.patch("builtins.open", mock.mock_open())as mock_open:
- gen_pheno_txt_file(samples=samples, vals=vals, trait_filename=trait_filename)
+ gen_pheno_txt_file(samples=samples, vals=vals,
+ trait_filename=trait_filename)
mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w")
filehandler = mock_open()
- write_calls = [mock.call('Trait\t'), mock.call('S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
+ write_calls = [mock.call('Trait\t'), mock.call(
+ 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
filehandler.write.assert_has_calls(write_calls)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 6267ce9a..6996c275 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -20,7 +20,8 @@ class TestRqtlMapping(unittest.TestCase):
def test_get_trait_data(self, mock_logger, mock_db):
"""test for getting trait data_type return True"""
query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'"""
- mock_db.db.execute.return_value.fetchone.return_value = ["""{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
+ mock_db.db.execute.return_value.fetchone.return_value = [
+ """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
results = get_trait_data_type("traid_id")
mock_db.db.execute.assert_called_with(query_value)
self.assertEqual(results, "fer434f")
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
index a29d8cfb..78cd3be9 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_run_mapping.py
@@ -187,7 +187,8 @@ class TestRunMapping(unittest.TestCase):
mock.call('Time/Date: 09/01/19 / 10:12:12\n'),
mock.call('Population: Human GP1_\n'), mock.call(
'Data Set: dataser_1\n'),
- mock.call('N Samples: 100\n'), mock.call('Transform - Quantile Normalized\n'),
+ mock.call('N Samples: 100\n'), mock.call(
+ 'Transform - Quantile Normalized\n'),
mock.call('Gene Symbol: IGFI\n'), mock.call(
'Location: X1 @ 123313 Mb\n'),
mock.call('Cofactors (dataset - trait):\n'),
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
index 4f91d8ca..69977146 100644
--- a/wqflask/tests/unit/wqflask/test_server_side.py
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -22,10 +22,13 @@ class TestServerSideTableTests(unittest.TestCase):
{'first': 'c', 'second': 1, 'third': 'ss'},
]
headers = ['first', 'second', 'third']
- request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1', 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
+ request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1',
+ 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
- test_page = ServerSideTable(rows_count, table_rows, headers, request_args).get_page()
+ test_page = ServerSideTable(
+ rows_count, table_rows, headers, request_args).get_page()
self.assertEqual(test_page['sEcho'], '1')
self.assertEqual(test_page['iTotalRecords'], 'nan')
self.assertEqual(test_page['iTotalDisplayRecords'], '3')
- self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])
+ self.assertEqual(test_page['data'], [{'first': 'b', 'second': 2, 'third': 'aa'}, {
+ 'first': 'c', 'second': 1, 'third': 'ss'}, {'first': 'd', 'second': 4, 'third': 'zz'}])
diff --git a/wqflask/tests/wqflask/show_trait/testSampleList.py b/wqflask/tests/wqflask/show_trait/testSampleList.py
index 441a88a7..305586ce 100644
--- a/wqflask/tests/wqflask/show_trait/testSampleList.py
+++ b/wqflask/tests/wqflask/show_trait/testSampleList.py
@@ -13,4 +13,5 @@ class TestSampleList(unittest.TestCase):
sorted_list_a = natural_sort(characters_list)
sorted_list_b = natural_sort(names_list)
self.assertEqual(sorted_list_a, ["a", "f", "g", "q", "s", "t", "z"])
- self.assertEqual(sorted_list_b, ["Dataset", "Sample", "publish", "temp1"])
+ self.assertEqual(
+ sorted_list_b, ["Dataset", "Sample", "publish", "temp1"])
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 24c3923e..63df2ba5 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -72,7 +72,8 @@ class TestTraits(unittest.TestCase):
mock_get.return_value = get_return_obj
results = get_ncbi_summary(trait)
mock_exists.assert_called_once()
- mock_get.assert_called_once_with(f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json")
+ mock_get.assert_called_once_with(
+ f"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={trait.geneid}&retmode=json")
self.assertEqual(results, "this is a summary of the geneid")
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index d35b2089..4f5691c1 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -178,7 +178,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
# draw drawing region
im_drawer.rectangle(
- xy=((xLeftOffset, yTopOffset), (xLeftOffset + plotWidth, yTopOffset + plotHeight))
+ xy=((xLeftOffset, yTopOffset),
+ (xLeftOffset + plotWidth, yTopOffset + plotHeight))
)
# draw scale
@@ -199,11 +200,13 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
y = yLow
for i in range(int(stepY) + 1):
yc = yTopOffset + plotHeight - (y - yLow) * yScale
- im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor)
+ im_drawer.line(
+ xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor)
strY = "%d" % y
im_drawer.text(
text=strY,
- xy=(xLeftOffset - im_drawer.textsize(strY, font=scaleFont)[0] - 6, yc + 5),
+ xy=(xLeftOffset - im_drawer.textsize(strY,
+ font=scaleFont)[0] - 6, yc + 5),
font=scaleFont)
y += (yTop - yLow) / stepY
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 48ab1dc0..6ece2f21 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -19,7 +19,8 @@ class Bench:
if self.name:
logger.debug("Starting benchmark: %s" % (self.name))
else:
- logger.debug("Starting benchmark at: %s [%i]" % (inspect.stack()[1][3], inspect.stack()[1][2]))
+ logger.debug("Starting benchmark at: %s [%i]" % (
+ inspect.stack()[1][3], inspect.stack()[1][2]))
self.start_time = time.time()
def __exit__(self, type, value, traceback):
@@ -33,11 +34,13 @@ class Bench:
logger.info(" %s took: %f seconds" % (name, (time_taken)))
if self.name:
- Bench.entries[self.name] = Bench.entries.get(self.name, 0) + time_taken
+ Bench.entries[self.name] = Bench.entries.get(
+ self.name, 0) + time_taken
@classmethod
def report(cls):
- total_time = sum((time_taken for time_taken in list(cls.entries.values())))
+ total_time = sum(
+ (time_taken for time_taken in list(cls.entries.values())))
print("\nTiming report\n")
for name, time_taken in list(cls.entries.items()):
percent = int(round((time_taken / total_time) * 100))
diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py
index 523280a1..da0a21db 100644
--- a/wqflask/utility/corestats.py
+++ b/wqflask/utility/corestats.py
@@ -65,7 +65,8 @@ class Stats:
if len(self.sequence) < 1:
value = None
elif (percentile >= 100):
- sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n' % percentile)
+ sys.stderr.write(
+ 'ERROR: percentile must be < 100. you supplied: %s\n' % percentile)
value = None
else:
element_idx = int(len(self.sequence) * (percentile / 100.0))
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 9415cef0..55907dd5 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -49,7 +49,8 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
def test_elasticsearch_connection():
- es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True)
+ es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + \
+ ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True)
if not es.ping():
logger.warning("Elasticsearch is DOWN")
@@ -88,7 +89,8 @@ def setup_users_index(es_connection):
"type": "keyword"}}}
es_connection.indices.create(index='users', ignore=400)
- es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local")
+ es_connection.indices.put_mapping(
+ body=index_settings, index="users", doc_type="local")
def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 24604e58..e619b7b6 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -38,13 +38,15 @@ class genotype:
def read_rdata_output(self, qtl_results):
# ZS: This is necessary because R/qtl requires centimorgan marker positions, which it normally gets from the .geno file, but that doesn't exist for HET3-ITP (which only has RData), so it needs to read in the marker cM positions from the results
- self.chromosomes = [] # ZS: Overwriting since the .geno file's contents are just placeholders
+ # ZS: Overwriting since the .geno file's contents are just placeholders
+ self.chromosomes = []
this_chr = "" # ZS: This is so it can track when the chromosome changes as it iterates through markers
chr_ob = None
for marker in qtl_results:
locus = Locus(self)
- if (str(marker['chr']) != this_chr) and this_chr != "X": # ZS: This is really awkward but works as a temporary fix
+ # ZS: This is really awkward but works as a temporary fix
+ if (str(marker['chr']) != this_chr) and this_chr != "X":
if this_chr != "":
self.chromosomes.append(chr_ob)
this_chr = str(marker['chr'])
@@ -156,9 +158,11 @@ class Locus:
try:
self.cM = float(marker_row[geno_ob.cm_column])
except:
- self.cM = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0
+ self.cM = float(
+ marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else 0
try:
- self.Mb = float(marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None
+ self.Mb = float(
+ marker_row[geno_ob.mb_column]) if geno_ob.mb_exists else None
except:
self.Mb = self.cM
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 94a08c17..09100bd9 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -92,7 +92,8 @@ class ConvertGenoFile:
genotypes = row_items[2:]
for item_count, genotype in enumerate(genotypes):
if genotype.upper().strip() in self.configurations:
- this_marker.genotypes.append(self.configurations[genotype.upper().strip()])
+ this_marker.genotypes.append(
+ self.configurations[genotype.upper().strip()])
else:
print("WARNING:", genotype.upper())
this_marker.genotypes.append("NA")
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 47079818..d706e32a 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -151,5 +151,6 @@ def getLogger(name, level=None):
else:
logger.setLevel(LOG_LEVEL)
- logger.info("Log level of " + name + " set to " + logging.getLevelName(logger.getEffectiveLevel()))
+ logger.info("Log level of " + name + " set to " + \
+ logging.getLevelName(logger.getEffectiveLevel()))
return gnlogger
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 8052035f..96a4be12 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -133,8 +133,10 @@ def get_user_groups(user_id):
for key in groups_list:
try:
group_ob = json.loads(groups_list[key])
- group_admins = set([this_admin.encode('utf-8') if this_admin else None for this_admin in group_ob['admins']])
- group_members = set([this_member.encode('utf-8') if this_member else None for this_member in group_ob['members']])
+ group_admins = set([this_admin.encode(
+ 'utf-8') if this_admin else None for this_admin in group_ob['admins']])
+ group_members = set([this_member.encode(
+ 'utf-8') if this_member else None for this_member in group_ob['members']])
if user_id in group_admins:
admin_group_ids.append(group_ob['id'])
elif user_id in group_members:
@@ -203,7 +205,8 @@ def get_groups_like_unique_column(column_name, column_value):
if column_value in group_info[column_name]:
matched_groups.append(group_info)
else:
- matched_groups.append(load_json_from_redis(group_list, column_value))
+ matched_groups.append(
+ load_json_from_redis(group_list, column_value))
return matched_groups
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 92f944bc..05f8a2b0 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -28,7 +28,8 @@ def app_config():
port = get_setting_int("SERVER_PORT")
if get_setting_bool("USE_GN_SERVER"):
- print(("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]"))
+ print(
+ ("GN2 API server URL is [" + BLUE + get_setting("GN_SERVER_URL") + ENDC + "]"))
import requests
page = requests.get(get_setting("GN_SERVER_URL"))
if page.status_code != 200:
@@ -37,4 +38,5 @@ def app_config():
# import utility.elasticsearch_tools as es
# es.test_elasticsearch_connection()
- print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL"))))
+ print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" %
+ (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL"))))
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index f5ef81e1..8d2e13ab 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -239,19 +239,23 @@ class pathdata:
def smbezier(self, x2, y2, x, y):
"""smooth bezier with xy2 to xy absolut"""
- self.path.append('S' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
+ self.path.append('S' + str(x2) + ',' + str(y2) + \
+ ' ' + str(x) + ',' + str(y))
def relsmbezier(self, x2, y2, x, y):
"""smooth bezier with xy2 to xy relative"""
- self.path.append('s' + str(x2) + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
+ self.path.append('s' + str(x2) + ',' + str(y2) + \
+ ' ' + str(x) + ',' + str(y))
def qbezier(self, x1, y1, x, y):
"""quadratic bezier with xy1 to xy absolut"""
- self.path.append('Q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y))
+ self.path.append('Q' + str(x1) + ',' + str(y1) + \
+ ' ' + str(x) + ',' + str(y))
def relqbezier(self, x1, y1, x, y):
"""quadratic bezier with xy1 to xy relative"""
- self.path.append('q' + str(x1) + ',' + str(y1) + ' ' + str(x) + ',' + str(y))
+ self.path.append('q' + str(x1) + ',' + str(y1) + \
+ ' ' + str(x) + ',' + str(y))
def smqbezier(self, x, y):
"""smooth quadratic bezier to xy absolut"""
@@ -447,7 +451,8 @@ class rect(SVGelement):
if width == None or height == None:
raise ValueError('both height and width are required')
- SVGelement.__init__(self, 'rect', {'width': width, 'height': height}, **args)
+ SVGelement.__init__(
+ self, 'rect', {'width': width, 'height': height}, **args)
if x != None:
self.attributes['x'] = x
if y != None:
@@ -545,7 +550,8 @@ class polyline(SVGelement):
"""
def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
- SVGelement.__init__(self, 'polyline', {'points': _xypointlist(points)}, **args)
+ SVGelement.__init__(self, 'polyline', {
+ 'points': _xypointlist(points)}, **args)
if fill != None:
self.attributes['fill'] = fill
if stroke_width != None:
@@ -561,7 +567,8 @@ class polygon(SVGelement):
"""
def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
- SVGelement.__init__(self, 'polygon', {'points': _xypointlist(points)}, **args)
+ SVGelement.__init__(
+ self, 'polygon', {'points': _xypointlist(points)}, **args)
if fill != None:
self.attributes['fill'] = fill
if stroke_width != None:
@@ -745,7 +752,8 @@ class image(SVGelement):
def __init__(self, url, x=None, y=None, width=None,height=None,**args):
if width == None or height == None:
raise ValueError('both height and width are required')
- SVGelement.__init__(self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args)
+ SVGelement.__init__(
+ self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args)
if x != None:
self.attributes['x'] = x
if y != None:
@@ -886,7 +894,8 @@ class script(SVGelement):
"""
def __init__(self, type, cdata=None, **args):
- SVGelement.__init__(self, 'script', {'type': type}, cdata=cdata, **args)
+ SVGelement.__init__(
+ self, 'script', {'type': type}, cdata=cdata, **args)
class animate(SVGelement):
@@ -896,7 +905,8 @@ class animate(SVGelement):
"""
def __init__(self, attribute, fr=None, to=None, dur=None,**args):
- SVGelement.__init__(self, 'animate', {'attributeName': attribute}, **args)
+ SVGelement.__init__(
+ self, 'animate', {'attributeName': attribute}, **args)
if fr != None:
self.attributes['from'] = fr
if to != None:
@@ -926,7 +936,8 @@ class animateTransform(SVGelement):
"""
def __init__(self, type=None, fr=None, to=None, dur=None,**args):
- SVGelement.__init__(self, 'animateTransform', {'attributeName': 'transform'}, **args)
+ SVGelement.__init__(self, 'animateTransform', {
+ 'attributeName': 'transform'}, **args)
# As far as I know the attributeName is always transform
if type != None:
self.attributes['type'] = type
@@ -945,7 +956,8 @@ class animateColor(SVGelement):
"""
def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args):
- SVGelement.__init__(self, 'animateColor', {'attributeName': attribute}, **args)
+ SVGelement.__init__(self, 'animateColor', {
+ 'attributeName': attribute}, **args)
if type != None:
self.attributes['type'] = type
if fr != None:
@@ -1020,11 +1032,13 @@ class drawing:
import io
xml = io.StringIO()
xml.write("\n")
- xml.write("\n" % (item, self.entity[item]))
+ xml.write("\n" %
+ (item, self.entity[item]))
xml.write("]")
xml.write(">\n")
self.svg.toXml(0, xml)
@@ -1042,7 +1056,8 @@ class drawing:
else:
if filename[-4:] == 'svgz':
import gzip
- f = gzip.GzipFile(filename=filename, mode="wb", compresslevel=9)
+ f = gzip.GzipFile(filename=filename,
+ mode="wb", compresslevel=9)
f.write(xml.getvalue())
f.close()
else:
@@ -1057,7 +1072,8 @@ class drawing:
writes a svg drawing to the screen or to a file
compresses if filename ends with svgz or if compress is true
"""
- doctype = implementation.createDocumentType('svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
+ doctype = implementation.createDocumentType(
+ 'svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
global root
# root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
@@ -1076,8 +1092,10 @@ class drawing:
if element.text:
textnode = root.createTextNode(element.text)
e.appendChild(textnode)
- for attribute in list(element.attributes.keys()): # in element.attributes is supported from python 2.2
- e.setAttribute(attribute, str(element.attributes[attribute]))
+ # in element.attributes is supported from python 2.2
+ for attribute in list(element.attributes.keys()):
+ e.setAttribute(attribute, str(
+ element.attributes[attribute]))
if element.elements:
for el in element.elements:
e = appender(el, e)
@@ -1105,7 +1123,8 @@ class drawing:
import io
xml = io.StringIO()
PrettyPrint(root, xml)
- f = gzip.GzipFile(filename=filename, mode='wb', compresslevel=9)
+ f = gzip.GzipFile(filename=filename,
+ mode='wb', compresslevel=9)
f.write(xml.getvalue())
f.close()
else:
@@ -1119,7 +1138,8 @@ class drawing:
try:
import xml.parsers.xmlproc.xmlval
except:
- raise exceptions.ImportError('PyXml is required for validating SVG')
+ raise exceptions.ImportError(
+ 'PyXml is required for validating SVG')
svg = self.toXml()
xv = xml.parsers.xmlproc.xmlval.XMLValidator()
try:
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 4fe4db08..263c3948 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -64,7 +64,8 @@ def get_setting(command_id, guess=None):
command = value(guess)
if command is None or command == "":
# print command
- raise Exception(command_id + ' setting unknown or faulty (update default_settings.py?).')
+ raise Exception(
+ command_id + ' setting unknown or faulty (update default_settings.py?).')
# print("Set "+command_id+"="+str(command))
return command
@@ -113,7 +114,8 @@ def js_path(module=None):
try_guix = get_setting("JS_GUIX_PATH") + "/" + module
if valid_path(try_guix):
return try_guix
- raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)"
+ raise "No JS path found for " + module + \
+ " (if not in Guix check JS_GN_PATH)"
def reaper_command(guess=None):
@@ -292,7 +294,8 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
ORCID_AUTH_URL = None
if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \
- ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
+ ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + \
+ "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
@@ -320,7 +323,8 @@ assert_dir(JS_GUIX_PATH + '/cytoscape-panzoom')
CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS
# assert_dir(JS_PATH)
-JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher"))
+JS_TWITTER_POST_FETCHER_PATH = get_setting(
+ "JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher"))
assert_dir(JS_TWITTER_POST_FETCHER_PATH)
assert_file(JS_TWITTER_POST_FETCHER_PATH + "/js/twitterFetcher_min.js")
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index f1dd148f..52026a82 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -25,13 +25,16 @@ def do_correlation(start_vars):
assert('trait_id' in start_vars)
this_dataset = data_set.create_dataset(dataset_name=start_vars['db'])
- target_dataset = data_set.create_dataset(dataset_name=start_vars['target_db'])
- this_trait = create_trait(dataset=this_dataset, name=start_vars['trait_id'])
+ target_dataset = data_set.create_dataset(
+ dataset_name=start_vars['target_db'])
+ this_trait = create_trait(dataset=this_dataset,
+ name=start_vars['trait_id'])
this_trait = retrieve_sample_data(this_trait, this_dataset)
corr_params = init_corr_params(start_vars)
- corr_results = calculate_results(this_trait, this_dataset, target_dataset, corr_params)
+ corr_results = calculate_results(
+ this_trait, this_dataset, target_dataset, corr_params)
#corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0])))
final_results = []
@@ -75,54 +78,66 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
if corr_params['type'] == "tissue":
trait_symbol_dict = this_dataset.retrieve_genes("Symbol")
- corr_results = do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params)
+ corr_results = do_tissue_correlation_for_all_traits(
+ this_trait, trait_symbol_dict, corr_params)
sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
key=lambda t: -abs(t[1][1])))
- elif corr_params['type'] == "literature" or corr_params['type'] == "lit": # ZS: Just so a user can use either "lit" or "literature"
+ # ZS: Just so a user can use either "lit" or "literature"
+ elif corr_params['type'] == "literature" or corr_params['type'] == "lit":
trait_geneid_dict = this_dataset.retrieve_genes("GeneId")
- corr_results = do_literature_correlation_for_all_traits(this_trait, this_dataset, trait_geneid_dict, corr_params)
+ corr_results = do_literature_correlation_for_all_traits(
+ this_trait, this_dataset, trait_geneid_dict, corr_params)
sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
key=lambda t: -abs(t[1][1])))
else:
for target_trait, target_vals in list(target_dataset.trait_data.items()):
- result = get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, corr_params['type'])
+ result = get_sample_r_and_p_values(
+ this_trait, this_dataset, target_vals, target_dataset, corr_params['type'])
if result is not None:
corr_results[target_trait] = result
- sorted_results = collections.OrderedDict(sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0])))
+ sorted_results = collections.OrderedDict(
+ sorted(list(corr_results.items()), key=lambda t: -abs(t[1][0])))
return sorted_results
def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1):
# Gets tissue expression values for the primary trait
- primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=[this_trait.symbol])
+ primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
+ symbol_list=[this_trait.symbol])
if this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
- primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower()]
+ primary_trait_tissue_values = primary_trait_tissue_vals_dict[this_trait.symbol.lower(
+ )]
- corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=list(trait_symbol_dict.values()))
+ corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
+ symbol_list=list(trait_symbol_dict.values()))
tissue_corr_data = {}
for trait, symbol in list(trait_symbol_dict.items()):
if symbol and symbol.lower() in corr_result_tissue_vals_dict:
- this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
+ this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower(
+ )]
result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
this_trait_tissue_values,
corr_params['method'])
- tissue_corr_data[trait] = [result[0], result[1], result[2], symbol]
+ tissue_corr_data[trait] = [
+ result[0], result[1], result[2], symbol]
return tissue_corr_data
def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params):
- input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid)
+ input_trait_mouse_gene_id = convert_to_mouse_gene_id(
+ target_dataset.group.species.lower(), this_trait.geneid)
lit_corr_data = {}
for trait, gene_id in list(trait_geneid_dict.items()):
- mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), gene_id)
+ mouse_gene_id = convert_to_mouse_gene_id(
+ target_dataset.group.species.lower(), gene_id)
if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
result = g.db.execute(
@@ -168,12 +183,15 @@ def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_data
this_trait_vals.append(this_sample_value)
shared_target_vals.append(target_sample_value)
- this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, shared_target_vals)
+ this_trait_vals, shared_target_vals, num_overlap = corr_result_helpers.normalize_values(
+ this_trait_vals, shared_target_vals)
if type == 'pearson':
- sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, shared_target_vals)
+ sample_r, sample_p = scipy.stats.pearsonr(
+ this_trait_vals, shared_target_vals)
else:
- sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, shared_target_vals)
+ sample_r, sample_p = scipy.stats.spearmanr(
+ this_trait_vals, shared_target_vals)
if num_overlap > 5:
if scipy.isnan(sample_r):
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index 662090d5..c22b44a9 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -37,20 +37,25 @@ def do_mapping_for_api(start_vars):
mapping_params = initialize_parameters(start_vars, dataset, this_trait)
- covariates = "" # ZS: It seems to take an empty string as default. This should probably be changed.
+ # ZS: It seems to take an empty string as default. This should probably be changed.
+ covariates = ""
if mapping_params['mapping_method'] == "gemma":
header_row = ["name", "chr", "Mb", "lod_score", "p_value"]
- if mapping_params['use_loco'] == "True": # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api
- result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0]
+ # ZS: gemma_mapping returns both results and the filename for LOCO, so need to only grab the former for api
+ if mapping_params['use_loco'] == "True":
+ result_markers = gemma_mapping.run_gemma(
+ this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])[0]
else:
- result_markers = gemma_mapping.run_gemma(this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])
+ result_markers = gemma_mapping.run_gemma(
+ this_trait, dataset, samples, vals, covariates, mapping_params['use_loco'], mapping_params['maf'])
elif mapping_params['mapping_method'] == "rqtl":
header_row = ["name", "chr", "cM", "lod_score"]
if mapping_params['num_perm'] > 0:
_sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'],
mapping_params['perm_check'], mapping_params['num_perm'],
- mapping_params['do_control'], mapping_params['control_marker'],
+ mapping_params['do_control'], mapping_params[
+ 'control_marker'],
mapping_params['manhattan_plot'], mapping_params['pair_scan'])
else:
result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'],
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 4f9cc6e5..e7dfa4e0 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -35,7 +35,8 @@ def hello_world():
@app.route("/api/v_{}/species".format(version))
def get_species_list():
- results = g.db.execute("SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;")
+ results = g.db.execute(
+ "SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;")
the_species = results.fetchall()
species_list = []
for species in the_species:
@@ -313,7 +314,8 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
@app.route("/api/v_{}/traits/".format(version), methods=("GET",))
@app.route("/api/v_{}/traits/.".format(version), methods=("GET",))
def fetch_traits(dataset_name, file_format="json"):
- trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args)
+ trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(
+ dataset_name, request.args)
if ("ids_only" in request.args) and (len(trait_ids) > 0):
if file_format == "json":
filename = dataset_name + "_trait_ids.json"
@@ -361,7 +363,8 @@ def fetch_traits(dataset_name, file_format="json"):
ProbeSet.Id
"""
- field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb", "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"]
+ field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb",
+ "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"]
elif data_type == "Geno":
query = """
SELECT
@@ -378,7 +381,8 @@ def fetch_traits(dataset_name, file_format="json"):
Geno.Id
"""
- field_list = ["Id", "Name", "Marker_Name", "Chr", "Mb", "Sequence", "Source"]
+ field_list = ["Id", "Name", "Marker_Name",
+ "Chr", "Mb", "Sequence", "Source"]
else:
query = """
SELECT
@@ -394,7 +398,8 @@ def fetch_traits(dataset_name, file_format="json"):
PublishXRef.Id
"""
- field_list = ["Id", "PhenotypeId", "PublicationId", "Locus", "LRS", "Additive", "Sequence"]
+ field_list = ["Id", "PhenotypeId", "PublicationId",
+ "Locus", "LRS", "Additive", "Sequence"]
if 'limit_to' in request.args:
limit_number = request.args['limit_to']
@@ -442,7 +447,8 @@ def fetch_traits(dataset_name, file_format="json"):
@app.route("/api/v_{}/sample_data/".format(version))
@app.route("/api/v_{}/sample_data/.".format(version))
def all_sample_data(dataset_name, file_format="csv"):
- trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(dataset_name, request.args)
+ trait_ids, trait_names, data_type, dataset_id = get_dataset_trait_ids(
+ dataset_name, request.args)
if len(trait_ids) > 0:
sample_list = get_samplelist(dataset_name)
@@ -676,7 +682,8 @@ def get_trait_info(dataset_name, trait_name, file_format="json"):
return flask.jsonify(trait_dict)
else:
- if "Publish" in dataset_name: # ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish"
+ # ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish"
+ if "Publish" in dataset_name:
dataset_name = dataset_name.replace("Publish", "")
group_id = get_group_id(dataset_name)
@@ -711,7 +718,8 @@ def get_corr_results():
results = correlation.do_correlation(request.args)
if len(results) > 0:
- return flask.jsonify(results) # ZS: I think flask.jsonify expects a dict/list instead of JSON
+ # ZS: I think flask.jsonify expects a dict/list instead of JSON
+ return flask.jsonify(results)
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
@@ -768,7 +776,8 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
output_lines.append(line.split())
i += 1
- csv_writer = csv.writer(si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE)
+ csv_writer = csv.writer(
+ si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE)
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
elif file_format == "rqtl2":
@@ -779,18 +788,23 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
filename = group_name
if os.path.isfile("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name)):
- yaml_file = json.load(open("{0}/{1}.json".format(flat_files("genotype/rqtl2"), group_name)))
+ yaml_file = json.load(
+ open("{0}/{1}.json".format(flat_files("genotype/rqtl2"), group_name)))
yaml_file["geno"] = filename + "_geno.csv"
yaml_file["gmap"] = filename + "_gmap.csv"
yaml_file["pheno"] = filename + "_pheno.csv"
config_file = [filename + ".json", json.dumps(yaml_file)]
#config_file = [filename + ".yaml", open("{0}/{1}.yaml".format(flat_files("genotype/rqtl2"), group_name))]
- geno_file = [filename + "_geno.csv", open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))]
- gmap_file = [filename + "_gmap.csv", open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))]
+ geno_file = [filename + "_geno.csv",
+ open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))]
+ gmap_file = [filename + "_gmap.csv",
+ open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))]
if dataset_name:
- phenotypes = requests.get("http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name)
+ phenotypes = requests.get(
+ "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name)
else:
- phenotypes = requests.get("http://gn2.genenetwork.org/api/v_pre1/sample_data/" + group_name + "Publish")
+ phenotypes = requests.get(
+ "http://gn2.genenetwork.org/api/v_pre1/sample_data/" + group_name + "Publish")
with ZipFile(memory_file, 'w', compression=ZIP_DEFLATED) as zf:
zf.writestr(config_file[0], config_file[1])
@@ -813,7 +827,8 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
for line in genofile:
if limit_num and i >= limit_num:
break
- output_lines.append([line.strip() for line in line.split(",")])
+ output_lines.append([line.strip()
+ for line in line.split(",")])
i += 1
csv_writer = csv.writer(si, delimiter=",")
@@ -898,7 +913,8 @@ def get_dataset_trait_ids(dataset_name, start_vars):
results = g.db.execute(query).fetchall()
trait_ids = [result[0] for result in results]
- trait_names = [str(result[2]) + "_" + str(result[1]) for result in results]
+ trait_names = [str(result[2]) + "_" + str(result[1])
+ for result in results]
return trait_ids, trait_names, data_type, dataset_id
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 61f73106..1fcf15f0 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -158,7 +158,8 @@ def remove_traits():
traits_to_remove = params['trait_list']
traits_to_remove = process_traits(traits_to_remove)
- members_now = g.user_session.remove_traits_from_collection(uc_id, traits_to_remove)
+ members_now = g.user_session.remove_traits_from_collection(
+ uc_id, traits_to_remove)
return redirect(url_for("view_collection", uc_id=uc_id))
@@ -181,7 +182,8 @@ def delete_collection():
else:
flash("We've deleted the selected collection.", "alert-info")
else:
- flash("We've deleted the collection: {}.".format(collection_name), "alert-info")
+ flash("We've deleted the collection: {}.".format(
+ collection_name), "alert-info")
return redirect(url_for('list_collections'))
@@ -191,7 +193,8 @@ def view_collection():
params = request.args
uc_id = params['uc_id']
- uc = next((collection for collection in g.user_session.user_collections if collection["id"] == uc_id))
+ uc = next(
+ (collection for collection in g.user_session.user_collections if collection["id"] == uc_id))
traits = uc["members"]
trait_obs = []
@@ -203,12 +206,14 @@ def view_collection():
name, dataset_name = atrait.split(':')
if dataset_name == "Temp":
group = name.split("_")[2]
- dataset = create_dataset(dataset_name, dataset_type="Temp", group_name=group)
+ dataset = create_dataset(
+ dataset_name, dataset_type="Temp", group_name=group)
trait_ob = create_trait(name=name, dataset=dataset)
else:
dataset = create_dataset(dataset_name)
trait_ob = create_trait(name=name, dataset=dataset)
- trait_ob = retrieve_trait_info(trait_ob, dataset, get_qtl_info=True)
+ trait_ob = retrieve_trait_info(
+ trait_ob, dataset, get_qtl_info=True)
trait_obs.append(trait_ob)
json_version.append(jsonable(trait_ob))
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index c135faa3..0fabb833 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -34,14 +34,16 @@ from flask import Flask, g
class ComparisonBarChart:
def __init__(self, start_vars):
- trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+ trait_db_list = [trait.strip()
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
self.all_sample_list = []
self.traits = []
self.insufficient_shared_samples = False
- this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop
+ # ZS: Getting initial group name before verifying all traits are in the same group in the following loop
+ this_group = self.trait_list[0][1].group.name
for trait_db in self.trait_list:
if trait_db[1].group.name != this_group:
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 6afea715..f9a0ea11 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -17,17 +17,21 @@ class CorrScatterPlot:
def __init__(self, params):
if "Temp" in params['dataset_1']:
- self.dataset_1 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1])
+ self.dataset_1 = data_set.create_dataset(
+ dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1])
else:
self.dataset_1 = data_set.create_dataset(params['dataset_1'])
if "Temp" in params['dataset_2']:
- self.dataset_2 = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1])
+ self.dataset_2 = data_set.create_dataset(
+ dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1])
else:
self.dataset_2 = data_set.create_dataset(params['dataset_2'])
#self.dataset_3 = data_set.create_dataset(params['dataset_3'])
- self.trait_1 = create_trait(name=params['trait_1'], dataset=self.dataset_1)
- self.trait_2 = create_trait(name=params['trait_2'], dataset=self.dataset_2)
+ self.trait_1 = create_trait(
+ name=params['trait_1'], dataset=self.dataset_1)
+ self.trait_2 = create_trait(
+ name=params['trait_2'], dataset=self.dataset_2)
#self.trait_3 = create_trait(name=params['trait_3'], dataset=self.dataset_3)
self.method = params['method']
@@ -38,10 +42,13 @@ class CorrScatterPlot:
if self.dataset_1.group.f1list != None:
primary_samples += self.dataset_1.group.f1list
- self.trait_1 = retrieve_sample_data(self.trait_1, self.dataset_1, primary_samples)
- self.trait_2 = retrieve_sample_data(self.trait_2, self.dataset_2, primary_samples)
+ self.trait_1 = retrieve_sample_data(
+ self.trait_1, self.dataset_1, primary_samples)
+ self.trait_2 = retrieve_sample_data(
+ self.trait_2, self.dataset_2, primary_samples)
- samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(self.trait_1.data, self.trait_2.data)
+ samples_1, samples_2, num_overlap = corr_result_helpers.normalize_values_with_samples(
+ self.trait_1.data, self.trait_2.data)
self.data = []
self.indIDs = list(samples_1.keys())
@@ -54,7 +61,8 @@ class CorrScatterPlot:
vals_2.append(samples_2[sample].value)
self.data.append(vals_2)
- slope, intercept, r_value, p_value, std_err = stats.linregress(vals_1, vals_2)
+ slope, intercept, r_value, p_value, std_err = stats.linregress(
+ vals_1, vals_2)
if slope < 0.001:
slope_string = '%.3E' % slope
@@ -67,14 +75,16 @@ class CorrScatterPlot:
x_range = [min(vals_1) - x_buffer, max(vals_1) + x_buffer]
y_range = [min(vals_2) - y_buffer, max(vals_2) + y_buffer]
- intercept_coords = get_intercept_coords(slope, intercept, x_range, y_range)
+ intercept_coords = get_intercept_coords(
+ slope, intercept, x_range, y_range)
rx = stats.rankdata(vals_1)
ry = stats.rankdata(vals_2)
self.rdata = []
self.rdata.append(rx.tolist())
self.rdata.append(ry.tolist())
- srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(rx, ry)
+ srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(
+ rx, ry)
if srslope < 0.001:
srslope_string = '%.3E' % srslope
@@ -86,7 +96,8 @@ class CorrScatterPlot:
sr_range = [min(rx) - x_buffer, max(rx) + x_buffer]
- sr_intercept_coords = get_intercept_coords(srslope, srintercept, sr_range, sr_range)
+ sr_intercept_coords = get_intercept_coords(
+ srslope, srintercept, sr_range, sr_range)
self.collections_exist = "False"
if g.user_session.num_collections > 0:
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index e2fe1ff4..e75c4a85 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -78,7 +78,8 @@ class CorrelationResults:
with Bench("Doing correlations"):
if start_vars['dataset'] == "Temp":
- self.dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group'])
+ self.dataset = data_set.create_dataset(
+ dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group'])
self.trait_id = start_vars['trait_id']
self.this_trait = create_trait(dataset=self.dataset,
name=self.trait_id,
@@ -129,12 +130,15 @@ class CorrelationResults:
if corr_samples_group == 'samples_other':
primary_samples = [x for x in primary_samples if x not in (
self.dataset.group.parlist + self.dataset.group.f1list)]
- self.process_samples(start_vars, list(self.this_trait.data.keys()), primary_samples)
+ self.process_samples(start_vars, list(
+ self.this_trait.data.keys()), primary_samples)
- self.target_dataset = data_set.create_dataset(start_vars['corr_dataset'])
+ self.target_dataset = data_set.create_dataset(
+ start_vars['corr_dataset'])
self.target_dataset.get_trait_data(list(self.sample_data.keys()))
- self.header_fields = get_header_fields(self.target_dataset.type, self.corr_method)
+ self.header_fields = get_header_fields(
+ self.target_dataset.type, self.corr_method)
if self.target_dataset.type == "ProbeSet":
self.filter_cols = [7, 6]
@@ -153,7 +157,8 @@ class CorrelationResults:
tissue_corr_data = self.do_tissue_correlation_for_all_traits()
if tissue_corr_data != None:
for trait in list(tissue_corr_data.keys())[:self.return_number]:
- self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
+ self.get_sample_r_and_p_values(
+ trait, self.target_dataset.trait_data[trait])
else:
for trait, values in list(self.target_dataset.trait_data.items()):
self.get_sample_r_and_p_values(trait, values)
@@ -163,7 +168,8 @@ class CorrelationResults:
lit_corr_data = self.do_lit_correlation_for_all_traits()
for trait in list(lit_corr_data.keys())[:self.return_number]:
- self.get_sample_r_and_p_values(trait, self.target_dataset.trait_data[trait])
+ self.get_sample_r_and_p_values(
+ trait, self.target_dataset.trait_data[trait])
elif self.corr_type == "sample":
for trait, values in list(self.target_dataset.trait_data.items()):
@@ -180,7 +186,8 @@ class CorrelationResults:
range_chr_as_int = order_id
for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]):
- trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
+ trait_object = create_trait(
+ dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
if not trait_object:
continue
@@ -235,7 +242,8 @@ class CorrelationResults:
if self.corr_type != "tissue" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet":
self.do_tissue_correlation_for_trait_list()
- self.json_results = generate_corr_json(self.correlation_results, self.this_trait, self.dataset, self.target_dataset)
+ self.json_results = generate_corr_json(
+ self.correlation_results, self.this_trait, self.dataset, self.target_dataset)
############################################################################################################################################
@@ -263,15 +271,18 @@ class CorrelationResults:
symbol_list=[self.this_trait.symbol])
if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
- primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
- gene_symbol_list = [trait.symbol for trait in self.correlation_results if trait.symbol]
+ primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower(
+ )]
+ gene_symbol_list = [
+ trait.symbol for trait in self.correlation_results if trait.symbol]
corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
symbol_list=gene_symbol_list)
for trait in self.correlation_results:
if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict:
- this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower()]
+ this_trait_tissue_values = corr_result_tissue_vals_dict[trait.symbol.lower(
+ )]
result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
this_trait_tissue_values,
@@ -286,7 +297,8 @@ class CorrelationResults:
symbol_list=[self.this_trait.symbol])
if self.this_trait.symbol.lower() in primary_trait_tissue_vals_dict:
- primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower()]
+ primary_trait_tissue_values = primary_trait_tissue_vals_dict[self.this_trait.symbol.lower(
+ )]
#print("trait_gene_symbols: ", pf(trait_gene_symbols.values()))
corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
@@ -299,7 +311,8 @@ class CorrelationResults:
tissue_corr_data = {}
for trait, symbol in list(self.trait_symbol_dict.items()):
if symbol and symbol.lower() in corr_result_tissue_vals_dict:
- this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower()]
+ this_trait_tissue_values = corr_result_tissue_vals_dict[symbol.lower(
+ )]
result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
this_trait_tissue_values,
@@ -314,12 +327,14 @@ class CorrelationResults:
def do_lit_correlation_for_trait_list(self):
- input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
+ input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(
+ self.dataset.group.species.lower(), self.this_trait.geneid)
for trait in self.correlation_results:
if trait.geneid:
- trait.mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), trait.geneid)
+ trait.mouse_gene_id = self.convert_to_mouse_gene_id(
+ self.dataset.group.species.lower(), trait.geneid)
else:
trait.mouse_gene_id = None
@@ -348,11 +363,13 @@ class CorrelationResults:
trait.lit_corr = 0
def do_lit_correlation_for_all_traits(self):
- input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
+ input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(
+ self.dataset.group.species.lower(), self.this_trait.geneid)
lit_corr_data = {}
for trait, gene_id in list(self.trait_geneid_dict.items()):
- mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), gene_id)
+ mouse_gene_id = self.convert_to_mouse_gene_id(
+ self.dataset.group.species.lower(), gene_id)
if mouse_gene_id and str(mouse_gene_id).find(";") == -1:
#print("gene_symbols:", input_trait_mouse_gene_id + " / " + mouse_gene_id)
@@ -438,21 +455,26 @@ class CorrelationResults:
self.this_trait_vals.append(sample_value)
target_vals.append(target_sample_value)
- self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals)
+ self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
+ self.this_trait_vals, target_vals)
if num_overlap > 5:
# ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/
if self.corr_method == 'bicor':
- sample_r, sample_p = do_bicor(self.this_trait_vals, target_vals)
+ sample_r, sample_p = do_bicor(
+ self.this_trait_vals, target_vals)
elif self.corr_method == 'pearson':
- sample_r, sample_p = scipy.stats.pearsonr(self.this_trait_vals, target_vals)
+ sample_r, sample_p = scipy.stats.pearsonr(
+ self.this_trait_vals, target_vals)
else:
- sample_r, sample_p = scipy.stats.spearmanr(self.this_trait_vals, target_vals)
+ sample_r, sample_p = scipy.stats.spearmanr(
+ self.this_trait_vals, target_vals)
if numpy.isnan(sample_r):
pass
else:
- self.correlation_data[trait] = [sample_r, sample_p, num_overlap]
+ self.correlation_data[trait] = [
+ sample_r, sample_p, num_overlap]
def process_samples(self, start_vars, sample_names, excluded_samples=None):
if not excluded_samples:
@@ -478,7 +500,8 @@ def do_bicor(this_trait_vals, target_trait_vals):
this_vals = ro.Vector(this_trait_vals)
target_vals = ro.Vector(target_trait_vals)
- the_r, the_p, _fisher_transform, _the_t, _n_obs = [numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)]
+ the_r, the_p, _fisher_transform, _the_t, _n_obs = [
+ numpy.asarray(x) for x in r_bicor(x=this_vals, y=target_vals)]
return the_r, the_p
@@ -492,7 +515,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
results_dict['index'] = i + 1
results_dict['trait_id'] = trait.name
results_dict['dataset'] = trait.dataset.name
- results_dict['hmac'] = hmac.data_hmac('{}:{}'.format(trait.name, trait.dataset.name))
+ results_dict['hmac'] = hmac.data_hmac(
+ '{}:{}'.format(trait.name, trait.dataset.name))
if target_dataset.type == "ProbeSet":
results_dict['symbol'] = trait.symbol
results_dict['description'] = "N/A"
@@ -543,7 +567,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
if bool(trait.authors):
authors_list = trait.authors.split(',')
if len(authors_list) > 6:
- results_dict['authors_display'] = ", ".join(authors_list[:6]) + ", et al."
+ results_dict['authors_display'] = ", ".join(
+ authors_list[:6]) + ", et al."
else:
results_dict['authors_display'] = trait.authors
if bool(trait.pubmed_id):
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 331cb1dc..aefb4453 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -44,7 +44,8 @@ THIRTY_DAYS = 60 * 60 * 24 * 30
class CorrelationMatrix:
def __init__(self, start_vars):
- trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+ trait_db_list = [trait.strip()
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
@@ -52,7 +53,8 @@ class CorrelationMatrix:
self.traits = []
self.insufficient_shared_samples = False
self.do_PCA = True
- this_group = self.trait_list[0][1].group.name # ZS: Getting initial group name before verifying all traits are in the same group in the following loop
+ # ZS: Getting initial group name before verifying all traits are in the same group in the following loop
+ this_group = self.trait_list[0][1].group.name
for trait_db in self.trait_list:
this_group = trait_db[1].group.name
this_trait = trait_db[0]
@@ -76,10 +78,12 @@ class CorrelationMatrix:
this_trait_vals.append('')
self.sample_data.append(this_trait_vals)
- if len(this_trait_vals) < len(self.trait_list): # Shouldn't do PCA if there are more traits than observations/samples
+ # Shouldn't do PCA if there are more traits than observations/samples
+ if len(this_trait_vals) < len(self.trait_list):
self.do_PCA = False
- self.lowest_overlap = 8 # ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
+ # ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
+ self.lowest_overlap = 8
self.corr_results = []
self.pca_corr_results = []
@@ -112,7 +116,8 @@ class CorrelationMatrix:
if sample in self.shared_samples_list:
self.shared_samples_list.remove(sample)
- this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, target_vals)
+ this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
+ this_trait_vals, target_vals)
if num_overlap < self.lowest_overlap:
self.lowest_overlap = num_overlap
@@ -120,21 +125,25 @@ class CorrelationMatrix:
corr_result_row.append([target_trait, 0, num_overlap])
pca_corr_result_row.append(0)
else:
- pearson_r, pearson_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
+ pearson_r, pearson_p = scipy.stats.pearsonr(
+ this_trait_vals, target_vals)
if is_spearman == False:
sample_r, sample_p = pearson_r, pearson_p
if sample_r == 1:
is_spearman = True
else:
- sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
+ sample_r, sample_p = scipy.stats.spearmanr(
+ this_trait_vals, target_vals)
- corr_result_row.append([target_trait, sample_r, num_overlap])
+ corr_result_row.append(
+ [target_trait, sample_r, num_overlap])
pca_corr_result_row.append(pearson_r)
self.corr_results.append(corr_result_row)
self.pca_corr_results.append(pca_corr_result_row)
- self.export_filename, self.export_filepath = export_corr_matrix(self.corr_results)
+ self.export_filename, self.export_filepath = export_corr_matrix(
+ self.corr_results)
self.trait_data_array = []
for trait_db in self.trait_list:
@@ -156,12 +165,14 @@ class CorrelationMatrix:
try:
corr_result_eigen = np.linalg.eig(np.array(self.pca_corr_results))
- corr_eigen_value, corr_eigen_vectors = sortEigenVectors(corr_result_eigen)
+ corr_eigen_value, corr_eigen_vectors = sortEigenVectors(
+ corr_result_eigen)
if self.do_PCA == True:
self.pca_works = "True"
self.pca_trait_ids = []
- pca = self.calculate_pca(list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors)
+ pca = self.calculate_pca(
+ list(range(len(self.traits))), corr_eigen_value, corr_eigen_vectors)
self.loadings_array = self.process_loadings()
else:
self.pca_works = "False"
@@ -179,7 +190,8 @@ class CorrelationMatrix:
base = importr('base')
stats = importr('stats')
- corr_results_to_list = robjects.FloatVector([item for sublist in self.pca_corr_results for item in sublist])
+ corr_results_to_list = robjects.FloatVector(
+ [item for sublist in self.pca_corr_results for item in sublist])
m = robjects.r.matrix(corr_results_to_list, nrow=len(cols))
eigen = base.eigen(m)
@@ -198,10 +210,12 @@ class CorrelationMatrix:
pca_traits.append((vector * -1.0).tolist())
this_group_name = self.trait_list[0][1].group.name
- temp_dataset = data_set.create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = this_group_name)
+ temp_dataset = data_set.create_dataset(
+ dataset_name="Temp", dataset_type="Temp", group_name = this_group_name)
temp_dataset.group.get_samplelist()
for i, pca_trait in enumerate(pca_traits):
- trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
+ trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \
+ this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
this_vals_string = ""
position = 0
for sample in temp_dataset.group.all_samples_ordered():
@@ -235,17 +249,23 @@ class CorrelationMatrix:
def export_corr_matrix(corr_results):
- corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
- matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename)
+ corr_matrix_filename = "corr_matrix_" + \
+ ''.join(random.choice(string.ascii_uppercase + string.digits)
+ for _ in range(6))
+ matrix_export_path = "{}{}.csv".format(
+ GENERATED_TEXT_DIR, corr_matrix_filename)
with open(matrix_export_path, "w+") as output_file:
- output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
+ output_file.write(
+ "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
output_file.write("\n")
output_file.write("Correlation ")
for i, item in enumerate(corr_results[0]):
- output_file.write("Trait" + str(i + 1) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t")
+ output_file.write("Trait" + str(i + 1) + ": " + \
+ str(item[0].dataset.name) + "::" + str(item[0].name) + "\t")
output_file.write("\n")
for i, row in enumerate(corr_results):
- output_file.write("Trait" + str(i + 1) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t")
+ output_file.write("Trait" + str(i + 1) + ": " + \
+ str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t")
for item in row:
output_file.write(str(item[1]) + "\t")
output_file.write("\n")
@@ -254,10 +274,12 @@ def export_corr_matrix(corr_results):
output_file.write("\n")
output_file.write("N ")
for i, item in enumerate(corr_results[0]):
- output_file.write("Trait" + str(i) + ": " + str(item[0].dataset.name) + "::" + str(item[0].name) + "\t")
+ output_file.write("Trait" + str(i) + ": " + \
+ str(item[0].dataset.name) + "::" + str(item[0].name) + "\t")
output_file.write("\n")
for i, row in enumerate(corr_results):
- output_file.write("Trait" + str(i) + ": " + str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t")
+ output_file.write("Trait" + str(i) + ": " + \
+ str(row[0][0].dataset.name) + "::" + str(row[0][0].name) + "\t")
for item in row:
output_file.write(str(item[2]) + "\t")
output_file.write("\n")
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index ec66e59f..48a82435 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -46,13 +46,18 @@ class CTL:
#log = r_file("/tmp/genenetwork_ctl.log", open = "wt")
# r_sink(log) # Uncomment the r_sink() commands to log output from stdout/stderr to a file
#r_sink(log, type = "message")
- r_library("ctl") # Load CTL - Should only be done once, since it is quite expensive
+ # Load CTL - Should only be done once, since it is quite expensive
+ r_library("ctl")
r_options(stringsAsFactors=False)
logger.info("Initialization of CTL done, package loaded in R session")
- self.r_CTLscan = ro.r["CTLscan"] # Map the CTLscan function
- self.r_CTLsignificant = ro.r["CTLsignificant"] # Map the CTLsignificant function
- self.r_lineplot = ro.r["ctl.lineplot"] # Map the ctl.lineplot function
- self.r_plotCTLobject = ro.r["plot.CTLobject"] # Map the CTLsignificant function
+ # Map the CTLscan function
+ self.r_CTLscan = ro.r["CTLscan"]
+ # Map the CTLsignificant function
+ self.r_CTLsignificant = ro.r["CTLsignificant"]
+ # Map the ctl.lineplot function
+ self.r_lineplot = ro.r["ctl.lineplot"]
+ # Map the CTLsignificant function
+ self.r_plotCTLobject = ro.r["plot.CTLobject"]
self.nodes_list = []
self.edges_list = []
logger.info("Obtained pointers to CTL functions")
@@ -81,7 +86,8 @@ class CTL:
def run_analysis(self, requestform):
logger.info("Starting CTL analysis on dataset")
- self.trait_db_list = [trait.strip() for trait in requestform['trait_list'].split(',')]
+ self.trait_db_list = [trait.strip()
+ for trait in requestform['trait_list'].split(',')]
self.trait_db_list = [x for x in self.trait_db_list if x]
logger.debug("strategy:", requestform.get("strategy"))
@@ -113,9 +119,11 @@ class CTL:
markers.append(marker["genotypes"])
genotypes = list(itertools.chain(*markers))
- logger.debug(len(genotypes) / len(individuals), "==", len(parser.markers))
+ logger.debug(len(genotypes) / len(individuals),
+ "==", len(parser.markers))
- rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(individuals), dimnames=r_list(markernames, individuals), byrow=True))
+ rGeno = r_t(ro.r.matrix(r_unlist(genotypes), nrow=len(markernames), ncol=len(
+ individuals), dimnames=r_list(markernames, individuals), byrow=True))
# Create a phenotype matrix
traits = []
@@ -131,7 +139,8 @@ class CTL:
else:
traits.append("-999")
- rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True))
+ rPheno = r_t(ro.r.matrix(r_as_numeric(r_unlist(traits)), nrow=len(self.trait_db_list), ncol=len(
+ individuals), dimnames=r_list(self.trait_db_list, individuals), byrow=True))
logger.debug(rPheno)
@@ -144,7 +153,8 @@ class CTL:
#r_write_table(rPheno, "~/outputGN/pheno.csv")
# Perform the CTL scan
- res = self.r_CTLscan(rGeno, rPheno, strategy=strategy, nperm=nperm, parametric = parametric, nthreads=6)
+ res = self.r_CTLscan(rGeno, rPheno, strategy=strategy,
+ nperm=nperm, parametric = parametric, nthreads=6)
# Get significant interactions
significant = self.r_CTLsignificant(res, significance=significance)
@@ -155,20 +165,27 @@ class CTL:
self.results['imgloc1'] = GENERATED_IMAGE_DIR + self.results['imgurl1']
self.results['ctlresult'] = significant
- self.results['requestform'] = requestform # Store the user specified parameters for the output page
+ # Store the user specified parameters for the output page
+ self.results['requestform'] = requestform
# Create the lineplot
- r_png(self.results['imgloc1'], width=1000, height=600, type='cairo-png')
+ r_png(self.results['imgloc1'], width=1000,
+ height=600, type='cairo-png')
self.r_lineplot(res, significance=significance)
r_dev_off()
- n = 2 # We start from 2, since R starts from 1 :)
+ # We start from 2, since R starts from 1 :)
+ n = 2
for trait in self.trait_db_list:
# Create the QTL like CTL plots
- self.results['imgurl' + str(n)] = webqtlUtil.genRandStr("CTL_") + ".png"
- self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + self.results['imgurl' + str(n)]
- r_png(self.results['imgloc' + str(n)], width=1000, height=600, type='cairo-png')
- self.r_plotCTLobject(res, (n - 1), significance=significance, main='Phenotype ' + trait)
+ self.results['imgurl' + \
+ str(n)] = webqtlUtil.genRandStr("CTL_") + ".png"
+ self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + \
+ self.results['imgurl' + str(n)]
+ r_png(self.results['imgloc' + str(n)],
+ width=1000, height=600, type='cairo-png')
+ self.r_plotCTLobject(
+ res, (n - 1), significance=significance, main='Phenotype ' + trait)
r_dev_off()
n = n + 1
@@ -178,17 +195,24 @@ class CTL:
# Create the interactive graph for cytoscape visualization (Nodes and Edges)
if not isinstance(significant, ri.RNULLType):
for x in range(len(significant[0])):
- logger.debug(significant[0][x], significant[1][x], significant[2][x]) # Debug to console
- tsS = significant[0][x].split(':') # Source
- tsT = significant[2][x].split(':') # Target
- gtS = create_trait(name=tsS[0], dataset_name=tsS[1]) # Retrieve Source info from the DB
- gtT = create_trait(name=tsT[0], dataset_name=tsT[1]) # Retrieve Target info from the DB
+ logger.debug(significant[0][x], significant[1]
+ [x], significant[2][x]) # Debug to console
+ # Source
+ tsS = significant[0][x].split(':')
+ # Target
+ tsT = significant[2][x].split(':')
+ # Retrieve Source info from the DB
+ gtS = create_trait(name=tsS[0], dataset_name=tsS[1])
+ # Retrieve Target info from the DB
+ gtT = create_trait(name=tsT[0], dataset_name=tsT[1])
self.addNode(gtS)
self.addNode(gtT)
self.addEdge(gtS, gtT, significant, x)
- significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name) # Update the trait name for the displayed table
- significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name) # Update the trait name for the displayed table
+ # Update the trait name for the displayed table
+ significant[0][x] = "{} ({})".format(gtS.symbol, gtS.name)
+ # Update the trait name for the displayed table
+ significant[2][x] = "{} ({})".format(gtT.symbol, gtT.name)
self.elements = json.dumps(self.nodes_list + self.edges_list)
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 7442dc72..e50ff50b 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -26,14 +26,16 @@ class DoSearch:
def __init__(self, search_term, search_operator=None, dataset=None, search_type=None):
self.search_term = search_term
# Make sure search_operator is something we expect
- assert search_operator in (None, "=", "<", ">", "<=", ">="), "Bad search operator"
+ assert search_operator in (
+ None, "=", "<", ">", "<=", ">="), "Bad search operator"
self.search_operator = search_operator
self.dataset = dataset
self.search_type = search_type
if self.dataset:
# Get group information for dataset and the species id
- self.species_id = webqtlDatabaseFunction.retrieve_species_id(self.dataset.group.name)
+ self.species_id = webqtlDatabaseFunction.retrieve_species_id(
+ self.dataset.group.name)
def execute(self, query):
"""Executes query and returns results"""
@@ -104,7 +106,8 @@ class MrnaAssaySearch(DoSearch):
search_string = escape(self.search_term[0])
if self.search_term[0] != "*":
- match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % (search_string)
+ match_clause = """((MATCH (ProbeSet.symbol) AGAINST ('%s' IN BOOLEAN MODE))) and """ % (
+ search_string)
else:
match_clause = ""
@@ -223,16 +226,19 @@ class PhenotypeSearch(DoSearch):
# and comment here
# if "'" not in self.search_term[0]:
- search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0]) + "[[:>:]]"
+ search_term = "[[:<:]]" + \
+ self.handle_wildcard(self.search_term[0]) + "[[:>:]]"
if "_" in self.search_term[0]:
if len(self.search_term[0].split("_")[0]) == 3:
- search_term = "[[:<:]]" + self.handle_wildcard(self.search_term[0].split("_")[1]) + "[[:>:]]"
+ search_term = "[[:<:]]" + self.handle_wildcard(
+ self.search_term[0].split("_")[1]) + "[[:>:]]"
# This adds a clause to the query that matches the search term
# against each field in the search_fields tuple
where_clause_list = []
for field in self.search_fields:
- where_clause_list.append('''%s REGEXP "%s"''' % (field, search_term))
+ where_clause_list.append('''%s REGEXP "%s"''' %
+ (field, search_term))
where_clause = "(%s) " % ' OR '.join(where_clause_list)
return where_clause
@@ -364,7 +370,8 @@ class GenotypeSearch(DoSearch):
if self.search_term[0] == "*":
self.query = self.compile_final_query()
else:
- self.query = self.compile_final_query(where_clause=self.get_where_clause())
+ self.query = self.compile_final_query(
+ where_clause=self.get_where_clause())
return self.execute(self.query)
@@ -497,7 +504,8 @@ class LrsSearch(DoSearch):
where_clause = """ %sXRef.LRS > %s and
%sXRef.LRS < %s """ % self.mescape(self.dataset.type,
- min(lrs_min, lrs_max),
+ min(lrs_min,
+ lrs_max),
self.dataset.type,
max(lrs_min, lrs_max))
@@ -537,7 +545,8 @@ class LrsSearch(DoSearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(self.from_clause, self.where_clause)
+ self.query = self.compile_final_query(
+ self.from_clause, self.where_clause)
return self.execute(self.query)
@@ -551,7 +560,8 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause)
+ self.query = self.compile_final_query(
+ from_clause=self.from_clause, where_clause=self.where_clause)
return self.execute(self.query)
@@ -566,7 +576,8 @@ class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(from_clause=self.from_clause, where_clause=self.where_clause)
+ self.query = self.compile_final_query(
+ from_clause=self.from_clause, where_clause=self.where_clause)
return self.execute(self.query)
@@ -593,7 +604,8 @@ class CisTransLrsSearch(DoSearch):
elif len(self.search_term) == 3:
lrs_min, lrs_max, self.mb_buffer = self.search_term
elif len(self.search_term) == 4:
- lrs_min, lrs_max, self.mb_buffer = [float(value) for value in self.search_term[:3]]
+ lrs_min, lrs_max, self.mb_buffer = [
+ float(value) for value in self.search_term[:3]]
chromosome = self.search_term[3]
if "Chr" in chromosome or "chr" in chromosome:
chromosome = int(chromosome[3:])
@@ -636,14 +648,19 @@ class CisTransLrsSearch(DoSearch):
if chromosome:
location_clause = "(%s.Chr = '%s' and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) or (%s.Chr != Geno.Chr and Geno.Chr = '%s')" % (escape(self.dataset.type),
chromosome,
- escape(self.dataset.type),
- escape(self.dataset.type),
+ escape(
+ self.dataset.type),
+ escape(
+ self.dataset.type),
the_operator,
- escape(str(self.mb_buffer)),
- escape(self.dataset.type),
+ escape(
+ str(self.mb_buffer)),
+ escape(
+ self.dataset.type),
chromosome)
else:
- location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type))
+ location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(
+ self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type))
where_clause = sub_clause + """
%sXRef.Locus = Geno.name and
Geno.SpeciesId = %s and
@@ -683,7 +700,8 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(self.from_clause, self.where_clause)
+ self.query = self.compile_final_query(
+ self.from_clause, self.where_clause)
return self.execute(self.query)
@@ -714,7 +732,8 @@ class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
self.from_clause = self.get_from_clause()
self.where_clause = self.get_where_clause()
- self.query = self.compile_final_query(self.from_clause, self.where_clause)
+ self.query = self.compile_final_query(
+ self.from_clause, self.where_clause)
return self.execute(self.query)
@@ -733,7 +752,8 @@ class MeanSearch(MrnaAssaySearch):
where_clause = """ %sXRef.mean > %s and
%sXRef.mean < %s """ % self.mescape(self.dataset.type,
- min(self.mean_min, self.mean_max),
+ min(self.mean_min,
+ self.mean_max),
self.dataset.type,
max(self.mean_min, self.mean_max))
else:
@@ -796,7 +816,8 @@ class PositionSearch(DoSearch):
DoSearch.search_types[search_key] = "PositionSearch"
def get_where_clause(self):
- self.search_term = [float(value) if is_number(value) else value for value in self.search_term]
+ self.search_term = [float(value) if is_number(
+ value) else value for value in self.search_term]
chr, self.mb_min, self.mb_max = self.search_term[:3]
self.chr = str(chr).lower()
self.get_chr()
@@ -806,7 +827,8 @@ class PositionSearch(DoSearch):
%s.Mb < %s """ % self.mescape(self.dataset.type,
self.chr,
self.dataset.type,
- min(self.mb_min, self.mb_max),
+ min(self.mb_min,
+ self.mb_max),
self.dataset.type,
max(self.mb_min, self.mb_max))
@@ -923,7 +945,8 @@ def get_aliases(symbol, species):
return []
filtered_aliases = []
- response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string)
+ response = requests.get(
+ GN2_BASE_URL + "/gn3/gene/aliases/" + symbol_string)
if response:
alias_list = json.loads(response.content)
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 81424b9c..fc93248a 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -35,11 +35,13 @@ class Docs:
def update_text(start_vars):
content = start_vars['ckcontent']
- content = content.replace('%', '%%').replace('"', '\\"').replace("'", "\\'")
+ content = content.replace('%', '%%').replace(
+ '"', '\\"').replace("'", "\\'")
try:
if g.user_session.record['user_email_address'] == "zachary.a.sloan@gmail.com" or g.user_session.record['user_email_address'] == "labwilliams@gmail.com":
- sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format(content, start_vars['entry_type'])
+ sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format(
+ content, start_vars['entry_type'])
g.db.execute(sql)
except:
pass
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index d0745ef7..5bd54f9d 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -35,9 +35,12 @@ def export_search_results_csv(targs):
metadata.append(["Data Set: " + targs['database_name']])
if 'accession_id' in targs:
if targs['accession_id'] != "None":
- metadata.append(["Metadata Link: http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + targs['accession_id']])
- metadata.append(["Export Date: " + datetime.datetime.now().strftime("%B %d, %Y")])
- metadata.append(["Export Time: " + datetime.datetime.now().strftime("%H:%M GMT")])
+ metadata.append(
+ ["Metadata Link: http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=" + targs['accession_id']])
+ metadata.append(
+ ["Export Date: " + datetime.datetime.now().strftime("%B %d, %Y")])
+ metadata.append(
+ ["Export Time: " + datetime.datetime.now().strftime("%H:%M GMT")])
if 'search_string' in targs:
if targs['search_string'] != "None":
metadata.append(["Search Query: " + targs['search_string']])
@@ -52,10 +55,12 @@ def export_search_results_csv(targs):
for trait in table_rows:
trait_name, dataset_name, _hash = trait.split(":")
trait_ob = create_trait(name=trait_name, dataset_name=dataset_name)
- trait_ob = retrieve_trait_info(trait_ob, trait_ob.dataset, get_qtl_info=True)
+ trait_ob = retrieve_trait_info(
+ trait_ob, trait_ob.dataset, get_qtl_info=True)
trait_list.append(trait_ob)
- table_headers = ['Index', 'URL', 'Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID', 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression']
+ table_headers = ['Index', 'URL', 'Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID',
+ 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression']
traits_by_group = sort_traits_by_group(trait_list)
@@ -87,7 +92,8 @@ def export_search_results_csv(targs):
trait_symbol = "N/A"
row_contents = [
i + 1,
- "https://genenetwork.org/show_trait?trait_id=" + str(trait.name) + "&dataset=" + str(trait.dataset.name),
+ "https://genenetwork.org/show_trait?trait_id=" + \
+ str(trait.name) + "&dataset=" + str(trait.dataset.name),
trait.dataset.group.species,
trait.dataset.group.name,
trait.dataset.name,
@@ -117,13 +123,15 @@ def export_search_results_csv(targs):
for sample in trait.dataset.group.samplelist:
if sample in trait.data:
- row_contents += [trait.data[sample].value, trait.data[sample].variance]
+ row_contents += [trait.data[sample].value,
+ trait.data[sample].variance]
else:
row_contents += ["x", "x"]
csv_rows.append(row_contents)
- csv_rows = list(map(list, itertools.zip_longest(*[row for row in csv_rows])))
+ csv_rows = list(
+ map(list, itertools.zip_longest(*[row for row in csv_rows])))
writer.writerows(csv_rows)
csv_data = buff.getvalue()
buff.close()
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index 1556c6a0..3c0f2ca7 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -27,7 +27,8 @@ logger = utility.logger.getLogger(__name__)
class SendToBNW:
def __init__(self, start_vars):
- trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+ trait_db_list = [trait.strip()
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
trait_samples_list = []
@@ -39,7 +40,8 @@ class SendToBNW:
trait1_samples = list(this_sample_data.keys())
trait_samples_list.append(trait1_samples)
- shared_samples = list(set(trait_samples_list[0]).intersection(*trait_samples_list))
+ shared_samples = list(
+ set(trait_samples_list[0]).intersection(*trait_samples_list))
self.form_value = "" # ZS: string that is passed to BNW through form
values_list = []
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index c55c43e6..8af9bee9 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -32,7 +32,8 @@ logger = utility.logger.getLogger(__name__)
class SendToGeneWeaver:
def __init__(self, start_vars):
- trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+ trait_db_list = [trait.strip()
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
self.chip_name = test_chip(self.trait_list)
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index 6b78725c..fd12562f 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -32,7 +32,8 @@ logger = utility.logger.getLogger(__name__)
class SendToWebGestalt:
def __init__(self, start_vars):
- trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+ trait_db_list = [trait.strip()
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
self.chip_name = test_chip(self.trait_list)
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index 69ce3e7a..55a7da0e 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -77,8 +77,10 @@ def remove_users():
admin_ids_to_remove = request.form['selected_admin_ids']
member_ids_to_remove = request.form['selected_member_ids']
- remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(":"), group_id, user_type="admins")
- remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(":"), group_id, user_type="members")
+ remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(
+ ":"), group_id, user_type="admins")
+ remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(
+ ":"), group_id, user_type="members")
return redirect(url_for('view_group', id=group_id))
@@ -88,10 +90,12 @@ def add_users(user_type='members'):
group_id = request.form['group_id']
if user_type == "admins":
user_emails = request.form['admin_emails_to_add'].split(",")
- add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=True)
+ add_users_to_group(g.user_session.user_id, group_id,
+ user_emails, admins=True)
elif user_type == "members":
user_emails = request.form['member_emails_to_add'].split(",")
- add_users_to_group(g.user_session.user_id, group_id, user_emails, admins=False)
+ add_users_to_group(g.user_session.user_id, group_id,
+ user_emails, admins=False)
return redirect(url_for('view_group', id=group_id))
@@ -111,7 +115,8 @@ def add_or_edit_group():
if "group_name" in params:
member_user_ids = set()
admin_user_ids = set()
- admin_user_ids.add(g.user_session.user_id) # ZS: Always add the user creating the group as an admin
+ # ZS: Always add the user creating the group as an admin
+ admin_user_ids.add(g.user_session.user_id)
if "admin_emails_to_add" in params:
admin_emails = params['admin_emails_to_add'].split(",")
for email in admin_emails:
@@ -127,7 +132,8 @@ def add_or_edit_group():
member_user_ids.add(user_details['user_id'])
#send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
- create_group(list(admin_user_ids), list(member_user_ids), params['group_name'])
+ create_group(list(admin_user_ids), list(
+ member_user_ids), params['group_name'])
return redirect(url_for('manage_groups'))
else:
return render_template("admin/create_group.html")
@@ -149,9 +155,11 @@ def send_group_invites(group_id, user_email_list=[], user_type="members"):
((user_type == "members") and (user_details['user_id'] in group_info['members'])):
continue
else:
- send_verification_email(user_details, template_name="email/group_verification.txt", key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group")
+ send_verification_email(user_details, template_name="email/group_verification.txt",
+ key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group")
else:
- temp_password = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+ temp_password = ''.join(random.choice(
+ string.ascii_uppercase + string.digits) for _ in range(6))
user_details = {
'user_id': str(uuid.uuid4()),
'email_address': user_email,
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index a21dae84..9548d130 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -77,18 +77,21 @@ class GSearch:
this_trait['name'] = line[5]
this_trait['dataset'] = line[3]
this_trait['dataset_fullname'] = line[4]
- this_trait['hmac'] = hmac.data_hmac('{}:{}'.format(line[5], line[3]))
+ this_trait['hmac'] = hmac.data_hmac(
+ '{}:{}'.format(line[5], line[3]))
this_trait['species'] = line[0]
this_trait['group'] = line[1]
this_trait['tissue'] = line[2]
this_trait['symbol'] = line[6]
if line[7]:
- this_trait['description'] = line[7].decode('utf-8', 'replace')
+ this_trait['description'] = line[7].decode(
+ 'utf-8', 'replace')
else:
this_trait['description'] = "N/A"
this_trait['location_repr'] = 'N/A'
if (line[8] != "NULL" and line[8] != "") and (line[9] != 0):
- this_trait['location_repr'] = 'Chr%s: %.6f' % (line[8], float(line[9]))
+ this_trait['location_repr'] = 'Chr%s: %.6f' % (
+ line[8], float(line[9]))
try:
this_trait['mean'] = '%.3f' % line[10]
except:
@@ -103,7 +106,8 @@ class GSearch:
this_trait['locus_chr'] = line[16]
this_trait['locus_mb'] = line[17]
- dataset_ob = SimpleNamespace(id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"])
+ dataset_ob = SimpleNamespace(
+ id=this_trait["dataset_id"], type="ProbeSet", species=this_trait["species"])
if dataset_ob.id not in dataset_to_permissions:
permissions = check_resource_availability(dataset_ob)
dataset_to_permissions[dataset_ob.id] = permissions
@@ -118,7 +122,9 @@ class GSearch:
max_lrs_text = "N/A"
if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None:
- max_lrs_text = "Chr" + str(this_trait['locus_chr']) + ": " + str(this_trait['locus_mb'])
+ max_lrs_text = "Chr" + \
+ str(this_trait['locus_chr']) + \
+ ": " + str(this_trait['locus_mb'])
this_trait['max_lrs_text'] = max_lrs_text
trait_list.append(this_trait)
@@ -146,7 +152,8 @@ class GSearch:
if "_" in self.terms:
if len(self.terms.split("_")[0]) == 3:
search_term = self.terms.split("_")[1]
- group_clause = "AND InbredSet.`InbredSetCode` = '{}'".format(self.terms.split("_")[0])
+ group_clause = "AND InbredSet.`InbredSetCode` = '{}'".format(
+ self.terms.split("_")[0])
sql = """
SELECT
Species.`Name`,
@@ -192,18 +199,22 @@ class GSearch:
this_trait['index'] = i + 1
this_trait['name'] = str(line[4])
if len(str(line[12])) == 3:
- this_trait['display_name'] = str(line[12]) + "_" + this_trait['name']
+ this_trait['display_name'] = str(
+ line[12]) + "_" + this_trait['name']
else:
this_trait['display_name'] = this_trait['name']
this_trait['dataset'] = line[2]
this_trait['dataset_fullname'] = line[3]
- this_trait['hmac'] = hmac.data_hmac('{}:{}'.format(line[4], line[2]))
+ this_trait['hmac'] = hmac.data_hmac(
+ '{}:{}'.format(line[4], line[2]))
this_trait['species'] = line[0]
this_trait['group'] = line[1]
if line[9] != None and line[6] != None:
- this_trait['description'] = line[6].decode('utf-8', 'replace')
+ this_trait['description'] = line[6].decode(
+ 'utf-8', 'replace')
elif line[5] != None:
- this_trait['description'] = line[5].decode('utf-8', 'replace')
+ this_trait['description'] = line[5].decode(
+ 'utf-8', 'replace')
else:
this_trait['description'] = "N/A"
if line[13] != None and line[13] != "":
@@ -221,7 +232,8 @@ class GSearch:
else:
this_trait['pubmed_link'] = "N/A"
if line[12]:
- this_trait['display_name'] = line[12] + "_" + str(this_trait['name'])
+ this_trait['display_name'] = line[12] + \
+ "_" + str(this_trait['name'])
this_trait['LRS_score_repr'] = "N/A"
if line[10] != "" and line[10] != None:
this_trait['LRS_score_repr'] = '%3.1f' % line[10]
@@ -230,13 +242,16 @@ class GSearch:
this_trait['additive'] = '%.3f' % line[11]
this_trait['max_lrs_text'] = "N/A"
- trait_ob = create_trait(dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
+ trait_ob = create_trait(
+ dataset_name=this_trait['dataset'], name=this_trait['name'], get_qtl_info=True, get_sample_info=False)
if not trait_ob:
continue
if this_trait['dataset'] == this_trait['group'] + "Publish":
try:
if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
- this_trait['max_lrs_text'] = "Chr" + str(trait_ob.locus_chr) + ": " + str(trait_ob.locus_mb)
+ this_trait['max_lrs_text'] = "Chr" + \
+ str(trait_ob.locus_chr) + \
+ ": " + str(trait_ob.locus_mb)
except:
this_trait['max_lrs_text'] = "N/A"
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 0b477446..aa11caa8 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -18,7 +18,8 @@ logger = getLogger(__name__)
class Heatmap:
def __init__(self, start_vars, temp_uuid):
- trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
+ trait_db_list = [trait.strip()
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
self.temp_uuid = temp_uuid
@@ -33,7 +34,8 @@ class Heatmap:
chrnames = []
self.species = species.TheSpecies(dataset=self.trait_list[0][1])
for key in list(self.species.chromosomes.chromosomes.keys()):
- chrnames.append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length])
+ chrnames.append([self.species.chromosomes.chromosomes[key].name,
+ self.species.chromosomes.chromosomes[key].mb_length])
for trait_db in self.trait_list:
@@ -108,10 +110,13 @@ class Heatmap:
trimmed_samples.append(str(samples[i]))
trimmed_values.append(values[i])
- trait_filename = str(this_trait.name) + "_" + str(self.dataset.name) + "_pheno"
+ trait_filename = str(this_trait.name) + "_" + \
+ str(self.dataset.name) + "_pheno"
gen_pheno_txt_file(trimmed_samples, trimmed_values, trait_filename)
- output_filename = self.dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+ output_filename = self.dataset.group.name + "_GWA_" + \
+ ''.join(random.choice(string.ascii_uppercase + string.digits)
+ for _ in range(6))
reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt -n 1000 -o {4}{5}.txt'.format(flat_files('genotype'),
genofile_name,
@@ -129,9 +134,11 @@ class Heatmap:
self.trait_results[this_trait.name] = []
for qtl in reaper_results:
if qtl['additive'] > 0:
- self.trait_results[this_trait.name].append(-float(qtl['lrs_value']))
+ self.trait_results[this_trait.name].append(
+ -float(qtl['lrs_value']))
else:
- self.trait_results[this_trait.name].append(float(qtl['lrs_value']))
+ self.trait_results[this_trait.name].append(
+ float(qtl['lrs_value']))
def gen_pheno_txt_file(samples, vals, filename):
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 8dd1c7c0..cadff080 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -54,7 +54,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
Mb >= %2.6f AND Mb < %2.6f AND
StrainId1 = %d AND StrainId2 = %d
""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0]
- newdict["snpDensity"] = newdict["snpCount"] / (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0
+ newdict["snpDensity"] = newdict["snpCount"] / \
+ (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0
else:
newdict["snpDensity"] = newdict["snpCount"] = 0
@@ -86,12 +87,14 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
StrainId1 = %d AND StrainId2 = %d
""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0]
- newdict2["snpDensity"] = newdict2["snpCount"] / (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0
+ newdict2["snpDensity"] = newdict2["snpCount"] / \
+ (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0
else:
newdict2["snpDensity"] = newdict2["snpCount"] = 0
try:
- newdict2['GeneLength'] = 1000.0 * (newdict2['TxEnd'] - newdict2['TxStart'])
+ newdict2['GeneLength'] = 1000.0 * \
+ (newdict2['TxEnd'] - newdict2['TxStart'])
except:
pass
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 5c7b81dd..cde822e8 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -307,7 +307,8 @@ class DisplayMappingResults:
if 'color_scheme' in start_vars:
self.color_scheme = start_vars['color_scheme']
if self.color_scheme == "single":
- self.manhattan_single_color = ImageColor.getrgb("#" + start_vars['manhattan_single_color'])
+ self.manhattan_single_color = ImageColor.getrgb(
+ "#" + start_vars['manhattan_single_color'])
if 'permCheck' in list(start_vars.keys()):
self.permChecked = start_vars['permCheck']
@@ -357,7 +358,8 @@ class DisplayMappingResults:
if 'reaper_version' in list(start_vars.keys()) and self.mapping_method == "reaper":
self.reaper_version = start_vars['reaper_version']
if 'output_files' in start_vars:
- self.output_files = ",".join([(the_file if the_file is not None else "") for the_file in start_vars['output_files']])
+ self.output_files = ",".join(
+ [(the_file if the_file is not None else "") for the_file in start_vars['output_files']])
self.categorical_vars = ""
self.perm_strata = ""
@@ -386,16 +388,19 @@ class DisplayMappingResults:
self.dataset.group.genofile = self.genofile_string.split(":")[0]
if self.mapping_method == "reaper" and self.manhattan_plot != True:
- self.genotype = self.dataset.group.read_genotype_file(use_reaper=True)
+ self.genotype = self.dataset.group.read_genotype_file(
+ use_reaper=True)
else:
self.genotype = self.dataset.group.read_genotype_file()
# Darwing Options
try:
if self.selectedChr > -1:
- self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
+ self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(
+ self.GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
else:
- self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
+ self.graphWidth = min(self.GRAPH_MAX_WIDTH, max(
+ self.MULT_GRAPH_MIN_WIDTH, int(start_vars['graphWidth'])))
except:
if self.selectedChr > -1:
self.graphWidth = self.GRAPH_DEFAULT_WIDTH
@@ -472,9 +477,11 @@ class DisplayMappingResults:
""" % (self.dataset.group.name, ", ".join(["'%s'" % X[0] for X in self.ChrList[1:]])))
self.ChrLengthMbList = [x[0] / 1000000.0 for x in self.ChrLengthMbList]
- self.ChrLengthMbSum = reduce(lambda x, y: x + y, self.ChrLengthMbList, 0.0)
+ self.ChrLengthMbSum = reduce(
+ lambda x, y: x + y, self.ChrLengthMbList, 0.0)
if self.ChrLengthMbList:
- self.MbGraphInterval = self.ChrLengthMbSum / (len(self.ChrLengthMbList) * 12) # Empirical Mb interval
+ self.MbGraphInterval = self.ChrLengthMbSum / \
+ (len(self.ChrLengthMbList) * 12) # Empirical Mb interval
else:
self.MbGraphInterval = 1
@@ -482,7 +489,8 @@ class DisplayMappingResults:
for i, _chr in enumerate(self.genotype):
self.ChrLengthCMList.append(_chr[-1].cM - _chr[0].cM)
- self.ChrLengthCMSum = reduce(lambda x, y: x + y, self.ChrLengthCMList, 0.0)
+ self.ChrLengthCMSum = reduce(
+ lambda x, y: x + y, self.ChrLengthCMList, 0.0)
if self.plotScale == 'physic':
self.GraphInterval = self.MbGraphInterval # Mb
@@ -496,7 +504,8 @@ class DisplayMappingResults:
smd = []
for sample in self.sample_vals_dict.keys():
if self.sample_vals_dict[sample] != "x":
- temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
+ temp = GeneralObject(name=sample, value=float(
+ self.sample_vals_dict[sample]))
smd.append(temp)
else:
continue
@@ -506,7 +515,8 @@ class DisplayMappingResults:
if item.name == samplelist[j]:
self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
# default:
- self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT
+ self.graphHeight = self.graphHeight + 2 * \
+ (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT
# END HaplotypeAnalyst
#########################
@@ -529,7 +539,8 @@ class DisplayMappingResults:
self.diffCol = []
for i, strain in enumerate(self.diffCol):
- self.diffCol[i] = g.db.execute("select Id from Strain where Symbol = %s", strain).fetchone()[0]
+ self.diffCol[i] = g.db.execute(
+ "select Id from Strain where Symbol = %s", strain).fetchone()[0]
################################################################
# GeneCollection goes here
@@ -552,13 +563,15 @@ class DisplayMappingResults:
chrName = "X"
else:
chrName = self.selectedChr
- self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "mouse")
+ self.geneCol = GeneUtil.loadGenes(
+ chrName, self.diffCol, self.startMb, self.endMb, "mouse")
elif self.dataset.group.species == "rat":
if self.selectedChr == 21:
chrName = "X"
else:
chrName = self.selectedChr
- self.geneCol = GeneUtil.loadGenes(chrName, self.diffCol, self.startMb, self.endMb, "rat")
+ self.geneCol = GeneUtil.loadGenes(
+ chrName, self.diffCol, self.startMb, self.endMb, "rat")
if self.geneCol and self.intervalAnalystChecked:
#######################################################################
@@ -577,7 +590,8 @@ class DisplayMappingResults:
showLocusForm = ""
intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight))
with Bench("Drawing Plot"):
- gifmap = self.plotIntMapping(intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm)
+ gifmap = self.plotIntMapping(
+ intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm)
self.gifmap = gifmap.__str__()
@@ -593,8 +607,10 @@ class DisplayMappingResults:
# Scales plot differently for high resolution
if self.draw2X:
- intCanvasX2 = Image.new("RGBA", size=(self.graphWidth * 2, self.graphHeight * 2))
- gifmapX2 = self.plotIntMapping(intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2)
+ intCanvasX2 = Image.new("RGBA", size=(
+ self.graphWidth * 2, self.graphHeight * 2))
+ gifmapX2 = self.plotIntMapping(
+ intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2)
intCanvasX2.save(
"{}.png".format(
os.path.join(webqtlConfig.GENERATED_IMAGE_DIR,
@@ -612,7 +628,8 @@ class DisplayMappingResults:
name=showLocusForm,
submit=HtmlGenWrapper.create_input_tag(type_='hidden'))
- hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+"Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
+ hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+ \
+ "Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
for key in hddn.keys():
showLocusForm.append(HtmlGenWrapper.create_input_tag(
name=key, value=hddn[key], type_='hidden'))
@@ -631,7 +648,8 @@ class DisplayMappingResults:
if self.traitList and self.traitList[0].dataset and self.traitList[0].dataset.type == 'Geno':
btminfo.append(HtmlGenWrapper.create_br_tag())
- btminfo.append('Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
+ btminfo.append(
+ 'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb= None, endMb = None, showLocusForm = ""):
im_drawer = ImageDraw.Draw(canvas)
@@ -673,7 +691,8 @@ class DisplayMappingResults:
else:
drawAreaHeight -= 3 * self.BAND_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom
if self.geneChecked:
- drawAreaHeight -= self.NUM_GENE_ROWS * self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom
+ drawAreaHeight -= self.NUM_GENE_ROWS * \
+ self.EACH_GENE_HEIGHT + 3 * self.BAND_SPACING + 10 * zoom
else:
if self.selectedChr > -1:
drawAreaHeight -= 20
@@ -682,7 +701,8 @@ class DisplayMappingResults:
# BEGIN HaplotypeAnalyst
if self.haplotypeAnalystChecked and self.selectedChr > -1:
- drawAreaHeight -= self.EACH_GENE_HEIGHT * (self.NR_INDIVIDUALS + 10) * 2 * zoom
+ drawAreaHeight -= self.EACH_GENE_HEIGHT * \
+ (self.NR_INDIVIDUALS + 10) * 2 * zoom
# END HaplotypeAnalyst
if zoom == 2:
@@ -693,38 +713,48 @@ class DisplayMappingResults:
newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
# Draw the alternating-color background first and get plotXScale
- plotXScale = self.drawGraphBackground(canvas, gifmap, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
+ plotXScale = self.drawGraphBackground(
+ canvas, gifmap, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
# draw bootstap
if self.bootChecked and not self.multipleInterval:
- self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
+ self.drawBootStrapResult(canvas, self.nboot, drawAreaHeight, plotXScale,
+ offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
# Draw clickable region and gene band if selected
if self.plotScale == 'physic' and self.selectedChr > -1:
- self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
+ self.drawClickBand(canvas, gifmap, plotXScale, offset=newoffset,
+ zoom=zoom, startMb=startMb, endMb=endMb)
if self.geneChecked and self.geneCol:
- self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
+ self.drawGeneBand(canvas, gifmap, plotXScale, offset=newoffset,
+ zoom=zoom, startMb=startMb, endMb=endMb)
if self.SNPChecked:
- self.drawSNPTrackNew(canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb)
+ self.drawSNPTrackNew(
+ canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb)
# BEGIN HaplotypeAnalyst
if self.haplotypeAnalystChecked:
- self.drawHaplotypeBand(canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
+ self.drawHaplotypeBand(
+ canvas, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
# END HaplotypeAnalyst
# Draw X axis
- self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
+ self.drawXAxis(canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm,
+ offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
# Draw QTL curve
- self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale, offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
+ self.drawQTL(canvas, drawAreaHeight, gifmap, plotXScale,
+ offset=newoffset, zoom=zoom, startMb=startMb, endMb=endMb)
# draw legend
if self.multipleInterval:
- self.drawMultiTraitName(fd, canvas, gifmap, showLocusForm, offset=newoffset)
+ self.drawMultiTraitName(
+ fd, canvas, gifmap, showLocusForm, offset=newoffset)
elif self.legendChecked:
self.drawLegendPanel(canvas, offset=newoffset, zoom=zoom)
else:
pass
# draw position, no need to use a separate function
- self.drawProbeSetPosition(canvas, plotXScale, offset=newoffset, zoom=zoom)
+ self.drawProbeSetPosition(
+ canvas, plotXScale, offset=newoffset, zoom=zoom)
return gifmap
@@ -756,19 +786,24 @@ class DisplayMappingResults:
if previous_chr_as_int != 1:
BootCoord.append(BootChrCoord)
BootChrCoord = []
- startX += (self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval) * plotXScale
+ startX += (
+ self.ChrLengthDistList[previous_chr_as_int - 2] + self.GraphInterval) * plotXScale
if self.plotScale == 'physic':
Xc = startX + (result['Mb'] - self.startMb) * plotXScale
else:
- Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale
+ Xc = startX + \
+ (result['cM'] - self.qtlresults[0]['cM']) * plotXScale
BootChrCoord.append([Xc, self.bootResult[i]])
else:
for i, result in enumerate(self.qtlresults):
if str(result['chr']) == str(self.ChrList[self.selectedChr][0]):
if self.plotScale == 'physic':
- Xc = startX + (result['Mb'] - self.startMb) * plotXScale
+ Xc = startX + (result['Mb'] - \
+ self.startMb) * plotXScale
else:
- Xc = startX + (result['cM'] - self.qtlresults[0]['cM']) * plotXScale
+ Xc = startX + \
+ (result['cM'] - self.qtlresults[0]
+ ['cM']) * plotXScale
BootChrCoord.append([Xc, self.bootResult[i]])
BootCoord = [BootChrCoord]
@@ -793,14 +828,16 @@ class DisplayMappingResults:
if maxBootCount < bootCount:
maxBootCount = bootCount
# end if
- reducedBootCoord.append([bootStartPixX, BootChrCoord[i][0], bootCount])
+ reducedBootCoord.append(
+ [bootStartPixX, BootChrCoord[i][0], bootCount])
bootStartPixX = BootChrCoord[i][0]
bootCount = BootChrCoord[i][1]
# end else
# end for
# add last piece
if BootChrCoord[-1][0] - bootStartPixX > stepBootStrap / 2.0:
- reducedBootCoord.append([bootStartPixX, BootChrCoord[-1][0], bootCount])
+ reducedBootCoord.append(
+ [bootStartPixX, BootChrCoord[-1][0], bootCount])
else:
reducedBootCoord[-1][2] += bootCount
reducedBootCoord[-1][1] = BootChrCoord[-1][0]
@@ -827,11 +864,13 @@ class DisplayMappingResults:
# draw boot scale
highestPercent = (maxBootCount * 100.0) / nboot
bootScale = Plot.detScale(0, highestPercent)
- bootScale = Plot.frange(bootScale[0], bootScale[1], bootScale[1] / bootScale[2])
+ bootScale = Plot.frange(
+ bootScale[0], bootScale[1], bootScale[1] / bootScale[2])
bootScale = bootScale[:-1] + [highestPercent]
bootOffset = 50 * fontZoom
- bootScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=13 * fontZoom)
+ bootScaleFont = ImageFont.truetype(
+ font=VERDANA_FILE, size=13 * fontZoom)
im_drawer.rectangle(
xy=((canvas.size[0] - bootOffset, yZero - bootHeightThresh),
(canvas.size[0] - bootOffset - 15*zoom, yZero)),
@@ -860,10 +899,12 @@ class DisplayMappingResults:
startPosY = 30
else:
startPosY = 15
- smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom)
+ smallLabelFont = ImageFont.truetype(
+ font=TREBUC_FILE, size=12 * fontZoom)
leftOffset = canvas.size[0] - xRightOffset - 190
im_drawer.rectangle(
- xy=((leftOffset, startPosY - 6), (leftOffset + 12, startPosY + 6)),
+ xy=((leftOffset, startPosY - 6),
+ (leftOffset + 12, startPosY + 6)),
fill=YELLOW, outline=BLACK)
im_drawer.text(xy=(canvas.size[0] - xRightOffset - 170, startPosY + TEXT_Y_DISPLACEMENT),
text='Frequency of the Peak LRS',
@@ -905,7 +946,8 @@ class DisplayMappingResults:
locPixel = xLeftOffset
for i, _chr in enumerate(self.ChrList[1:]):
if _chr[0] != Chr:
- locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale
+ locPixel += (self.ChrLengthDistList[i] + \
+ self.GraphInterval) * plotXScale
else:
locPixel += Mb * plotXScale
break
@@ -921,7 +963,8 @@ class DisplayMappingResults:
# the trait's position is between two traits
if i > 0 and self.qtlresults[i - 1]['Mb'] < Mb and qtlresult['Mb'] >= Mb:
- locPixel = xLeftOffset + plotXScale * (self.qtlresults[i - 1]['Mb'] + (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']) * (Mb - self.qtlresults[i - 1]['Mb']) / (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']))
+ locPixel = xLeftOffset + plotXScale * (self.qtlresults[i - 1]['Mb'] + (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']) * (
+ Mb - self.qtlresults[i - 1]['Mb']) / (qtlresult['Mb'] - self.qtlresults[i - 1]['Mb']))
break
# the trait's position is on the right of the last genotype
@@ -932,12 +975,15 @@ class DisplayMappingResults:
for i, _chr in enumerate(self.ChrList):
if i < (len(self.ChrList) - 1):
if _chr != Chr:
- locPixel += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale
+ locPixel += (self.ChrLengthDistList[i] + \
+ self.GraphInterval) * plotXScale
else:
- locPixel += (Mb * (_chr[-1].cM - _chr[0].cM) / self.ChrLengthCMList[i]) * plotXScale
+ locPixel += (Mb * (_chr[-1].cM - _chr[0].cM) / \
+ self.ChrLengthCMList[i]) * plotXScale
break
if locPixel >= 0 and self.plotScale == 'physic':
- traitPixel = ((locPixel, yZero), (locPixel - 7, yZero + 14), (locPixel + 7, yZero + 14))
+ traitPixel = ((locPixel, yZero), (locPixel - 7,
+ yZero + 14), (locPixel + 7, yZero + 14))
draw_open_polygon(canvas, xy=traitPixel, outline=BLACK,
fill=self.TRANSCRIPT_LOCATION_COLOR)
@@ -979,7 +1025,8 @@ class DisplayMappingResults:
maxCount = max(SNPCounts)
if maxCount > 0:
for i in range(xLeftOffset, xLeftOffset + plotWidth):
- snpDensity = float(SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount)
+ snpDensity = float(
+ SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount)
im_drawer.line(
xy=((i, drawSNPLocationY + (snpDensity) * zoom),
(i, drawSNPLocationY - (snpDensity) * zoom)),
@@ -1015,12 +1062,16 @@ class DisplayMappingResults:
(rectWidth + rightShift, yPaddingTop + 10+kstep*15)),
fill=thisLRSColor, outline=BLACK)
im_drawer.text(
- text=name, xy=(rectWidth + 2 + rightShift, yPaddingTop + 10 + kstep * 15),
+ text=name, xy=(rectWidth + 2 + rightShift,
+ yPaddingTop + 10 + kstep * 15),
font=colorFont, fill=BLACK)
if thisTrait.db:
- COORDS = "%d,%d,%d,%d" % (rectWidth + 2 + rightShift, yPaddingTop + kstep * 15, rectWidth + 2 + rightShift + nameWidth, yPaddingTop + 10 + kstep * 15,)
- HREF = "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
- Areas = HtmlGenWrapper.create_area_tag(shape='rect', coords=COORDS, href=HREF)
+ COORDS = "%d,%d,%d,%d" % (rectWidth + 2 + rightShift, yPaddingTop + kstep * \
+ 15, rectWidth + 2 + rightShift + nameWidth, yPaddingTop + 10 + kstep * 15,)
+ HREF = "javascript:showDatabase3('%s','%s','%s','');" % (
+ showLocusForm, thisTrait.db.name, thisTrait.name)
+ Areas = HtmlGenWrapper.create_area_tag(
+ shape='rect', coords=COORDS, href=HREF)
gifmap.append(Areas) # TODO
def drawLegendPanel(self, canvas, offset=(40, 120, 80, 10), zoom=1):
@@ -1042,7 +1093,8 @@ class DisplayMappingResults:
if hasattr(self.traitList[0], 'chr') and hasattr(self.traitList[0], 'mb'):
startPosY = 15
nCol = 2
- smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12 * fontZoom)
+ smallLabelFont = ImageFont.truetype(
+ font=TREBUC_FILE, size=12 * fontZoom)
leftOffset = canvas.size[0] - xRightOffset - 190
draw_open_polygon(
@@ -1064,7 +1116,8 @@ class DisplayMappingResults:
xy=((startPosX, startPosY), (startPosX + 32, startPosY)),
fill=self.LRS_COLOR, width=2)
im_drawer.text(
- text=self.LRS_LOD, xy=(startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT),
+ text=self.LRS_LOD, xy=(
+ startPosX + 40, startPosY + TEXT_Y_DISPLACEMENT),
font=labelFont, fill=BLACK)
startPosY += stepPosY
@@ -1118,10 +1171,12 @@ class DisplayMappingResults:
xy=((thisStartX, startPosY), (startPosX + 32, startPosY)),
fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
im_drawer.line(
- xy=((thisStartX, startPosY + stepPosY), (startPosX + 32, startPosY + stepPosY)),
+ xy=((thisStartX, startPosY + stepPosY),
+ (startPosX + 32, startPosY + stepPosY)),
fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
im_drawer.text(
- text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant),
+ text='Significant %s = %2.2f' % (
+ self.LRS_LOD, self.significant),
xy=(thisStartX + 40, startPosY + TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
im_drawer.text(
text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
@@ -1134,7 +1189,8 @@ class DisplayMappingResults:
if self.dataset.type == "Publish" or self.dataset.type == "Geno":
dataset_label = self.dataset.fullname
else:
- dataset_label = "%s - %s" % (self.dataset.group.name, self.dataset.fullname)
+ dataset_label = "%s - %s" % (self.dataset.group.name,
+ self.dataset.fullname)
string1 = 'Dataset: %s' % (dataset_label)
@@ -1151,7 +1207,8 @@ class DisplayMappingResults:
string3 = 'Using GEMMA mapping method with '
if self.covariates != "":
string3 += 'the cofactors below:'
- cofactor_names = ", ".join([covar.split(":")[0] for covar in self.covariates.split(",")])
+ cofactor_names = ", ".join(
+ [covar.split(":")[0] for covar in self.covariates.split(",")])
string4 = cofactor_names
else:
string3 += 'no cofactors'
@@ -1159,7 +1216,8 @@ class DisplayMappingResults:
string3 = 'Using R/qtl mapping method with '
if self.covariates != "":
string3 += 'the cofactors below:'
- cofactor_names = ", ".join([covar.split(":")[0] for covar in self.covariates.split(",")])
+ cofactor_names = ", ".join(
+ [covar.split(":")[0] for covar in self.covariates.split(",")])
string4 = cofactor_names
elif self.controlLocus and self.doControl != "false":
string3 += '%s as control' % self.controlLocus
@@ -1177,15 +1235,19 @@ class DisplayMappingResults:
if self.selectedChr == -1:
identification = "Mapping on All Chromosomes for "
else:
- identification = "Mapping on Chromosome %s for " % (self.ChrList[self.selectedChr][0])
+ identification = "Mapping on Chromosome %s for " % (
+ self.ChrList[self.selectedChr][0])
if self.this_trait.symbol:
- identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.symbol)
+ identification += "Trait: %s - %s" % (
+ self.this_trait.name, self.this_trait.symbol)
elif self.dataset.type == "Publish":
if self.this_trait.post_publication_abbreviation:
- identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.post_publication_abbreviation)
+ identification += "Trait: %s - %s" % (
+ self.this_trait.name, self.this_trait.post_publication_abbreviation)
elif self.this_trait.pre_publication_abbreviation:
- identification += "Trait: %s - %s" % (self.this_trait.name, self.this_trait.pre_publication_abbreviation)
+ identification += "Trait: %s - %s" % (
+ self.this_trait.name, self.this_trait.pre_publication_abbreviation)
else:
identification += "Trait: %s" % (self.this_trait.name)
else:
@@ -1265,7 +1327,8 @@ class DisplayMappingResults:
tenPercentLength = geneLength * 0.0001
SNPdensity = theGO["snpCount"] / geneLength
- exonStarts = list(map(float, theGO['exonStarts'].split(",")[:-1]))
+ exonStarts = list(
+ map(float, theGO['exonStarts'].split(",")[:-1]))
exonEnds = list(map(float, theGO['exonEnds'].split(",")[:-1]))
cdsStart = theGO['cdsStart']
cdsEnd = theGO['cdsEnd']
@@ -1274,8 +1337,10 @@ class DisplayMappingResults:
strand = theGO["Strand"]
exonCount = theGO["exonCount"]
- geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb)
- geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel
+ geneStartPix = xLeftOffset + \
+ plotXScale * (float(txStart) - startMb)
+ geneEndPix = xLeftOffset + plotXScale * \
+ (float(txEnd) - startMb) # at least one pixel
if (geneEndPix < xLeftOffset):
return; # this gene is not on the screen
@@ -1290,7 +1355,8 @@ class DisplayMappingResults:
# found earlier, needs to be recomputed as snps are added
# always apply colors now, even if SNP Track not checked - Zach 11/24/2010
- densities = [1.0000000000000001e-05, 0.094094033555233408, 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
+ densities = [1.0000000000000001e-05, 0.094094033555233408,
+ 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
if SNPdensity < densities[0]:
myColor = BLACK
elif SNPdensity < densities[1]:
@@ -1309,7 +1375,8 @@ class DisplayMappingResults:
outlineColor = myColor
fillColor = myColor
- TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % (geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount)
+ TITLE = "Gene: %s (%s)\nFrom %2.3f to %2.3f Mb (%s)\nNum. exons: %d." % (
+ geneSymbol, accession, float(txStart), float(txEnd), strand, exonCount)
# NL: 06-02-2011 Rob required to change this link for gene related
HREF = geneNCBILink % geneSymbol
@@ -1324,8 +1391,10 @@ class DisplayMappingResults:
strand = theGO["Strand"]
exonCount = 0
- geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb)
- geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) # at least one pixel
+ geneStartPix = xLeftOffset + \
+ plotXScale * (float(txStart) - startMb)
+ geneEndPix = xLeftOffset + plotXScale * \
+ (float(txEnd) - startMb) # at least one pixel
if (geneEndPix < xLeftOffset):
return; # this gene is not on the screen
@@ -1338,7 +1407,8 @@ class DisplayMappingResults:
outlineColor = DARKBLUE
fillColor = DARKBLUE
- TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (geneSymbol, float(txStart), float(txEnd), strand)
+ TITLE = "Gene: %s\nFrom %2.3f to %2.3f Mb (%s)" % (
+ geneSymbol, float(txStart), float(txEnd), strand)
# NL: 06-02-2011 Rob required to change this link for gene related
HREF = geneNCBILink % geneSymbol
else:
@@ -1347,7 +1417,8 @@ class DisplayMappingResults:
TITLE = "Gene: %s" % geneSymbol
# Draw Genes
- geneYLocation = yPaddingTop + (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT * zoom
+ geneYLocation = yPaddingTop + \
+ (gIndex % self.NUM_GENE_ROWS) * self.EACH_GENE_HEIGHT * zoom
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING
else:
@@ -1361,7 +1432,8 @@ class DisplayMappingResults:
# draw the line that runs the entire length of the gene
im_drawer.line(
xy=(
- (geneStartPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 * zoom),
+ (geneStartPix, geneYLocation + \
+ self.EACH_GENE_HEIGHT / 2 * zoom),
(geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 *zoom)),
fill=outlineColor, width=1)
@@ -1401,8 +1473,10 @@ class DisplayMappingResults:
# draw the blocks for the exon regions
for i in range(0, len(exonStarts)):
- exonStartPix = (exonStarts[i] - startMb) * plotXScale + xLeftOffset
- exonEndPix = (exonEnds[i] - startMb) * plotXScale + xLeftOffset
+ exonStartPix = (
+ exonStarts[i] - startMb) * plotXScale + xLeftOffset
+ exonEndPix = (exonEnds[i] - startMb) * \
+ plotXScale + xLeftOffset
if (exonStartPix < xLeftOffset):
exonStartPix = xLeftOffset
if (exonEndPix < xLeftOffset):
@@ -1418,7 +1492,8 @@ class DisplayMappingResults:
# draw gray blocks for 3' and 5' UTR blocks
if cdsStart and cdsEnd:
- utrStartPix = (txStart - startMb) * plotXScale + xLeftOffset
+ utrStartPix = (txStart - startMb) * \
+ plotXScale + xLeftOffset
utrEndPix = (cdsStart - startMb) * plotXScale + xLeftOffset
if (utrStartPix < xLeftOffset):
utrStartPix = xLeftOffset
@@ -1436,7 +1511,8 @@ class DisplayMappingResults:
labelText = "5'"
im_drawer.text(
text=labelText,
- xy=(utrStartPix - 9, geneYLocation + self.EACH_GENE_HEIGHT),
+ xy=(utrStartPix - 9, geneYLocation + \
+ self.EACH_GENE_HEIGHT),
font=ImageFont.truetype(font=ARIAL_FILE, size=2))
# the second UTR region
@@ -1459,7 +1535,8 @@ class DisplayMappingResults:
labelText = "3'"
im_drawer.text(
text=labelText,
- xy=(utrEndPix + 2, geneYLocation + self.EACH_GENE_HEIGHT),
+ xy=(utrEndPix + 2, geneYLocation + \
+ self.EACH_GENE_HEIGHT),
font=ImageFont.truetype(font=ARIAL_FILE, size=2))
# draw the genes as rectangles
@@ -1469,7 +1546,8 @@ class DisplayMappingResults:
(geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT * zoom))),
outline=outlineColor, fill=fillColor)
- COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
+ COORDS = "%d, %d, %d, %d" % (
+ geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
# NL: 06-02-2011 Rob required to display NCBI info in a new window
gifmap.append(
HtmlGenWrapper.create_area_tag(
@@ -1496,7 +1574,8 @@ class DisplayMappingResults:
smd = []
for sample in self.sample_vals_dict.keys():
if self.sample_vals_dict[sample] != "x" and sample in samplelist:
- temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
+ temp = GeneralObject(name=sample, value=float(
+ self.sample_vals_dict[sample]))
smd.append(temp)
else:
continue
@@ -1517,8 +1596,10 @@ class DisplayMappingResults:
txStart = _chr[i].Mb
txEnd = _chr[i].Mb
- geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0
- geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) - 0
+ geneStartPix = xLeftOffset + plotXScale * \
+ (float(txStart) - startMb) - 0
+ geneEndPix = xLeftOffset + plotXScale * \
+ (float(txEnd) - startMb) - 0
drawit = 1
if (geneStartPix < xLeftOffset):
@@ -1546,8 +1627,10 @@ class DisplayMappingResults:
txStart = _chr[j].Mb
txEnd = _chr[j].Mb
- geneStartPix = xLeftOffset + plotXScale * (float(txStart) - startMb) - 0
- geneEndPix = xLeftOffset + plotXScale * (float(txEnd) - startMb) + 0
+ geneStartPix = xLeftOffset + plotXScale * \
+ (float(txStart) - startMb) - 0
+ geneEndPix = xLeftOffset + plotXScale * \
+ (float(txEnd) - startMb) + 0
if oldgeneEndPix >= xLeftOffset:
drawStart = oldgeneEndPix + 4
@@ -1585,7 +1668,8 @@ class DisplayMappingResults:
# Draw Genes
- geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * (self.EACH_GENE_HEIGHT) * zoom
+ geneYLocation = yPaddingTop + self.NUM_GENE_ROWS * \
+ (self.EACH_GENE_HEIGHT) * zoom
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
geneYLocation += 4 * self.BAND_HEIGHT + 4 * self.BAND_SPACING
else:
@@ -1606,7 +1690,8 @@ class DisplayMappingResults:
if (plotbxd == 1):
ind = 0
if samplelist[k] in [item.name for item in smd]:
- ind = [item.name for item in smd].index(samplelist[k])
+ ind = [item.name for item in smd].index(
+ samplelist[k])
maxind = max(ind, maxind)
@@ -1637,8 +1722,10 @@ class DisplayMappingResults:
geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)),
outline=outlineColor, fill=fillColor)
- COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT))
- TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
+ COORDS = "%d, %d, %d, %d" % (
+ geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT))
+ TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (
+ samplelist[k], _chr[j].name, float(txStart))
HREF = ''
gifmap.append(
HtmlGenWrapper.create_area_tag(
@@ -1683,7 +1770,8 @@ class DisplayMappingResults:
plotbxd = 1
if (plotbxd == 1):
- ind = [item.name for item in smd].index(samplelist[j]) - 1
+ ind = [item.name for item in smd].index(
+ samplelist[j]) - 1
expr = smd[ind].value
# Place where font is hardcoded
@@ -1691,13 +1779,15 @@ class DisplayMappingResults:
text="%s" % (samplelist[j]),
xy=((xLeftOffset + plotWidth + 10),
geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
- font=ImageFont.truetype(font=VERDANA_FILE, size=12),
+ font=ImageFont.truetype(
+ font=VERDANA_FILE, size=12),
fill=BLACK)
im_drawer.text(
text="%2.2f" % (expr),
xy=((xLeftOffset + plotWidth + 60),
geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
- font=ImageFont.truetype(font=VERDANA_FILE, size=12),
+ font=ImageFont.truetype(
+ font=VERDANA_FILE, size=12),
fill=BLACK)
# END HaplotypeAnalyst
@@ -1719,12 +1809,16 @@ class DisplayMappingResults:
# but it makes the HTML huge, and takes forever to render the page in the first place)
# Draw the bands that you can click on to go to UCSC / Ensembl
MAX_CLICKABLE_REGION_DIVISIONS = 100
- clickableRegionLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=9)
- pixelStep = max(5, int(float(plotWidth) / MAX_CLICKABLE_REGION_DIVISIONS))
+ clickableRegionLabelFont = ImageFont.truetype(
+ font=VERDANA_FILE, size=9)
+ pixelStep = max(
+ 5, int(float(plotWidth) / MAX_CLICKABLE_REGION_DIVISIONS))
# pixelStep: every N pixels, we make a new clickable area for the user to go to that area of the genome.
- numBasesCurrentlyOnScreen = self.kONE_MILLION * abs(startMb - endMb) # Number of bases on screen now
- flankingWidthInBases = int (min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION)))
+ numBasesCurrentlyOnScreen = self.kONE_MILLION * \
+ abs(startMb - endMb) # Number of bases on screen now
+ flankingWidthInBases = int (
+ min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION)))
webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0
# Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing.
@@ -1733,23 +1827,33 @@ class DisplayMappingResults:
paddingTop = yTopOffset
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
- phenogenPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING)
- ucscPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING)
- ensemblPaddingTop = paddingTop + 3 * (self.BAND_HEIGHT + self.BAND_SPACING)
+ phenogenPaddingTop = paddingTop + \
+ (self.BAND_HEIGHT + self.BAND_SPACING)
+ ucscPaddingTop = paddingTop + 2 * \
+ (self.BAND_HEIGHT + self.BAND_SPACING)
+ ensemblPaddingTop = paddingTop + 3 * \
+ (self.BAND_HEIGHT + self.BAND_SPACING)
else:
- ucscPaddingTop = paddingTop + (self.BAND_HEIGHT + self.BAND_SPACING)
- ensemblPaddingTop = paddingTop + 2 * (self.BAND_HEIGHT + self.BAND_SPACING)
+ ucscPaddingTop = paddingTop + \
+ (self.BAND_HEIGHT + self.BAND_SPACING)
+ ensemblPaddingTop = paddingTop + 2 * \
+ (self.BAND_HEIGHT + self.BAND_SPACING)
if zoom == 1:
for pixel in range(xLeftOffset, xLeftOffset + plotWidth, pixelStep):
- calBase = self.kONE_MILLION * (startMb + (endMb - startMb) * (pixel - xLeftOffset - 0.0) / plotWidth)
+ calBase = self.kONE_MILLION * \
+ (startMb + (endMb - startMb) * \
+ (pixel - xLeftOffset - 0.0) / plotWidth)
xBrowse1 = pixel
- xBrowse2 = min(xLeftOffset + plotWidth, (pixel + pixelStep - 1))
+ xBrowse2 = min(xLeftOffset + plotWidth,
+ (pixel + pixelStep - 1))
- WEBQTL_COORDS = "%d, %d, %d, %d" % (xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT))
- WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase - webqtlZoomWidth)) / 1000000.0, (calBase + webqtlZoomWidth) / 1000000.0)
+ WEBQTL_COORDS = "%d, %d, %d, %d" % (
+ xBrowse1, paddingTop, xBrowse2, (paddingTop + self.BAND_HEIGHT))
+ WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(
+ 0, (calBase - webqtlZoomWidth)) / 1000000.0, (calBase + webqtlZoomWidth) / 1000000.0)
WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
gifmap.append(
@@ -1764,15 +1868,19 @@ class DisplayMappingResults:
outline=self.CLICKABLE_WEBQTL_REGION_COLOR,
fill=self.CLICKABLE_WEBQTL_REGION_COLOR)
im_drawer.line(
- xy=((xBrowse1, paddingTop), (xBrowse1, (paddingTop + self.BAND_HEIGHT))),
+ xy=((xBrowse1, paddingTop), (xBrowse1,
+ (paddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
- PHENOGEN_COORDS = "%d, %d, %d, %d" % (xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT))
+ PHENOGEN_COORDS = "%d, %d, %d, %d" % (
+ xBrowse1, phenogenPaddingTop, xBrowse2, (phenogenPaddingTop + self.BAND_HEIGHT))
if self.dataset.group.species == "mouse":
- PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
+ PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (
+ self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
else:
- PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
+ PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (
+ self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
gifmap.append(
HtmlGenWrapper.create_area_tag(
@@ -1786,14 +1894,18 @@ class DisplayMappingResults:
outline=self.CLICKABLE_PHENOGEN_REGION_COLOR,
fill=self.CLICKABLE_PHENOGEN_REGION_COLOR)
im_drawer.line(
- xy=((xBrowse1, phenogenPaddingTop), (xBrowse1, (phenogenPaddingTop + self.BAND_HEIGHT))),
+ xy=((xBrowse1, phenogenPaddingTop), (xBrowse1,
+ (phenogenPaddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
- UCSC_COORDS = "%d, %d, %d, %d" % (xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT))
+ UCSC_COORDS = "%d, %d, %d, %d" % (
+ xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop + self.BAND_HEIGHT))
if self.dataset.group.species == "mouse":
- UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr)
+ UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=%s/snp/chr%s" % (
+ self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases, webqtlConfig.PORTADDR, self.selectedChr)
else:
- UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
+ UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (
+ self._ucscDb, self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
gifmap.append(
HtmlGenWrapper.create_area_tag(
@@ -1811,11 +1923,14 @@ class DisplayMappingResults:
(xBrowse1, (ucscPaddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_UCSC_REGION_OUTLINE_COLOR)
- ENSEMBL_COORDS = "%d, %d, %d, %d" % (xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT))
+ ENSEMBL_COORDS = "%d, %d, %d, %d" % (
+ xBrowse1, ensemblPaddingTop, xBrowse2, (ensemblPaddingTop + self.BAND_HEIGHT))
if self.dataset.group.species == "mouse":
- ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
+ ENSEMBL_HREF = "http://www.ensembl.org/Mus_musculus/contigview?highlight=&chr=%s&vc_start=%d&vc_end=%d&x=35&y=12" % (
+ self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
else:
- ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
+ ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (
+ self.selectedChr, max(0, calBase - flankingWidthInBases), calBase + flankingWidthInBases)
ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
gifmap.append(HtmlGenWrapper.create_area_tag(
shape='rect',
@@ -1841,19 +1956,23 @@ class DisplayMappingResults:
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
im_drawer.text(
text="Click to view the corresponding section of the genome in PhenoGen",
- xy=((xLeftOffset + 10), phenogenPaddingTop), # + self.BAND_HEIGHT/2),
+ # + self.BAND_HEIGHT/2),
+ xy=((xLeftOffset + 10), phenogenPaddingTop),
font=clickableRegionLabelFont, fill=self.CLICKABLE_PHENOGEN_TEXT_COLOR)
im_drawer.text(
text="Click to view the corresponding section of the genome in the UCSC Genome Browser",
- xy=((xLeftOffset + 10), ucscPaddingTop), # + self.BAND_HEIGHT/2),
+ # + self.BAND_HEIGHT/2),
+ xy=((xLeftOffset + 10), ucscPaddingTop),
font=clickableRegionLabelFont, fill=self.CLICKABLE_UCSC_TEXT_COLOR)
im_drawer.text(
text="Click to view the corresponding section of the genome in the Ensembl Genome Browser",
- xy=((xLeftOffset + 10), ensemblPaddingTop), # + self.BAND_HEIGHT/2),
+ # + self.BAND_HEIGHT/2),
+ xy=((xLeftOffset + 10), ensemblPaddingTop),
font=clickableRegionLabelFont, fill=self.CLICKABLE_ENSEMBL_TEXT_COLOR)
# draw the gray text
- chrFont = ImageFont.truetype(font=VERDANA_BOLD_FILE, size=26 * zoom)
+ chrFont = ImageFont.truetype(
+ font=VERDANA_BOLD_FILE, size=26 * zoom)
chrX = xLeftOffset + plotWidth - 2 - im_drawer.textsize(
"Chr %s" % self.ChrList[self.selectedChr][0], font=chrFont)[0]
im_drawer.text(
@@ -1922,8 +2041,10 @@ class DisplayMappingResults:
(Xc, yZero + xMajorTickHeight)),
fill=xAxisTickMarkColor,
width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
- labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
- strWidth, strHeight = im_drawer.textsize(labelStr, font=MBLabelFont)
+ # What Mbase location to put on the label
+ labelStr = str(formatStr % _Mb)
+ strWidth, strHeight = im_drawer.textsize(
+ labelStr, font=MBLabelFont)
drawStringXc = (Xc - (strWidth / 2.0))
im_drawer.text(xy=(drawStringXc, strYLoc),
text=labelStr, font=MBLabelFont,
@@ -1956,9 +2077,11 @@ class DisplayMappingResults:
canvas, text=str(tickdists), font=MBLabelFont,
xy=(startPosX + tickdists * plotXScale,
yZero + 10 * zoom), fill=BLACK, angle=270)
- startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale
+ startPosX += (self.ChrLengthDistList[i] + \
+ self.GraphInterval) * plotXScale
- megabaseLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5))
+ megabaseLabelFont = ImageFont.truetype(
+ font=VERDANA_FILE, size=int(18 * zoom * 1.5))
im_drawer.text(
text="Megabases",
xy=(
@@ -1984,7 +2107,8 @@ class DisplayMappingResults:
if _locus.cM != preLpos:
distinctCount += 1
preLpos = _locus.cM
- thisChr.append([_locus.name, _locus.cM - Locus0CM])
+ thisChr.append(
+ [_locus.name, _locus.cM - Locus0CM])
else:
for j in (0, nLoci / 4, nLoci / 2, nLoci*3/4, -1):
while _chr[j].name == ' - ':
@@ -1992,7 +2116,8 @@ class DisplayMappingResults:
if _chr[j].cM != preLpos:
distinctCount += 1
preLpos = _chr[j].cM
- thisChr.append([_chr[j].name, _chr[j].cM - Locus0CM])
+ thisChr.append(
+ [_chr[j].name, _chr[j].cM - Locus0CM])
ChrAInfo.append(thisChr)
else:
for i, _chr in enumerate(self.genotype):
@@ -2004,7 +2129,8 @@ class DisplayMappingResults:
if _locus.cM != preLpos:
distinctCount += 1
preLpos = _locus.cM
- thisChr.append([_locus.name, _locus.cM - Locus0CM])
+ thisChr.append(
+ [_locus.name, _locus.cM - Locus0CM])
ChrAInfo.append(thisChr)
stepA = (plotWidth + 0.0) / distinctCount
@@ -2053,7 +2179,8 @@ class DisplayMappingResults:
outline=rectColor, fill=rectColor, width=0)
COORDS = "%d,%d,%d,%d" % (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth)
- HREF = "/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name + "Geno")
+ HREF = "/show_trait?trait_id=%s&dataset=%s" % (
+ Lname, self.dataset.group.name + "Geno")
#HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
Areas = HtmlGenWrapper.create_area_tag(
shape='rect',
@@ -2067,9 +2194,11 @@ class DisplayMappingResults:
im_drawer.line(
xy=((startPosX, yZero), (startPosX, yZero + 40)),
fill=lineColor)
- startPosX += (self.ChrLengthDistList[j] + self.GraphInterval) * plotXScale
+ startPosX += (self.ChrLengthDistList[j] + \
+ self.GraphInterval) * plotXScale
- centimorganLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5))
+ centimorganLabelFont = ImageFont.truetype(
+ font=VERDANA_FILE, size=int(18 * zoom * 1.5))
im_drawer.text(
text="Centimorgans",
xy=(xLeftOffset + (plotWidth - im_drawer.textsize(
@@ -2100,29 +2229,39 @@ class DisplayMappingResults:
# ZS: This is a mess, but I don't know a better way to account for different mapping methods returning results in different formats + the option to change between LRS and LOD
if self.lrsMax <= 0: # sliding scale
if "lrs_value" in self.qtlresults[0]:
- LRS_LOD_Max = max([result['lrs_value'] for result in self.qtlresults])
+ LRS_LOD_Max = max([result['lrs_value']
+ for result in self.qtlresults])
if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
- self.significant = min(self.significant / self.LODFACTOR, webqtlConfig.MAXLRS)
- self.suggestive = min(self.suggestive / self.LODFACTOR, webqtlConfig.MAXLRS)
+ self.significant = min(
+ self.significant / self.LODFACTOR, webqtlConfig.MAXLRS)
+ self.suggestive = min(
+ self.suggestive / self.LODFACTOR, webqtlConfig.MAXLRS)
else:
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
- self.significant = min(self.significant, webqtlConfig.MAXLRS)
- self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)
+ self.significant = min(
+ self.significant, webqtlConfig.MAXLRS)
+ self.suggestive = min(
+ self.suggestive, webqtlConfig.MAXLRS)
else:
pass
else:
- LRS_LOD_Max = max([result['lod_score'] for result in self.qtlresults])
+ LRS_LOD_Max = max([result['lod_score']
+ for result in self.qtlresults])
if self.LRS_LOD == "LRS":
LRS_LOD_Max = LRS_LOD_Max * self.LODFACTOR
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
- self.significant = min(self.significant * self.LODFACTOR, webqtlConfig.MAXLRS)
- self.suggestive = min(self.suggestive * self.LODFACTOR, webqtlConfig.MAXLRS)
+ self.significant = min(
+ self.significant * self.LODFACTOR, webqtlConfig.MAXLRS)
+ self.suggestive = min(
+ self.suggestive * self.LODFACTOR, webqtlConfig.MAXLRS)
else:
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
- self.significant = min(self.significant, webqtlConfig.MAXLRS)
- self.suggestive = min(self.suggestive, webqtlConfig.MAXLRS)
+ self.significant = min(
+ self.significant, webqtlConfig.MAXLRS)
+ self.suggestive = min(
+ self.suggestive, webqtlConfig.MAXLRS)
else:
pass
@@ -2143,7 +2282,8 @@ class DisplayMappingResults:
self.js_data = json.dumps(js_data)
LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom)
- LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5))
+ LRSLODFont = ImageFont.truetype(
+ font=VERDANA_FILE, size=int(18 * zoom * 1.5))
yZero = yTopOffset + plotHeight
# LRSHeightThresh = drawAreaHeight
@@ -2188,7 +2328,8 @@ class DisplayMappingResults:
# draw the "LRS" or "LOD" string to the left of the axis
LRSScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom)
- LRSLODFont = ImageFont.truetype(font=VERDANA_FILE, size=int(18 * zoom * 1.5))
+ LRSLODFont = ImageFont.truetype(
+ font=VERDANA_FILE, size=int(18 * zoom * 1.5))
yZero = yTopOffset + plotHeight
# TEXT_X_DISPLACEMENT = -20
@@ -2239,7 +2380,8 @@ class DisplayMappingResults:
# ZS: I don't know if what I did here with this inner function is clever or overly complicated, but it's the only way I could think of to avoid duplicating the code inside this function
def add_suggestive_significant_lines_and_legend(start_pos_x, chr_length_dist):
- rightEdge = int(start_pos_x + chr_length_dist * plotXScale - self.SUGGESTIVE_WIDTH / 1.5)
+ rightEdge = int(start_pos_x + chr_length_dist * \
+ plotXScale - self.SUGGESTIVE_WIDTH / 1.5)
im_drawer.line(
xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, suggestiveY),
(rightEdge, suggestiveY)),
@@ -2253,15 +2395,19 @@ class DisplayMappingResults:
width=self.SIGNIFICANT_WIDTH * zoom
# , clipX=(xLeftOffset, xLeftOffset + plotWidth-2)
)
- sugg_coords = "%d, %d, %d, %d" % (start_pos_x, suggestiveY - 2, rightEdge + 2 * zoom, suggestiveY + 2)
- sig_coords = "%d, %d, %d, %d" % (start_pos_x, significantY - 2, rightEdge + 2 * zoom, significantY + 2)
+ sugg_coords = "%d, %d, %d, %d" % (
+ start_pos_x, suggestiveY - 2, rightEdge + 2 * zoom, suggestiveY + 2)
+ sig_coords = "%d, %d, %d, %d" % (
+ start_pos_x, significantY - 2, rightEdge + 2 * zoom, significantY + 2)
if self.LRS_LOD == 'LRS':
sugg_title = "Suggestive LRS = %0.2f" % self.suggestive
sig_title = "Significant LRS = %0.2f" % self.significant
else:
- sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive / 4.61)
- sig_title = "Significant LOD = %0.2f" % (self.significant / 4.61)
+ sugg_title = "Suggestive LOD = %0.2f" % (
+ self.suggestive / 4.61)
+ sig_title = "Significant LOD = %0.2f" % (
+ self.significant / 4.61)
Areas1 = HtmlGenWrapper.create_area_tag(
shape='rect',
coords=sugg_coords,
@@ -2273,24 +2419,28 @@ class DisplayMappingResults:
gifmap.append(Areas1)
gifmap.append(Areas2)
- start_pos_x += (chr_length_dist + self.GraphInterval) * plotXScale
+ start_pos_x += (chr_length_dist + \
+ self.GraphInterval) * plotXScale
return start_pos_x
for i, _chr in enumerate(self.genotype):
if self.selectedChr != -1:
if _chr.name == self.ChrList[self.selectedChr][0]:
- startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[0])
+ startPosX = add_suggestive_significant_lines_and_legend(
+ startPosX, self.ChrLengthDistList[0])
break
else:
continue
else:
- startPosX = add_suggestive_significant_lines_and_legend(startPosX, self.ChrLengthDistList[i])
+ startPosX = add_suggestive_significant_lines_and_legend(
+ startPosX, self.ChrLengthDistList[i])
if self.multipleInterval:
lrsEdgeWidth = 1
else:
if self.additiveChecked:
- additiveMax = max([abs(X['additive']) for X in self.qtlresults])
+ additiveMax = max([abs(X['additive'])
+ for X in self.qtlresults])
lrsEdgeWidth = 3
if zoom == 2:
@@ -2300,7 +2450,8 @@ class DisplayMappingResults:
AdditiveCoordXY = []
DominanceCoordXY = []
- symbolFont = ImageFont.truetype(font=FNT_BS_FILE, size=5) # ZS: For Manhattan Plot
+ symbolFont = ImageFont.truetype(
+ font=FNT_BS_FILE, size=5) # ZS: For Manhattan Plot
previous_chr = 1
previous_chr_as_int = 0
@@ -2332,7 +2483,8 @@ class DisplayMappingResults:
if Xc == Xc0: # genotype , locus distance is 0
Xcm = Xc
else:
- Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0
+ Xcm = (yZero - Yc0) / \
+ ((Yc - Yc0) / (Xc - Xc0)) + Xc0
if Yc0 < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xcm, yZero)),
@@ -2340,7 +2492,8 @@ class DisplayMappingResults:
# , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
im_drawer.line(
- xy=((Xcm, yZero), (Xc, yZero - (Yc - yZero))),
+ xy=((Xcm, yZero),
+ (Xc, yZero - (Yc - yZero))),
fill=minusColor, width=lineWidth
# , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
@@ -2391,7 +2544,8 @@ class DisplayMappingResults:
AdditiveCoordXY = []
previous_chr = qtlresult['chr']
previous_chr_as_int += 1
- newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1] + self.GraphInterval) * plotXScale
+ newStartPosX = (
+ self.ChrLengthDistList[previous_chr_as_int - 1] + self.GraphInterval) * plotXScale
if newStartPosX != oldStartPosX:
startPosX += newStartPosX
oldStartPosX = newStartPosX
@@ -2408,10 +2562,12 @@ class DisplayMappingResults:
if self.genotype.filler:
if self.selectedChr != -1:
start_cm = self.genotype[self.selectedChr - 1][0].cM
- Xc = startPosX + (qtlresult['Mb'] - start_cm) * plotXScale
+ Xc = startPosX + \
+ (qtlresult['Mb'] - start_cm) * plotXScale
else:
start_cm = self.genotype[previous_chr_as_int][0].cM
- Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * (((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale))
+ Xc = startPosX + ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) * (
+ ((qtlresult['Mb'] - start_cm - startMb) * plotXScale) / ((qtlresult['Mb'] - start_cm - startMb + self.GraphInterval) * plotXScale))
else:
Xc = startPosX + (qtlresult['Mb'] - startMb) * plotXScale
@@ -2425,17 +2581,23 @@ class DisplayMappingResults:
if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR)
- Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR)
+ Yc = yZero - webqtlConfig.MAXLRS * \
+ LRSHeightThresh / \
+ (LRS_LOD_Max * self.LODFACTOR)
else:
#Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR)
- Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / (LRS_LOD_Max * self.LODFACTOR)
+ Yc = yZero - \
+ qtlresult['lrs_value'] * LRSHeightThresh / \
+ (LRS_LOD_Max * self.LODFACTOR)
else:
if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1]
Yc = yZero - webqtlConfig.MAXLRS * LRSHeightThresh / LRS_LOD_Max
else:
#Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1]
- Yc = yZero - qtlresult['lrs_value'] * LRSHeightThresh / LRS_LOD_Max
+ Yc = yZero - \
+ qtlresult['lrs_value'] * \
+ LRSHeightThresh / LRS_LOD_Max
else:
if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf':
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1]
@@ -2443,10 +2605,14 @@ class DisplayMappingResults:
else:
if self.LRS_LOD == "LRS":
#Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1]
- Yc = yZero - qtlresult['lod_score'] * self.LODFACTOR * LRSHeightThresh / LRS_LOD_Max
+ Yc = yZero - \
+ qtlresult['lod_score'] * self.LODFACTOR * \
+ LRSHeightThresh / LRS_LOD_Max
else:
#Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1]
- Yc = yZero - qtlresult['lod_score'] * LRSHeightThresh / LRS_LOD_Max
+ Yc = yZero - \
+ qtlresult['lod_score'] * \
+ LRSHeightThresh / LRS_LOD_Max
if self.manhattan_plot == True:
if self.color_scheme == "single":
@@ -2462,7 +2628,8 @@ class DisplayMappingResults:
im_drawer.text(
text="5",
xy=(
- Xc - im_drawer.textsize("5", font=symbolFont)[0] / 2 + 1,
+ Xc - im_drawer.textsize("5",
+ font=symbolFont)[0] / 2 + 1,
Yc - 4),
fill=point_color, font=symbolFont)
else:
@@ -2471,7 +2638,8 @@ class DisplayMappingResults:
if not self.multipleInterval and self.additiveChecked:
if additiveMax == 0.0:
additiveMax = 0.000001
- Yc = yZero - qtlresult['additive'] * AdditiveHeightThresh / additiveMax
+ Yc = yZero - qtlresult['additive'] * \
+ AdditiveHeightThresh / additiveMax
AdditiveCoordXY.append((Xc, Yc))
m += 1
@@ -2496,7 +2664,8 @@ class DisplayMappingResults:
if Xc == Xc0: # genotype , locus distance is 0
Xcm = Xc
else:
- Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0
+ Xcm = (yZero - Yc0) / \
+ ((Yc - Yc0) / (Xc - Xc0)) + Xc0
if Yc0 < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xcm, yZero)),
@@ -2561,7 +2730,8 @@ class DisplayMappingResults:
if Xc == Xc0: # genotype , locus distance is 0
Xcm = Xc
else:
- Xcm = (yZero - Yc0) / ((Yc - Yc0) / (Xc - Xc0)) + Xc0
+ Xcm = (yZero - Yc0) / \
+ ((Yc - Yc0) / (Xc - Xc0)) + Xc0
if Yc0 < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xcm, yZero)),
@@ -2616,9 +2786,11 @@ class DisplayMappingResults:
# draw additive scale
if not self.multipleInterval and self.additiveChecked:
- additiveScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom)
+ additiveScaleFont = ImageFont.truetype(
+ font=VERDANA_FILE, size=16 * zoom)
additiveScale = Plot.detScaleOld(0, additiveMax)
- additiveStep = (additiveScale[1] - additiveScale[0]) / additiveScale[2]
+ additiveStep = (additiveScale[1] - \
+ additiveScale[0]) / additiveScale[2]
additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
addPlotScale = AdditiveHeightThresh / additiveMax
TEXT_Y_DISPLACEMENT = -8
@@ -2633,7 +2805,8 @@ class DisplayMappingResults:
scaleStr = "%2.3f" % item
im_drawer.text(
text=scaleStr,
- xy= (xLeftOffset + plotWidth + 6, additiveY + TEXT_Y_DISPLACEMENT),
+ xy= (xLeftOffset + plotWidth + 6,
+ additiveY + TEXT_Y_DISPLACEMENT),
font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE)
im_drawer.line(
@@ -2690,14 +2863,16 @@ class DisplayMappingResults:
plotXScale = plotWidth / drawRegionDistance
else: # multiple chromosome view
- plotXScale = plotWidth / ((len(self.genotype) - 1) * self.GraphInterval + drawRegionDistance)
+ plotXScale = plotWidth / \
+ ((len(self.genotype) - 1) * self.GraphInterval + drawRegionDistance)
startPosX = xLeftOffset
if fontZoom == 1.5:
chrFontZoom = 2
else:
chrFontZoom = 1
- chrLabelFont = ImageFont.truetype(font=VERDANA_FILE, size=24 * chrFontZoom)
+ chrLabelFont = ImageFont.truetype(
+ font=VERDANA_FILE, size=24 * chrFontZoom)
for i, _chr in enumerate(self.genotype):
if (i % 2 == 0):
@@ -2712,14 +2887,18 @@ class DisplayMappingResults:
outline=GAINSBORO,
fill=theBackColor)
- chrNameWidth, chrNameHeight = im_drawer.textsize(_chr.name, font=chrLabelFont)
- chrStartPix = startPosX + (self.ChrLengthDistList[i] * plotXScale - chrNameWidth) / 2
- chrEndPix = startPosX + (self.ChrLengthDistList[i] * plotXScale + chrNameWidth) / 2
+ chrNameWidth, chrNameHeight = im_drawer.textsize(
+ _chr.name, font=chrLabelFont)
+ chrStartPix = startPosX + \
+ (self.ChrLengthDistList[i] * plotXScale - chrNameWidth) / 2
+ chrEndPix = startPosX + \
+ (self.ChrLengthDistList[i] * plotXScale + chrNameWidth) / 2
TEXT_Y_DISPLACEMENT = 0
im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT),
text=_chr.name, font=chrLabelFont, fill=BLACK)
- COORDS = "%d,%d,%d,%d" % (chrStartPix, yTopOffset, chrEndPix, yTopOffset + 20)
+ COORDS = "%d,%d,%d,%d" % (
+ chrStartPix, yTopOffset, chrEndPix, yTopOffset + 20)
# add by NL 09-03-2010
HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList)
@@ -2729,7 +2908,8 @@ class DisplayMappingResults:
coords=COORDS,
href=HREF)
gifmap.append(Areas)
- startPosX += (self.ChrLengthDistList[i] + self.GraphInterval) * plotXScale
+ startPosX += (self.ChrLengthDistList[i] + \
+ self.GraphInterval) * plotXScale
return plotXScale
@@ -2746,7 +2926,8 @@ class DisplayMappingResults:
perm_output = self.perm_output
filename = webqtlUtil.genRandStr("Reg_")
- Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD, YLabel='Frequency', title=' Histogram of Permutation Test')
+ Plot.plotBar(myCanvas, perm_output, XLabel=self.LRS_LOD,
+ YLabel='Frequency', title=' Histogram of Permutation Test')
myCanvas.save("{}.gif".format(GENERATED_IMAGE_DIR + filename),
format='gif')
@@ -2825,7 +3006,8 @@ class DisplayMappingResults:
txEnd = theGO["TxEnd"]
theGO["snpDensity"] = theGO["snpCount"] / geneLength
if self.ALEX_DEBUG_BOOL_PRINT_GENE_LIST:
- geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO["GeneID"]
+ geneIdString = 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s' % theGO[
+ "GeneID"]
if theGO["snpCount"]:
snpString = HT.Link(
@@ -2842,7 +3024,9 @@ class DisplayMappingResults:
else:
snpString = 0
- mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit"
+ mouseStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Mouse&db=mm9&position=chr" + \
+ theGO["Chromosome"] + "%3A" + str(int(theGO["TxStart"] * 1000000.0)) + "-" + str(
+ int(theGO["TxEnd"] * 1000000.0)) + "&pix=620&Submit=submit"
# the chromosomes for human 1 are 1qXX.XX
if theGO['humanGene']:
@@ -2854,7 +3038,8 @@ class DisplayMappingResults:
humanChr = theGO['humanGene']["Chromosome"]
humanTxStart = theGO['humanGene']["TxStart"]
- humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (humanChr, int(1000000 * theGO['humanGene']["TxStart"]), int(1000000 * theGO['humanGene']["TxEnd"]))
+ humanStartString = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg17&position=chr%s:%d-%d" % (
+ humanChr, int(1000000 * theGO['humanGene']["TxStart"]), int(1000000 * theGO['humanGene']["TxEnd"]))
else:
humanStartString = humanChr = humanStartDisplay = "--"
@@ -2879,7 +3064,8 @@ class DisplayMappingResults:
else:
chr_as_int = int(theGO["Chromosome"]) - 1
if refGene:
- literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor, refGene, theGO['GeneID']) or "N/A")
+ literatureCorrelationString = str(self.getLiteratureCorrelation(
+ self.cursor, refGene, theGO['GeneID']) or "N/A")
this_row = [selectCheck.__str__(),
str(tableIterationsCnt),
@@ -2947,7 +3133,8 @@ class DisplayMappingResults:
if theGO["GeneID"] != "":
geneSymbolNCBI = str(HtmlGenWrapper.create_link_tag(
- "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format(theGO["GeneID"]),
+ "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={}".format(
+ theGO["GeneID"]),
theGO["GeneSymbol"],
Class="normalsize",
target="_blank"))
@@ -2960,7 +3147,8 @@ class DisplayMappingResults:
chr_as_int = int(theGO["Chromosome"]) - 1
geneLength = (float(theGO["TxEnd"]) - float(theGO["TxStart"]))
- geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1))
+ geneLengthURL = "javascript:rangeView('%s', %f, %f)" % (theGO["Chromosome"], float(
+ theGO["TxStart"]) - (geneLength * 0.1), float(theGO["TxEnd"]) + (geneLength * 0.1))
avgExprVal = []
if avgExprVal != "" and avgExprVal:
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 68689104..289f1d5c 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -149,7 +149,8 @@ def gen_covariates_file(this_dataset, covariates, samples):
dataset_name = covariate.split(":")[1]
if dataset_name == "Temp":
temp_group = trait_name.split("_")[2]
- dataset_ob = create_dataset(dataset_name="Temp", dataset_type="Temp", group_name = temp_group)
+ dataset_ob = create_dataset(
+ dataset_name="Temp", dataset_type="Temp", group_name = temp_group)
else:
dataset_ob = create_dataset(covariate.split(":")[1])
trait_ob = create_trait(dataset=dataset_ob,
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index 22a50bb8..2fa80841 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -10,7 +10,8 @@ logger = utility.logger.getLogger(__name__)
def run_plink(this_trait, dataset, species, vals, maf):
- plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_")
+ plink_output_filename = webqtlUtil.genRandStr(
+ f"{dataset.group.name}_{this_trait.name}_")
gen_pheno_txt_file(dataset, vals)
plink_command = f"{PLINK_COMMAND} --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc "
@@ -41,7 +42,8 @@ def gen_pheno_txt_file(this_dataset, vals):
this_val = -9
else:
this_val = vals[i]
- outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
+ outfile.write("0 " + line[1] + " " + line[2] + " " + \
+ line[3] + " " + line[4] + " " + str(this_val) + "\n")
def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''):
@@ -162,7 +164,8 @@ def parse_plink_output(output_filename, species):
def build_line_list(line=""):
- line_list = line.strip().split(' ') # irregular number of whitespaces between columns
+ # irregular number of whitespaces between columns
+ line_list = line.strip().split(' ')
line_list = [item for item in line_list if item != '']
line_list = [item.strip() for item in line_list]
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index b8fe2c37..f932498f 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -26,7 +26,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
gen_pheno_txt_file(samples, vals, trait_filename)
output_filename = (f"{this_dataset.group.name}_GWA_" +
- ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+ ''.join(random.choice(string.ascii_uppercase + string.digits)
+ for _ in range(6))
)
bootstrap_filename = None
permu_filename = None
@@ -34,19 +35,22 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list = []
if boot_check and num_bootstrap > 0:
bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" +
- ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+ ''.join(random.choice(string.ascii_uppercase + string.digits)
+ for _ in range(6))
)
opt_list.append("-b")
opt_list.append(f"--n_bootstrap {str(num_bootstrap)}")
- opt_list.append(f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
+ opt_list.append(
+ f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
if num_perm > 0:
permu_filename = ("{this_dataset.group.name}_PERM_" +
''.join(random.choice(string.ascii_uppercase +
string.digits) for _ in range(6))
)
opt_list.append("-n " + str(num_perm))
- opt_list.append("--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt")
+ opt_list.append(
+ "--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt")
if control_marker != "" and do_control == "true":
opt_list.append("-c " + control_marker)
if manhattan_plot != True:
@@ -58,7 +62,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
genofile_name,
TEMPDIR,
trait_filename,
- " ".join(opt_list),
+ " ".join(
+ opt_list),
webqtlConfig.GENERATED_IMAGE_DIR,
output_filename))
@@ -67,7 +72,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
else:
output_filename, permu_filename, bootstrap_filename = output_files
- marker_obs, permu_vals, bootstrap_vals = parse_reaper_output(output_filename, permu_filename, bootstrap_filename)
+ marker_obs, permu_vals, bootstrap_vals = parse_reaper_output(
+ output_filename, permu_filename, bootstrap_filename)
suggestive = 0
significant = 0
@@ -193,7 +199,8 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
suggestive = 0
significant = 0
else:
- perm_output = genotype.permutation(strains=trimmed_samples, trait=trimmed_values, nperm=num_perm)
+ perm_output = genotype.permutation(
+ strains=trimmed_samples, trait=trimmed_values, nperm=num_perm)
suggestive = perm_output[int(num_perm * 0.37 - 1)]
significant = perm_output[int(num_perm * 0.95 - 1)]
# highly_significant = perm_output[int(num_perm*0.99-1)] #ZS: Currently not used, but leaving it here just in case
@@ -257,7 +264,8 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
json_data['markernames'].append(reaper_locus.name)
# if self.additive:
# self.json_data['additive'].append(qtl.additive)
- locus = {"name": reaper_locus.name, "chr": reaper_locus.chr, "cM": reaper_locus.cM, "Mb": reaper_locus.Mb}
+ locus = {"name": reaper_locus.name, "chr": reaper_locus.chr,
+ "cM": reaper_locus.cM, "Mb": reaper_locus.Mb}
qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb,
"cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance}
qtl_results.append(qtl)
@@ -270,5 +278,6 @@ def natural_sort(marker_list):
Changed to return indices instead of values, though, since the same reordering needs to be applied to bootstrap results
"""
convert = lambda text: int(text) if text.isdigit() else text.lower()
- alphanum_key = lambda key: [convert(c) for c in re.split('([0-9]+)', str(marker_list[key]['chr']))]
+ alphanum_key = lambda key: [convert(c) for c in re.split(
+ '([0-9]+)', str(marker_list[key]['chr']))]
return sorted(list(range(len(marker_list))), key=alphanum_key)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 588600f5..c2b165a4 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -51,7 +51,8 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
# Get pointers to some R/qtl functions
scanone = ro.r["scanone"] # Map the scanone function
scantwo = ro.r["scantwo"] # Map the scantwo function
- calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function
+ # Map the calc.genoprob function
+ calc_genoprob = ro.r["calc.genoprob"]
crossname = dataset.group.name
# try:
@@ -67,14 +68,16 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
scale_units = "Mb"
generate_cross_from_geno(dataset, scale_units)
- GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
+ # Map the local GENOtoCSVR function
+ GENOtoCSVR = ro.r["GENOtoCSVR"]
crossfilelocation = TMPDIR + crossname + ".cross"
if dataset.group.genofile:
genofilelocation = locate(dataset.group.genofile, "genotype")
else:
genofilelocation = locate(dataset.group.name + ".geno", "genotype")
logger.info("Going to create a cross from geno");
- cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available
+ # TODO: Add the SEX if that is available
+ cross_object = GENOtoCSVR(genofilelocation, crossfilelocation)
logger.info("before calc_genoprob");
if manhattan_plot:
cross_object = calc_genoprob(cross_object)
@@ -85,14 +88,19 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
logger.info("phenostring done");
names_string = sanitize_rqtl_names(samples)
logger.info("sanitized pheno and names");
- cross_object = add_phenotype(cross_object, pheno_string, "the_pheno") # Add the phenotype
- cross_object = add_names(cross_object, names_string, "the_names") # Add the phenotype
+ # Add the phenotype
+ cross_object = add_phenotype(cross_object, pheno_string, "the_pheno")
+ # Add the phenotype
+ cross_object = add_names(cross_object, names_string, "the_names")
logger.info("Added pheno and names");
- marker_covars = create_marker_covariates(control_marker, cross_object) # Create the additive covariate markers
+ # Create the additive covariate markers
+ marker_covars = create_marker_covariates(control_marker, cross_object)
logger.info("Marker covars done");
if cofactors != "":
logger.info("Cofactors: " + cofactors);
- cross_object, trait_covars = add_cofactors(cross_object, dataset, cofactors, samples) # Create the covariates from selected traits
+ # Create the covariates from selected traits
+ cross_object, trait_covars = add_cofactors(
+ cross_object, dataset, cofactors, samples)
ro.r('all_covars <- cbind(marker_covars, trait_covars)')
else:
ro.r('all_covars <- marker_covars')
@@ -100,9 +108,11 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
# DEBUG to save the session object to file
if pair_scan:
if do_control == "true":
- logger.info("Using covariate"); result_data_frame = scantwo(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16)
+ logger.info("Using covariate"); result_data_frame = scantwo(
+ cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16)
else:
- logger.info("No covariates"); result_data_frame = scantwo(cross_object, pheno="the_pheno", model=model, method=method, n_cluster=16)
+ logger.info("No covariates"); result_data_frame = scantwo(
+ cross_object, pheno="the_pheno", model=model, method=method, n_cluster=16)
pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png"
png(file=TEMPDIR + pair_scan_filename)
@@ -112,25 +122,36 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
return process_pair_scan_results(result_data_frame)
else:
if do_control == "true" or cofactors != "":
- logger.info("Using covariate"); result_data_frame = scanone(cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method)
+ logger.info("Using covariate"); result_data_frame = scanone(
+ cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method)
ro.r('save.image(file = "/home/zas1024/gn2-zach/itp_cofactor_test.RData")')
else:
- logger.info("No covariates"); result_data_frame = scanone(cross_object, pheno="the_pheno", model=model, method=method)
-
- if num_perm > 0 and permCheck == "ON": # Do permutation (if requested by user)
- if len(perm_strata_list) > 0: # ZS: The strata list would only be populated if "Stratified" was checked on before mapping
- cross_object, strata_ob = add_perm_strata(cross_object, perm_strata_list)
+ logger.info("No covariates"); result_data_frame = scanone(
+ cross_object, pheno="the_pheno", model=model, method=method)
+
+ # Do permutation (if requested by user)
+ if num_perm > 0 and permCheck == "ON":
+ # ZS: The strata list would only be populated if "Stratified" was checked on before mapping
+ if len(perm_strata_list) > 0:
+ cross_object, strata_ob = add_perm_strata(
+ cross_object, perm_strata_list)
if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), perm_strata = strata_ob, model=model, method=method)
+ perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(
+ num_perm), perm_strata = strata_ob, model=model, method=method)
else:
- perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method)
+ perm_data_frame = scanone(
+ cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method)
else:
if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(num_perm), model=model, method=method)
+ perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(
+ num_perm), model=model, method=method)
else:
- perm_data_frame = scanone(cross_object, pheno_col="the_pheno", n_perm=num_perm, model=model, method=method)
+ perm_data_frame = scanone(
+ cross_object, pheno_col="the_pheno", n_perm=num_perm, model=model, method=method)
- perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
+ # Functions that sets the thresholds for the webinterface
+ perm_output, suggestive, significant = process_rqtl_perm_results(
+ num_perm, perm_data_frame)
return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species)
else:
return process_rqtl_results(result_data_frame, dataset.group.species)
@@ -147,7 +168,8 @@ def generate_cross_from_rdata(dataset):
""" % (rdata_location))
-def generate_cross_from_geno(dataset, scale_units): # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
+# TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
+def generate_cross_from_geno(dataset, scale_units):
ro.r("""
trim <- function( x ) { gsub("(^[[:space:]]+|[[:space:]]+$)", "", x) }
@@ -246,7 +268,8 @@ def sanitize_rqtl_names(vals):
def add_phenotype(cross, pheno_as_string, col_name):
ro.globalenv["the_cross"] = cross
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
- ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric(' + pheno_as_string + '))')
+ ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + \
+ ' = as.numeric(' + pheno_as_string + '))')
return ro.r["the_cross"]
@@ -270,7 +293,8 @@ def add_categorical_covar(cross, covar_as_string, i):
#logger.info("loop" + str(x));
col_name = "covar_" + str(i) + "_" + str(x)
#logger.info("col_name" + col_name);
- ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = newcovar[,' + str(x) + '])')
+ ro.r('the_cross$pheno <- cbind(pheno, ' + \
+ col_name + ' = newcovar[,' + str(x) + '])')
col_names.append(col_name)
#logger.info("loop" + str(x) + "done");
@@ -281,7 +305,8 @@ def add_categorical_covar(cross, covar_as_string, i):
def add_names(cross, names_as_string, col_name):
ro.globalenv["the_cross"] = cross
ro.r('pheno <- data.frame(pull.pheno(the_cross))')
- ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = ' + names_as_string + ')')
+ ro.r('the_cross$pheno <- cbind(pheno, ' + \
+ col_name + ' = ' + names_as_string + ')')
return ro.r["the_cross"]
@@ -330,9 +355,11 @@ def add_cofactors(cross, this_dataset, covariates, samples):
logger.info("Covariate: " + covariate + " is of type: " + datatype);
if(datatype == "categorical"): # Cat variable
logger.info("call of add_categorical_covar");
- cross, col_names = add_categorical_covar(cross, covar_as_string, i) # Expand and add it to the cross
+ cross, col_names = add_categorical_covar(
+ cross, covar_as_string, i) # Expand and add it to the cross
logger.info("add_categorical_covar returned");
- for z, col_name in enumerate(col_names): # Go through the additional covar names
+ # Go through the additional covar names
+ for z, col_name in enumerate(col_names):
if i < (len(covariate_list) - 1):
covar_name_string += '"' + col_name + '", '
else:
@@ -355,18 +382,22 @@ def add_cofactors(cross, this_dataset, covariates, samples):
def create_marker_covariates(control_marker, cross):
ro.globalenv["the_cross"] = cross
- ro.r('genotypes <- pull.geno(the_cross)') # Get the genotype matrix
- userinput_sanitized = control_marker.replace(" ", "").split(",") # TODO: sanitize user input, Never Ever trust a user
+ # Get the genotype matrix
+ ro.r('genotypes <- pull.geno(the_cross)')
+ # TODO: sanitize user input, Never Ever trust a user
+ userinput_sanitized = control_marker.replace(" ", "").split(",")
logger.debug(userinput_sanitized)
if len(userinput_sanitized) > 0:
- covariate_names = ', '.join('"{0}"'.format(w) for w in userinput_sanitized)
+ covariate_names = ', '.join('"{0}"'.format(w)
+ for w in userinput_sanitized)
ro.r('covnames <- c(' + covariate_names + ')')
else:
ro.r('covnames <- c()')
ro.r('covInGeno <- which(covnames %in% colnames(genotypes))')
ro.r('covnames <- covnames[covInGeno]')
ro.r("cat('covnames (purged): ', covnames,'\n')")
- ro.r('marker_covars <- genotypes[,covnames]') # Get the covariate matrix by using the marker name as index to the genotype file
+ # Get the covariate matrix by using the marker name as index to the genotype file
+ ro.r('marker_covars <- genotypes[,covnames]')
# TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc
return ro.r["marker_covars"]
@@ -375,7 +406,8 @@ def process_pair_scan_results(result):
pair_scan_results = []
result = result[1]
- output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+ output = [tuple([result[j][i] for j in range(result.ncol)])
+ for i in range(result.nrow)]
for i, line in enumerate(result.iter_row()):
marker = {}
@@ -401,14 +433,17 @@ def process_rqtl_perm_results(num_perm, results):
return perm_output, suggestive, significant
-def process_rqtl_results(result, species_name): # TODO: how to make this a one liner and not copy the stuff in a loop
+# TODO: how to make this a one liner and not copy the stuff in a loop
+def process_rqtl_results(result, species_name):
qtl_results = []
- output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+ output = [tuple([result[j][i] for j in range(result.ncol)])
+ for i in range(result.nrow)]
for i, line in enumerate(result.iter_row()):
marker = {}
marker['name'] = result.rownames[i]
- if species_name == "mouse" and output[i][0] == 20: # ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file
+ # ZS: This is awkward, but I'm not sure how to change the 20s to Xs in the RData file
+ if species_name == "mouse" and output[i][0] == 20:
marker['chr'] = "X"
else:
marker['chr'] = output[i][0]
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 31c58083..d9b28fba 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -51,7 +51,8 @@ class RunMapping:
def __init__(self, start_vars, temp_uuid):
helper_functions.get_species_dataset_trait(self, start_vars)
- self.temp_uuid = temp_uuid # needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py)
+ # needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py)
+ self.temp_uuid = temp_uuid
# ZS: Needed to zoom in or remap temp traits like PCA traits
if "temp_trait" in start_vars and start_vars['temp_trait'] != "False":
@@ -102,8 +103,11 @@ class RunMapping:
if "results_path" in start_vars:
self.mapping_results_path = start_vars['results_path']
else:
- mapping_results_filename = self.dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
- self.mapping_results_path = "{}{}.csv".format(webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
+ mapping_results_filename = self.dataset.group.name + "_" + \
+ ''.join(random.choice(string.ascii_uppercase + string.digits)
+ for _ in range(6))
+ self.mapping_results_path = "{}{}.csv".format(
+ webqtlConfig.GENERATED_IMAGE_DIR, mapping_results_filename)
self.manhattan_plot = False
if 'manhattan_plot' in start_vars:
@@ -122,7 +126,8 @@ class RunMapping:
self.use_loco = None
self.suggestive = ""
self.significant = ""
- self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
+ # Initializing this since it is checked in views to determine which template to use
+ self.pair_scan = False
if 'transform' in start_vars:
self.transform = start_vars['transform']
else:
@@ -140,7 +145,8 @@ class RunMapping:
# ZS: This is passed to GN1 code for single chr mapping
self.selected_chr = -1
if "selected_chr" in start_vars:
- if int(start_vars['selected_chr']) != -1: # ZS: Needs to be -1 if showing full map; there's probably a better way to fix this
+ # ZS: Needs to be -1 if showing full map; there's probably a better way to fix this
+ if int(start_vars['selected_chr']) != -1:
self.selected_chr = int(start_vars['selected_chr']) + 1
else:
self.selected_chr = int(start_vars['selected_chr'])
@@ -198,28 +204,33 @@ class RunMapping:
self.output_files = None
if 'output_files' in start_vars:
self.output_files = start_vars['output_files']
- if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
+ # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
+ if 'first_run' in start_vars:
self.first_run = False
self.score_type = "-logP"
self.manhattan_plot = True
with Bench("Running GEMMA"):
if self.use_loco == "True":
- marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
+ marker_obs, self.output_files = gemma_mapping.run_gemma(
+ self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
else:
- marker_obs, self.output_files = gemma_mapping.run_gemma(self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
+ marker_obs, self.output_files = gemma_mapping.run_gemma(
+ self.this_trait, self.dataset, self.samples, self.vals, self.covariates, self.use_loco, self.maf, self.first_run, self.output_files)
results = marker_obs
elif self.mapping_method == "rqtl_plink":
results = self.run_rqtl_plink()
elif self.mapping_method == "rqtl_geno":
perm_strata = []
if "perm_strata" in start_vars and "categorical_vars" in start_vars:
- self.categorical_vars = start_vars["categorical_vars"].split(",")
+ self.categorical_vars = start_vars["categorical_vars"].split(
+ ",")
if len(self.categorical_vars) and start_vars["perm_strata"] == "True":
primary_samples = SampleList(dataset=self.dataset,
sample_names=self.samples,
this_trait=self.this_trait)
- perm_strata = get_perm_strata(self.this_trait, primary_samples, self.categorical_vars, self.samples)
+ perm_strata = get_perm_strata(
+ self.this_trait, primary_samples, self.categorical_vars, self.samples)
self.score_type = "LOD"
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
@@ -231,9 +242,11 @@ class RunMapping:
# if start_vars['pair_scan'] == "true":
# self.pair_scan = True
if self.permCheck and self.num_perm > 0:
- self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(
+ self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
else:
- results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.mapping_scale, self.method, self.model, self.permCheck,
+ self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
elif self.mapping_method == "reaper":
if "startMb" in start_vars: # ZS: Check if first time page loaded, so it can default to ON
if "additiveCheck" in start_vars:
@@ -268,10 +281,12 @@ class RunMapping:
if self.reaper_version == "new":
self.first_run = True
self.output_files = None
- if 'first_run' in start_vars: # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
+ # ZS: check if first run so existing result files can be used if it isn't (for example zooming on a chromosome, etc)
+ if 'first_run' in start_vars:
self.first_run = False
if 'output_files' in start_vars:
- self.output_files = start_vars['output_files'].split(",")
+ self.output_files = start_vars['output_files'].split(
+ ",")
results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait,
self.dataset,
@@ -301,7 +316,8 @@ class RunMapping:
elif self.mapping_method == "plink":
self.score_type = "-logP"
self.manhattan_plot = True
- results = plink_mapping.run_plink(self.this_trait, self.dataset, self.species, self.vals, self.maf)
+ results = plink_mapping.run_plink(
+ self.this_trait, self.dataset, self.species, self.vals, self.maf)
#results = self.run_plink()
else:
logger.debug("RUNNING NOTHING")
@@ -353,7 +369,9 @@ class RunMapping:
chr=str(marker['chr']),
rs=marker['name'],
ps=this_ps,
- url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno"
+ url="/show_trait?trait_id=" + \
+ marker['name'] + "&dataset=" + \
+ self.dataset.group.name + "Geno"
)
if self.geno_db_exists == "True":
@@ -362,7 +380,9 @@ class RunMapping:
chr=str(marker['chr']),
rs=marker['name'],
pos=this_ps,
- url="/show_trait?trait_id=" + marker['name'] + "&dataset=" + self.dataset.group.name + "Geno"
+ url="/show_trait?trait_id=" + \
+ marker['name'] + "&dataset=" + \
+ self.dataset.group.name + "Geno"
)
else:
annot_marker = dict(
@@ -373,7 +393,8 @@ class RunMapping:
)
if 'lrs_value' in marker and marker['lrs_value'] > 0:
- browser_marker['p_wald'] = 10**-(marker['lrs_value'] / 4.61)
+ browser_marker['p_wald'] = 10**- \
+ (marker['lrs_value'] / 4.61)
elif 'lod_score' in marker and marker['lod_score'] > 0:
browser_marker['p_wald'] = 10**-(marker['lod_score'])
else:
@@ -386,9 +407,13 @@ class RunMapping:
highest_chr = marker['chr']
if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
if 'Mb' in marker.keys():
- marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.6f}".format(marker['Mb'])
+ marker['display_pos'] = "Chr" + \
+ str(marker['chr']) + ": " + \
+ "{:.6f}".format(marker['Mb'])
elif 'cM' in marker.keys():
- marker['display_pos'] = "Chr" + str(marker['chr']) + ": " + "{:.3f}".format(marker['cM'])
+ marker['display_pos'] = "Chr" + \
+ str(marker['chr']) + ": " + \
+ "{:.3f}".format(marker['cM'])
else:
marker['display_pos'] = "N/A"
self.qtl_results.append(marker)
@@ -396,12 +421,15 @@ class RunMapping:
total_markers = len(self.qtl_results)
with Bench("Exporting Results"):
- export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples)
+ export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path,
+ self.mapping_scale, self.score_type, self.transform, self.covariates, self.n_samples)
with Bench("Trimming Markers for Figure"):
if len(self.qtl_results) > 30000:
- self.qtl_results = trim_markers_for_figure(self.qtl_results)
- self.results_for_browser = trim_markers_for_figure(self.results_for_browser)
+ self.qtl_results = trim_markers_for_figure(
+ self.qtl_results)
+ self.results_for_browser = trim_markers_for_figure(
+ self.results_for_browser)
filtered_annotations = []
for marker in self.results_for_browser:
for annot_marker in self.annotations_for_browser:
@@ -409,14 +437,17 @@ class RunMapping:
filtered_annotations.append(annot_marker)
break
self.annotations_for_browser = filtered_annotations
- browser_files = write_input_for_browser(self.dataset, self.results_for_browser, self.annotations_for_browser)
+ browser_files = write_input_for_browser(
+ self.dataset, self.results_for_browser, self.annotations_for_browser)
else:
- browser_files = write_input_for_browser(self.dataset, self.results_for_browser, self.annotations_for_browser)
+ browser_files = write_input_for_browser(
+ self.dataset, self.results_for_browser, self.annotations_for_browser)
with Bench("Trimming Markers for Table"):
self.trimmed_markers = trim_markers_for_table(results)
- chr_lengths = get_chr_lengths(self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results)
+ chr_lengths = get_chr_lengths(
+ self.mapping_scale, self.mapping_method, self.dataset, self.qtl_results)
# ZS: For zooming into genome browser, need to pass chromosome name instead of number
if self.dataset.group.species == "mouse":
@@ -472,11 +503,14 @@ class RunMapping:
def run_rqtl_plink(self):
# os.chdir("") never do this inside a webserver!!
- output_filename = webqtlUtil.genRandStr("%s_%s_" % (self.dataset.group.name, self.this_trait.name))
+ output_filename = webqtlUtil.genRandStr("%s_%s_" % (
+ self.dataset.group.name, self.this_trait.name))
- plink_mapping.gen_pheno_txt_file_plink(self.this_trait, self.dataset, self.vals, pheno_filename=output_filename)
+ plink_mapping.gen_pheno_txt_file_plink(
+ self.this_trait, self.dataset, self.vals, pheno_filename=output_filename)
- rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename)
+ rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (
+ self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename)
os.system(rqtl_command)
@@ -508,8 +542,10 @@ class RunMapping:
def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples):
with open(results_path, "w+") as output_file:
- output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
- output_file.write("Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n")
+ output_file.write(
+ "Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
+ output_file.write(
+ "Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n")
output_file.write("Data Set: " + dataset.fullname + "\n")
output_file.write("N Samples: " + str(n_samples) + "\n")
if len(transform) > 0:
@@ -529,7 +565,8 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
output_file.write(transform_text + "\n")
if dataset.type == "ProbeSet":
output_file.write("Gene Symbol: " + trait.symbol + "\n")
- output_file.write("Location: " + str(trait.chr) + " @ " + str(trait.mb) + " Mb\n")
+ output_file.write("Location: " + str(trait.chr) + \
+ " @ " + str(trait.mb) + " Mb\n")
if len(covariates) > 0:
output_file.write("Cofactors (dataset - trait):\n")
for covariate in covariates.split(","):
@@ -630,9 +667,11 @@ def trim_markers_for_figure(markers):
def trim_markers_for_table(markers):
if 'lod_score' in list(markers[0].keys()):
- sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
+ sorted_markers = sorted(
+ markers, key=lambda k: k['lod_score'], reverse=True)
else:
- sorted_markers = sorted(markers, key=lambda k: k['lrs_value'], reverse=True)
+ sorted_markers = sorted(
+ markers, key=lambda k: k['lrs_value'], reverse=True)
# ZS: So we end up with a list of just 2000 markers
if len(sorted_markers) >= 2000:
@@ -643,7 +682,9 @@ def trim_markers_for_table(markers):
def write_input_for_browser(this_dataset, gwas_results, annotations):
- file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+ file_base = this_dataset.group.name + "_" + \
+ ''.join(random.choice(string.ascii_uppercase + string.digits)
+ for _ in range(6))
gwas_filename = file_base + "_GWAS"
annot_filename = file_base + "_ANNOT"
gwas_path = "{}/gn2/".format(TEMPDIR) + gwas_filename
@@ -659,7 +700,8 @@ def write_input_for_browser(this_dataset, gwas_results, annotations):
def geno_db_exists(this_dataset):
geno_db_name = this_dataset.group.name + "Geno"
try:
- geno_db = data_set.create_dataset(dataset_name=geno_db_name, get_samplelist=False)
+ geno_db = data_set.create_dataset(
+ dataset_name=geno_db_name, get_samplelist=False)
return "True"
except:
return "False"
@@ -689,9 +731,11 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
highest_pos = float(result['cM']) * 1000000
else:
highest_pos = float(result['Mb']) * 1000000
- chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)})
+ chr_lengths.append(
+ {"chr": str(this_chr), "size": str(highest_pos)})
else:
- chr_lengths.append({"chr": str(this_chr), "size": str(highest_pos)})
+ chr_lengths.append(
+ {"chr": str(this_chr), "size": str(highest_pos)})
this_chr = chr_as_num
else:
if mapping_method == "reaper":
@@ -722,7 +766,8 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
combined_string = ""
for var in categorical_vars:
if var in list(sample_list.sample_attribute_values[sample].keys()):
- combined_string += str(sample_list.sample_attribute_values[sample][var])
+ combined_string += str(
+ sample_list.sample_attribute_values[sample][var])
else:
combined_string += "NA"
else:
@@ -730,7 +775,8 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
perm_strata_strings.append(combined_string)
- d = dict([(y, x + 1) for x, y in enumerate(sorted(set(perm_strata_strings)))])
+ d = dict([(y, x + 1)
+ for x, y in enumerate(sorted(set(perm_strata_strings)))])
list_to_numbers = [d[x] for x in perm_strata_strings]
perm_strata = list_to_numbers
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index d7c9ef95..7b9ff8fe 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -17,7 +17,8 @@ from wqflask.database import Base, init_db
class User(Base):
__tablename__ = "user"
- id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
+ id = Column(Unicode(36), primary_key=True,
+ default=lambda: str(uuid.uuid4()))
email_address = Column(Unicode(50), unique=True, nullable=False)
# Todo: Turn on strict mode for Mysql
@@ -28,11 +29,13 @@ class User(Base):
active = Column(Boolean(), nullable=False, default=True)
- registration_info = Column(Text) # json detailing when they were registered, etc.
+ # json detailing when they were registered, etc.
+ registration_info = Column(Text)
confirmed = Column(Text) # json detailing when they confirmed, etc.
- superuser = Column(Text) # json detailing when they became a superuser, otherwise empty
+ # json detailing when they became a superuser, otherwise empty
+ superuser = Column(Text)
# if not superuser
logins = relationship("Login",
@@ -66,7 +69,8 @@ class User(Base):
def get_collection_by_name(self, collection_name):
try:
- collect = self.user_collections.filter_by(name=collection_name).first()
+ collect = self.user_collections.filter_by(
+ name=collection_name).first()
except sqlalchemy.orm.exc.NoResultFound:
collect = None
return collect
@@ -118,12 +122,15 @@ class User(Base):
class Login(Base):
__tablename__ = "login"
- id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
+ id = Column(Unicode(36), primary_key=True,
+ default=lambda: str(uuid.uuid4()))
user = Column(Unicode(36), ForeignKey('user.id'))
timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow())
ip_address = Column(Unicode(39))
- successful = Column(Boolean(), nullable=False) # False if wrong password was entered
- session_id = Column(Text) # Set only if successfully logged in, otherwise should be blank
+ # False if wrong password was entered
+ successful = Column(Boolean(), nullable=False)
+ # Set only if successfully logged in, otherwise should be blank
+ session_id = Column(Text)
# Set to user who assumes identity if this was a login for debugging purposes by a superuser
assumed_by = Column(Unicode(36), ForeignKey('user.id'))
@@ -137,13 +144,16 @@ class Login(Base):
class UserCollection(Base):
__tablename__ = "user_collection"
- id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
+ id = Column(Unicode(36), primary_key=True,
+ default=lambda: str(uuid.uuid4()))
user = Column(Unicode(36), ForeignKey('user.id'))
# I'd prefer this to not have a length, but for the index below it needs one
name = Column(Unicode(50))
- created_timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow())
- changed_timestamp = Column(DateTime(), default=lambda: datetime.datetime.utcnow())
+ created_timestamp = Column(
+ DateTime(), default=lambda: datetime.datetime.utcnow())
+ changed_timestamp = Column(
+ DateTime(), default=lambda: datetime.datetime.utcnow())
members = Column(Text) # We're going to store them as a json list
# This index ensures a user doesn't have more than one collection with the same name
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 4591710c..36d4cd61 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -47,7 +47,8 @@ def search_for_user():
params = request.form
user_list = []
user_list += get_users_like_unique_column("full_name", params['user_name'])
- user_list += get_users_like_unique_column("email_address", params['user_email'])
+ user_list += get_users_like_unique_column(
+ "email_address", params['user_email'])
return json.dumps(user_list)
@@ -61,7 +62,8 @@ def search_for_groups():
user_list = []
user_list += get_users_like_unique_column("full_name", params['user_name'])
- user_list += get_users_like_unique_column("email_address", params['user_email'])
+ user_list += get_users_like_unique_column(
+ "email_address", params['user_email'])
for user in user_list:
group_list += get_groups_like_unique_column("admins", user['user_id'])
group_list += get_groups_like_unique_column("members", user['user_id'])
@@ -124,7 +126,8 @@ def add_group_to_resource():
'admin': request.form['admin_privilege']
}
add_access_mask(resource_id, group_id, access_mask)
- flash("Privileges have been added for group {}.".format(group_name), "alert-info")
+ flash("Privileges have been added for group {}.".format(
+ group_name), "alert-info")
return redirect(url_for("manage_resource", resource_id=resource_id))
else:
return render_template("admin/search_for_groups.html", resource_id=resource_id)
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index ed5f9bad..273a97a4 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -52,7 +52,8 @@ class SearchResultPage:
search = self.search_terms
self.original_search_string = self.search_terms
# check for dodgy search terms
- rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE)
+ rx = re.compile(
+ r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE)
if rx.match(search):
logger.info("Regex failed search")
self.search_term_exists = False
@@ -96,7 +97,8 @@ class SearchResultPage:
trait_list = []
json_trait_list = []
- species = webqtlDatabaseFunction.retrieve_species(self.dataset.group.name)
+ species = webqtlDatabaseFunction.retrieve_species(
+ self.dataset.group.name)
# result_set represents the results for each search term; a search of
# "shh grin2b" would have two sets of results, one for each term
logger.debug("self.results is:", pf(self.results))
@@ -109,7 +111,8 @@ class SearchResultPage:
trait_dict = {}
trait_id = result[0]
- this_trait = create_trait(dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+ this_trait = create_trait(
+ dataset=self.dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
if this_trait:
trait_dict['index'] = index + 1
trait_dict['name'] = this_trait.name
@@ -118,7 +121,8 @@ class SearchResultPage:
else:
trait_dict['display_name'] = this_trait.name
trait_dict['dataset'] = this_trait.dataset.name
- trait_dict['hmac'] = hmac.data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))
+ trait_dict['hmac'] = hmac.data_hmac(
+ '{}:{}'.format(this_trait.name, this_trait.dataset.name))
if this_trait.dataset.type == "ProbeSet":
trait_dict['symbol'] = this_trait.symbol if this_trait.symbol else "N/A"
trait_dict['description'] = "N/A"
@@ -168,9 +172,11 @@ class SearchResultPage:
self.trait_list = trait_list
if self.dataset.type == "ProbeSet":
- self.header_data_names = ['index', 'display_name', 'symbol', 'description', 'location', 'mean', 'lrs_score', 'lrs_location', 'additive']
+ self.header_data_names = ['index', 'display_name', 'symbol', 'description',
+ 'location', 'mean', 'lrs_score', 'lrs_location', 'additive']
elif self.dataset.type == "Publish":
- self.header_data_names = ['index', 'display_name', 'description', 'mean', 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive']
+ self.header_data_names = ['index', 'display_name', 'description', 'mean',
+ 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive']
elif self.dataset.type == "Geno":
self.header_data_names = ['index', 'display_name', 'location']
@@ -184,7 +190,8 @@ class SearchResultPage:
combined_from_clause = ""
combined_where_clause = ""
- previous_from_clauses = [] # The same table can't be referenced twice in the from clause
+ # The same table can't be referenced twice in the from clause
+ previous_from_clauses = []
logger.debug("len(search_terms)>1")
symbol_list = []
@@ -198,7 +205,8 @@ class SearchResultPage:
for i, a_search in enumerate(alias_terms):
the_search = self.get_search_ob(a_search)
if the_search != None:
- get_from_clause = getattr(the_search, "get_from_clause", None)
+ get_from_clause = getattr(
+ the_search, "get_from_clause", None)
if callable(get_from_clause):
from_clause = the_search.get_from_clause()
if from_clause in previous_from_clauses:
@@ -222,7 +230,8 @@ class SearchResultPage:
else:
the_search = self.get_search_ob(a_search)
if the_search != None:
- get_from_clause = getattr(the_search, "get_from_clause", None)
+ get_from_clause = getattr(
+ the_search, "get_from_clause", None)
if callable(get_from_clause):
from_clause = the_search.get_from_clause()
if from_clause in previous_from_clauses:
@@ -241,7 +250,8 @@ class SearchResultPage:
self.search_term_exists = False
if self.search_term_exists:
combined_where_clause = "(" + combined_where_clause + ")"
- final_query = the_search.compile_final_query(combined_from_clause, combined_where_clause)
+ final_query = the_search.compile_final_query(
+ combined_from_clause, combined_where_clause)
results = the_search.execute(final_query)
self.results.extend(results)
@@ -312,7 +322,8 @@ def get_aliases(symbol_list, species):
symbols_string = ",".join(updated_symbols)
filtered_aliases = []
- response = requests.get(GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string)
+ response = requests.get(
+ GN2_BASE_URL + "/gn3/gene/aliases2/" + symbols_string)
if response:
alias_lists = json.loads(response.content)
seen = set()
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 496dee57..6419335e 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -74,14 +74,20 @@ class SampleList:
if 'rrid' in sample.extra_attributes:
if self.dataset.group.species == "mouse":
if len(sample.extra_attributes['rrid'].split(":")) > 1:
- the_rrid = sample.extra_attributes['rrid'].split(":")[1]
- sample.extra_attributes['rrid'] = [sample.extra_attributes['rrid']]
- sample.extra_attributes['rrid'].append(webqtlConfig.RRID_MOUSE_URL % the_rrid)
+ the_rrid = sample.extra_attributes['rrid'].split(":")[
+ 1]
+ sample.extra_attributes['rrid'] = [
+ sample.extra_attributes['rrid']]
+ sample.extra_attributes['rrid'].append(
+ webqtlConfig.RRID_MOUSE_URL % the_rrid)
elif self.dataset.group.species == "rat":
if len(str(sample.extra_attributes['rrid'])):
- the_rrid = sample.extra_attributes['rrid'].split("_")[1]
- sample.extra_attributes['rrid'] = [sample.extra_attributes['rrid']]
- sample.extra_attributes['rrid'].append(webqtlConfig.RRID_RAT_URL % the_rrid)
+ the_rrid = sample.extra_attributes['rrid'].split("_")[
+ 1]
+ sample.extra_attributes['rrid'] = [
+ sample.extra_attributes['rrid']]
+ sample.extra_attributes['rrid'].append(
+ webqtlConfig.RRID_RAT_URL % the_rrid)
self.sample_list.append(sample)
@@ -130,7 +136,8 @@ class SampleList:
self.attributes[key].name = name
self.attributes[key].distinct_values = [
item.Value for item in values]
- self.attributes[key].distinct_values = natural_sort(self.attributes[key].distinct_values)
+ self.attributes[key].distinct_values = natural_sort(
+ self.attributes[key].distinct_values)
all_numbers = True
for value in self.attributes[key].distinct_values:
try:
@@ -170,7 +177,8 @@ class SampleList:
except ValueError:
pass
- attribute_values[self.attributes[item.Id].name.lower()] = attribute_value
+ attribute_values[self.attributes[item.Id].name.lower(
+ )] = attribute_value
self.sample_attribute_values[sample_name] = attribute_values
def get_first_attr_col(self):
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index f0fcd27d..81e7903b 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -40,16 +40,23 @@ def get_export_metadata(trait_id, dataset_name):
metadata = []
if dataset.type == "Publish":
metadata.append(["Phenotype ID: " + trait_id])
- metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name])
+ metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + \
+ trait_id + "&dataset=" + dataset_name])
metadata.append(["Group: " + dataset.group.name])
- metadata.append(["Phenotype: " + this_trait.description_display.replace(",", "\",\"")])
- metadata.append(["Authors: " + (this_trait.authors if this_trait.authors else "N/A")])
- metadata.append(["Title: " + (this_trait.title if this_trait.title else "N/A")])
- metadata.append(["Journal: " + (this_trait.journal if this_trait.journal else "N/A")])
- metadata.append(["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name])
+ metadata.append(
+ ["Phenotype: " + this_trait.description_display.replace(",", "\",\"")])
+ metadata.append(
+ ["Authors: " + (this_trait.authors if this_trait.authors else "N/A")])
+ metadata.append(
+ ["Title: " + (this_trait.title if this_trait.title else "N/A")])
+ metadata.append(
+ ["Journal: " + (this_trait.journal if this_trait.journal else "N/A")])
+ metadata.append(
+ ["Dataset Link: http://gn1.genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName=" + dataset.name])
else:
metadata.append(["Record ID: " + trait_id])
- metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + trait_id + "&dataset=" + dataset_name])
+ metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + \
+ trait_id + "&dataset=" + dataset_name])
if this_trait.symbol:
metadata.append(["Symbol: " + this_trait.symbol])
metadata.append(["Dataset: " + dataset.name])
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index e5c67165..7fcbe984 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -27,9 +27,11 @@ class SnpBrowser:
self.table_rows = []
if self.limit_strains == "true":
- self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns)
+ self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(
+ variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns)
else:
- self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
+ self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(
+ variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
def initialize_parameters(self, start_vars):
if 'first_run' in start_vars:
@@ -53,10 +55,12 @@ class SnpBrowser:
self.rat_chr_list = []
mouse_species_ob = species.TheSpecies(species_name="Mouse")
for key in mouse_species_ob.chromosomes.chromosomes:
- self.mouse_chr_list.append(mouse_species_ob.chromosomes.chromosomes[key].name)
+ self.mouse_chr_list.append(
+ mouse_species_ob.chromosomes.chromosomes[key].name)
rat_species_ob = species.TheSpecies(species_name="Rat")
for key in rat_species_ob.chromosomes.chromosomes:
- self.rat_chr_list.append(rat_species_ob.chromosomes.chromosomes[key].name)
+ self.rat_chr_list.append(
+ rat_species_ob.chromosomes.chromosomes[key].name)
if self.species_id == 1:
self.this_chr_list = self.mouse_chr_list
@@ -109,9 +113,11 @@ class SnpBrowser:
"CAST/EiJ"]
self.chosen_strains_rat = ["BN", "F344", "WLI", "WMI"]
if 'chosen_strains_mouse' in start_vars:
- self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split(",")
+ self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split(
+ ",")
if 'chosen_strains_rat' in start_vars:
- self.chosen_strains_rat = start_vars['chosen_strains_rat'].split(",")
+ self.chosen_strains_rat = start_vars['chosen_strains_rat'].split(
+ ",")
if self.species_id == 1:
self.chosen_strains = self.chosen_strains_mouse
@@ -150,9 +156,11 @@ class SnpBrowser:
if self.gene_name != "":
if self.species_id != 0:
- query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE SpeciesId = %s AND geneSymbol = '%s'" % (self.species_id, self.gene_name)
+ query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE SpeciesId = %s AND geneSymbol = '%s'" % (
+ self.species_id, self.gene_name)
else:
- query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE geneSymbol = '%s'" % (self.gene_name)
+ query = "SELECT geneSymbol, chromosome, txStart, txEnd FROM GeneList WHERE geneSymbol = '%s'" % (
+ self.gene_name)
result = g.db.execute(query).fetchone()
if result:
self.gene_name, self.chr, self.start_mb, self.end_mb = result
@@ -163,9 +171,11 @@ class SnpBrowser:
query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll WHERE Rs = '%s'" % self.gene_name
else:
if self.species_id != 0:
- query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SpeciesId = %s AND SnpName = '%s'" % (self.species_id, self.gene_name)
+ query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SpeciesId = %s AND SnpName = '%s'" % (
+ self.species_id, self.gene_name)
else:
- query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SnpName = '%s'" % (self.gene_name)
+ query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SnpName = '%s'" % (
+ self.gene_name)
result_snp = g.db.execute(query).fetchall()
if result_snp:
self.snp_list = [item[0] for item in result_snp]
@@ -177,9 +187,11 @@ class SnpBrowser:
elif self.variant_type == "InDel":
if self.gene_name[0] == "I":
if self.species_id != 0:
- query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE SpeciesId = %s AND Name = '%s'" % (self.species_id, self.gene_name)
+ query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE SpeciesId = %s AND Name = '%s'" % (
+ self.species_id, self.gene_name)
else:
- query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE Name = '%s'" % (self.gene_name)
+ query = "SELECT Id, Chromosome, Mb_start, Mb_end FROM IndelAll WHERE Name = '%s'" % (
+ self.gene_name)
result_snp = g.db.execute(query).fetchall()
if result_snp:
self.snp_list = [item[0] for item in result_snp]
@@ -255,7 +267,8 @@ class SnpBrowser:
if self.limit_strains == "true" and len(self.chosen_strains) > 0:
for item in self.chosen_strains:
- index = self.strain_lists[self.species_name.lower()].index(item)
+ index = self.strain_lists[self.species_name.lower()].index(
+ item)
strain_index_list.append(index)
for seq, result in enumerate(results):
@@ -263,7 +276,8 @@ class SnpBrowser:
if self.variant_type == "SNP":
display_strains = []
- snp_id, species_id, snp_name, rs, chr, mb, mb_2016, alleles, snp_source, conservation_score = result[:10]
+ snp_id, species_id, snp_name, rs, chr, mb, mb_2016, alleles, snp_source, conservation_score = result[
+ :10]
effect_list = result[10:28]
if self.species_id == 1:
self.allele_list = result[30:]
@@ -279,7 +293,8 @@ class SnpBrowser:
self.allele_list = display_strains
effect_info_dict = get_effect_info(effect_list)
- coding_domain_list = ['Start Gained', 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
+ coding_domain_list = ['Start Gained', 'Start Lost',
+ 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
intron_domain_list = ['Splice Site', 'Nonsplice Site']
for key in effect_info_dict:
@@ -296,19 +311,22 @@ class SnpBrowser:
if 'Intergenic' in domain:
if self.gene_name != "":
- gene_id = get_gene_id(self.species_id, self.gene_name)
+ gene_id = get_gene_id(
+ self.species_id, self.gene_name)
gene = [gene_id, self.gene_name]
else:
gene = check_if_in_gene(species_id, chr, mb)
transcript = exon = function = function_details = ''
if self.redundant == "false" or last_mb != mb: # filter redundant
if self.include_record(domain, function, snp_source, conservation_score):
- info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id]
+ info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain,
+ function, function_details, snp_source, conservation_score, snp_id]
info_list.extend(self.allele_list)
filtered_results.append(info_list)
last_mb = mb
else:
- gene_list, transcript_list, exon_list, function_list, function_details_list = effect_info_dict[key]
+ gene_list, transcript_list, exon_list, function_list, function_details_list = effect_info_dict[
+ key]
for index, item in enumerate(gene_list):
gene = item
transcript = transcript_list[index]
@@ -325,13 +343,15 @@ class SnpBrowser:
function = ""
if function_details_list:
- function_details = "Biotype: " + function_details_list[index]
+ function_details = "Biotype: " + \
+ function_details_list[index]
else:
function_details = ""
if self.redundant == "false" or last_mb != mb:
if self.include_record(domain, function, snp_source, conservation_score):
- info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id]
+ info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain,
+ function, function_details, snp_source, conservation_score, snp_id]
info_list.extend(self.allele_list)
filtered_results.append(info_list)
last_mb = mb
@@ -345,7 +365,8 @@ class SnpBrowser:
gene = "No Gene"
domain = conservation_score = snp_id = snp_name = rs = flank_3 = flank_5 = ncbi = function = ""
if self.include_record(domain, function, source_name, conservation_score):
- filtered_results.append([indel_name, indel_chr, indel_mb_start, indel_mb_end, indel_strand, indel_type, indel_size, indel_sequence, source_name])
+ filtered_results.append([indel_name, indel_chr, indel_mb_start, indel_mb_end,
+ indel_strand, indel_type, indel_size, indel_sequence, source_name])
last_mb = indel_mb_start
else:
@@ -365,7 +386,8 @@ class SnpBrowser:
if gene_name and (gene_name not in gene_name_list):
gene_name_list.append(gene_name)
if len(gene_name_list) > 0:
- gene_id_name_dict = get_gene_id_name_dict(self.species_id, gene_name_list)
+ gene_id_name_dict = get_gene_id_name_dict(
+ self.species_id, gene_name_list)
# ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc)
self.empty_columns = {
@@ -383,7 +405,8 @@ class SnpBrowser:
for i, result in enumerate(self.filtered_results):
this_row = {}
if self.variant_type == "SNP":
- snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14]
+ snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[
+ :14]
allele_value_list = result[14:]
if rs:
snp_url = webqtlConfig.DBSNP % (rs)
@@ -394,9 +417,11 @@ class SnpBrowser:
end_bp = int(mb * 1000000 + 100)
position_info = "chr%s:%d-%d" % (chr, start_bp, end_bp)
if self.species_id == 2:
- snp_url = webqtlConfig.GENOMEBROWSER_URL % ("rn6", position_info)
+ snp_url = webqtlConfig.GENOMEBROWSER_URL % (
+ "rn6", position_info)
else:
- snp_url = webqtlConfig.GENOMEBROWSER_URL % ("mm10", position_info)
+ snp_url = webqtlConfig.GENOMEBROWSER_URL % (
+ "mm10", position_info)
mb = float(mb)
mb_formatted = "%2.6f" % mb
@@ -429,7 +454,8 @@ class SnpBrowser:
gene_link = ""
if transcript:
- transcript_link = webqtlConfig.ENSEMBLETRANSCRIPT_URL % (transcript)
+ transcript_link = webqtlConfig.ENSEMBLETRANSCRIPT_URL % (
+ transcript)
self.empty_columns['transcript'] = "true"
else:
transcript_link = ""
@@ -460,7 +486,8 @@ class SnpBrowser:
function_list = function_details.strip().split(",")
function_list = [item.strip() for item in function_list]
function_list[0] = function_list[0].title()
- function_details = ", ".join(item for item in function_list)
+ function_details = ", ".join(
+ item for item in function_list)
function_details = function_details.replace("_", " ")
function_details = function_details.replace("/", " -> ")
if function_details == "Biotype: Protein Coding":
@@ -675,8 +702,10 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None):
header_fields = []
header_data_names = []
if variant_type == "SNP":
- header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
- header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score', 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details']
+ header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore',
+ 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
+ header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score',
+ 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details']
header_fields.append(strain_list)
header_data_names += strain_list
@@ -712,8 +741,10 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None):
header_data_names.remove(col)
elif variant_type == "InDel":
- header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
- header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s', 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']
+ header_fields = ['Index', 'ID', 'Type', 'InDel Chr',
+ 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
+ header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
+ 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']
return header_fields, empty_field_count, header_data_names
@@ -726,10 +757,13 @@ def get_effect_details_by_category(effect_name=None, effect_value=None):
function_detail_list = []
tmp_list = []
- gene_group_list = ['Upstream', 'Downstream', 'Splice Site', 'Nonsplice Site', '3\' UTR']
- biotype_group_list = ['Unknown Effect In Exon', 'Start Gained', 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
+ gene_group_list = ['Upstream', 'Downstream',
+ 'Splice Site', 'Nonsplice Site', '3\' UTR']
+ biotype_group_list = ['Unknown Effect In Exon', 'Start Gained',
+ 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
new_codon_group_list = ['Start Gained']
- codon_effect_group_list = ['Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
+ codon_effect_group_list = [
+ 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
effect_detail_list = effect_value.strip().split('|')
effect_detail_list = [item.strip() for item in effect_detail_list]
@@ -773,8 +807,10 @@ def get_effect_info(effect_list):
effect_detail_list = []
effect_info_dict = {}
- prime3_utr, prime5_utr, upstream, downstream, intron, nonsplice_site, splice_site, intergenic = effect_list[:8]
- exon, non_synonymous_coding, synonymous_coding, start_gained, start_lost, stop_gained, stop_lost, unknown_effect_in_exon = effect_list[8:16]
+ prime3_utr, prime5_utr, upstream, downstream, intron, nonsplice_site, splice_site, intergenic = effect_list[
+ :8]
+ exon, non_synonymous_coding, synonymous_coding, start_gained, start_lost, stop_gained, stop_lost, unknown_effect_in_exon = effect_list[
+ 8:16]
if intergenic:
domain = "Intergenic"
@@ -783,59 +819,72 @@ def get_effect_info(effect_list):
# if not exon, get gene list/transcript list info
if upstream:
domain = "Upstream"
- effect_detail_list = get_effect_details_by_category(effect_name='Upstream', effect_value=upstream)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Upstream', effect_value=upstream)
effect_info_dict[domain] = effect_detail_list
if downstream:
domain = "Downstream"
- effect_detail_list = get_effect_details_by_category(effect_name='Downstream', effect_value=downstream)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Downstream', effect_value=downstream)
effect_info_dict[domain] = effect_detail_list
if intron:
if splice_site:
domain = "Splice Site"
- effect_detail_list = get_effect_details_by_category(effect_name='Splice Site', effect_value=splice_site)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Splice Site', effect_value=splice_site)
effect_info_dict[domain] = effect_detail_list
if nonsplice_site:
domain = "Nonsplice Site"
- effect_detail_list = get_effect_details_by_category(effect_name='Nonsplice Site', effect_value=nonsplice_site)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Nonsplice Site', effect_value=nonsplice_site)
effect_info_dict[domain] = effect_detail_list
# get gene, transcript_list, and exon info
if prime3_utr:
domain = "3\' UTR"
- effect_detail_list = get_effect_details_by_category(effect_name='3\' UTR', effect_value=prime3_utr)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='3\' UTR', effect_value=prime3_utr)
effect_info_dict[domain] = effect_detail_list
if prime5_utr:
domain = "5\' UTR"
- effect_detail_list = get_effect_details_by_category(effect_name='5\' UTR', effect_value=prime5_utr)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='5\' UTR', effect_value=prime5_utr)
effect_info_dict[domain] = effect_detail_list
if start_gained:
domain = "Start Gained"
- effect_detail_list = get_effect_details_by_category(effect_name='Start Gained', effect_value=start_gained)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Start Gained', effect_value=start_gained)
effect_info_dict[domain] = effect_detail_list
if unknown_effect_in_exon:
domain = "Unknown Effect In Exon"
- effect_detail_list = get_effect_details_by_category(effect_name='Unknown Effect In Exon', effect_value=unknown_effect_in_exon)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Unknown Effect In Exon', effect_value=unknown_effect_in_exon)
effect_info_dict[domain] = effect_detail_list
if start_lost:
domain = "Start Lost"
- effect_detail_list = get_effect_details_by_category(effect_name='Start Lost', effect_value=start_lost)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Start Lost', effect_value=start_lost)
effect_info_dict[domain] = effect_detail_list
if stop_gained:
domain = "Stop Gained"
- effect_detail_list = get_effect_details_by_category(effect_name='Stop Gained', effect_value=stop_gained)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Stop Gained', effect_value=stop_gained)
effect_info_dict[domain] = effect_detail_list
if stop_lost:
domain = "Stop Lost"
- effect_detail_list = get_effect_details_by_category(effect_name='Stop Lost', effect_value=stop_lost)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Stop Lost', effect_value=stop_lost)
effect_info_dict[domain] = effect_detail_list
if non_synonymous_coding:
domain = "Nonsynonymous"
- effect_detail_list = get_effect_details_by_category(effect_name='Nonsynonymous', effect_value=non_synonymous_coding)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Nonsynonymous', effect_value=non_synonymous_coding)
effect_info_dict[domain] = effect_detail_list
if synonymous_coding:
domain = "Synonymous"
- effect_detail_list = get_effect_details_by_category(effect_name='Synonymous', effect_value=synonymous_coding)
+ effect_detail_list = get_effect_details_by_category(
+ effect_name='Synonymous', effect_value=synonymous_coding)
effect_info_dict[domain] = effect_detail_list
return effect_info_dict
@@ -863,7 +912,8 @@ def get_gene_id_name_dict(species_id, gene_name_list):
gene_id_name_dict = {}
if len(gene_name_list) == 0:
return ""
- gene_name_str_list = ["'" + gene_name + "'" for gene_name in gene_name_list]
+ gene_name_str_list = ["'" + gene_name + \
+ "'" for gene_name in gene_name_list]
gene_name_str = ",".join(gene_name_str_list)
query = """
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 07073d6a..2e467dc8 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -52,10 +52,12 @@ class GSearch:
self.trait_list = []
with Bench("Creating trait objects"):
for line in re:
- dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
+ dataset = create_dataset(
+ line[3], "ProbeSet", get_samplelist=False)
trait_id = line[4]
# with Bench("Building trait object"):
- this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+ this_trait = GeneralTrait(
+ dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
self.trait_list.append(this_trait)
elif self.type == "phenotype":
@@ -97,7 +99,8 @@ class GSearch:
for line in re:
dataset = create_dataset(line[2], "Publish")
trait_id = line[3]
- this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
+ this_trait = GeneralTrait(
+ dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
self.trait_list.append(this_trait)
self.results = self.convert_to_json()
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 2a2f8484..708d43d2 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -70,7 +70,8 @@ def set_password(password):
assert len(password) >= 6, "Password shouldn't be shorter than 6 characters"
- encoded_password = encode_password(pass_gen_fields, pass_gen_fields['unencrypted_password'])
+ encoded_password = encode_password(
+ pass_gen_fields, pass_gen_fields['unencrypted_password'])
return encoded_password
@@ -161,12 +162,16 @@ def verify_email():
# As long as they have access to the email account
# We might as well log them in
session_id_signed = get_signed_session_id(user_details)
- flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success")
- response = make_response(redirect(url_for('index_page', import_collections=import_col, anon_id=anon_id)))
- response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None)
+ flash("Thank you for logging in {}.".format(
+ user_details['full_name']), "alert-success")
+ response = make_response(redirect(
+ url_for('index_page', import_collections=import_col, anon_id=anon_id)))
+ response.set_cookie(UserSession.user_cookie_name,
+ session_id_signed, max_age=None)
return response
else:
- flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+ flash(
+ "Invalid code: Password reset code does not exist or might have expired!", "error")
@app.route("/n/login", methods=('GET', 'POST'))
@@ -195,23 +200,28 @@ def login():
display_id = user_details['orcid']
else:
display_id = ""
- flash("Thank you for logging in {}.".format(display_id), "alert-success")
+ flash("Thank you for logging in {}.".format(
+ display_id), "alert-success")
response = make_response(redirect(url_for('index_page')))
- response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None)
+ response.set_cookie(
+ UserSession.user_cookie_name, session_id_signed, max_age=None)
else:
flash("Something went unexpectedly wrong.", "alert-danger")
response = make_response(redirect(url_for('index_page')))
return response
else:
- user_details = get_user_by_unique_column("email_address", params['email_address'])
+ user_details = get_user_by_unique_column(
+ "email_address", params['email_address'])
password_match = False
if user_details:
submitted_password = params['password']
pwfields = user_details['password']
if isinstance(pwfields, str):
pwfields = json.loads(pwfields)
- encrypted_pass_fields = encode_password(pwfields, submitted_password)
- password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password'])
+ encrypted_pass_fields = encode_password(
+ pwfields, submitted_password)
+ password_match = pbkdf2.safe_str_cmp(
+ encrypted_pass_fields['password'], pwfields['password'])
else: # Invalid e-mail
flash("Invalid e-mail address. Please try again.", "alert-danger")
@@ -227,12 +237,16 @@ def login():
anon_id = params['anon_id']
session_id_signed = get_signed_session_id(user_details)
- flash("Thank you for logging in {}.".format(user_details['full_name']), "alert-success")
- response = make_response(redirect(url_for('index_page', import_collections=import_col, anon_id=anon_id)))
- response.set_cookie(UserSession.user_cookie_name, session_id_signed, max_age=None)
+ flash("Thank you for logging in {}.".format(
+ user_details['full_name']), "alert-success")
+ response = make_response(redirect(
+ url_for('index_page', import_collections=import_col, anon_id=anon_id)))
+ response.set_cookie(
+ UserSession.user_cookie_name, session_id_signed, max_age=None)
return response
else:
- email_ob = send_verification_email(user_details, template_name="email/user_verification.txt")
+ email_ob = send_verification_email(
+ user_details, template_name="email/user_verification.txt")
return render_template("newsecurity/verification_still_needed.html", subject=email_ob['subject'])
else: # Incorrect password
# ZS: It previously seemed to store that there was an incorrect log-in attempt here, but it did so in the MySQL DB so this might need to be reproduced with Redis
@@ -252,8 +266,10 @@ def github_oauth2():
"code": code
}
- result = requests.post("https://github.com/login/oauth/access_token", json=data)
- result_dict = {arr[0]: arr[1] for arr in [tok.split("=") for tok in result.text.split("&")]}
+ result = requests.post(
+ "https://github.com/login/oauth/access_token", json=data)
+ result_dict = {arr[0]: arr[1]
+ for arr in [tok.split("=") for tok in result.text.split("&")]}
github_user = get_github_user_details(result_dict["access_token"])
@@ -277,7 +293,8 @@ def github_oauth2():
def get_github_user_details(access_token):
from utility.tools import GITHUB_API_URL
- result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
+ result = requests.get(GITHUB_API_URL, headers={
+ 'Authorization': 'token ' + access_token}).content
return json.loads(result)
@@ -323,7 +340,8 @@ def orcid_oauth2():
def get_github_user_details(access_token):
from utility.tools import GITHUB_API_URL
- result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
+ result = requests.get(GITHUB_API_URL, headers={
+ 'Authorization': 'token ' + access_token}).content
return json.loads(result)
@@ -389,13 +407,16 @@ def forgot_password_submit():
next_page = None
if email_address != "":
logger.debug("Wants to send password E-mail to ", email_address)
- user_details = get_user_by_unique_column("email_address", email_address)
+ user_details = get_user_by_unique_column(
+ "email_address", email_address)
if user_details:
- email_subject = send_forgot_password_email(user_details["email_address"])
+ email_subject = send_forgot_password_email(
+ user_details["email_address"])
return render_template("new_security/forgot_password_step2.html",
subject=email_subject)
else:
- flash("The e-mail entered is not associated with an account.", "alert-danger")
+ flash("The e-mail entered is not associated with an account.",
+ "alert-danger")
return redirect(url_for("forgot_password"))
else:
@@ -417,7 +438,8 @@ def password_reset():
return render_template(
"new_security/password_reset.html", user_encode=user_details["email_address"])
else:
- flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+ flash(
+ "Invalid code: Password reset code does not exist or might have expired!", "error")
return redirect(url_for("login"))
else:
return redirect(url_for("login"))
@@ -446,21 +468,27 @@ def register_user(params):
errors = []
user_details = {}
- user_details['email_address'] = params.get('email_address', '').encode("utf-8").strip()
+ user_details['email_address'] = params.get(
+ 'email_address', '').encode("utf-8").strip()
if not (5 <= len(user_details['email_address']) <= 50):
- errors.append('Email Address needs to be between 5 and 50 characters.')
+ errors.append(
+ 'Email Address needs to be between 5 and 50 characters.')
else:
- email_exists = get_user_by_unique_column("email_address", user_details['email_address'])
+ email_exists = get_user_by_unique_column(
+ "email_address", user_details['email_address'])
if email_exists:
errors.append('User already exists with that email')
- user_details['full_name'] = params.get('full_name', '').encode("utf-8").strip()
+ user_details['full_name'] = params.get(
+ 'full_name', '').encode("utf-8").strip()
if not (5 <= len(user_details['full_name']) <= 50):
errors.append('Full Name needs to be between 5 and 50 characters.')
- user_details['organization'] = params.get('organization', '').encode("utf-8").strip()
+ user_details['organization'] = params.get(
+ 'organization', '').encode("utf-8").strip()
if user_details['organization'] and not (5 <= len(user_details['organization']) <= 50):
- errors.append('Organization needs to be empty or between 5 and 50 characters.')
+ errors.append(
+ 'Organization needs to be empty or between 5 and 50 characters.')
password = str(params.get('password', ''))
if not (6 <= len(password)):
@@ -493,7 +521,8 @@ def register():
errors = register_user(params)
if len(errors) == 0:
- flash("Registration successful. You may login with your new account", "alert-info")
+ flash(
+ "Registration successful. You may login with your new account", "alert-info")
return redirect(url_for("login"))
return render_template("new_security/register_user.html", values=params, errors=errors)
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index a9bd65e6..5610833b 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -93,8 +93,10 @@ class AnonUser:
this_collection = {}
this_collection['id'] = collection['id']
this_collection['name'] = collection['name']
- this_collection['created_timestamp'] = collection['created_timestamp'].strftime('%b %d %Y %I:%M%p')
- this_collection['changed_timestamp'] = collection['changed_timestamp'].strftime('%b %d %Y %I:%M%p')
+ this_collection['created_timestamp'] = collection['created_timestamp'].strftime(
+ '%b %d %Y %I:%M%p')
+ this_collection['changed_timestamp'] = collection['changed_timestamp'].strftime(
+ '%b %d %Y %I:%M%p')
this_collection['num_members'] = collection['num_members']
this_collection['members'] = collection['members']
updated_collections.append(this_collection)
@@ -108,21 +110,26 @@ class AnonUser:
else:
collections = json.loads(json_collections)
for collection in collections:
- collection['created_timestamp'] = datetime.datetime.strptime(collection['created_timestamp'], '%b %d %Y %I:%M%p')
- collection['changed_timestamp'] = datetime.datetime.strptime(collection['changed_timestamp'], '%b %d %Y %I:%M%p')
+ collection['created_timestamp'] = datetime.datetime.strptime(
+ collection['created_timestamp'], '%b %d %Y %I:%M%p')
+ collection['changed_timestamp'] = datetime.datetime.strptime(
+ collection['changed_timestamp'], '%b %d %Y %I:%M%p')
- collections = sorted(collections, key=lambda i: i['changed_timestamp'], reverse=True)
+ collections = sorted(
+ collections, key=lambda i: i['changed_timestamp'], reverse=True)
return collections
def import_traits_to_user(self):
result = Redis.get(self.key)
collections_list = json.loads(result if result else "[]")
for collection in collections_list:
- collection_exists = g.user_session.get_collection_by_name(collection['name'])
+ collection_exists = g.user_session.get_collection_by_name(
+ collection['name'])
if collection_exists:
continue
else:
- g.user_session.add_collection(collection['name'], collection['members'])
+ g.user_session.add_collection(
+ collection['name'], collection['members'])
def display_num_collections(self):
"""
@@ -148,7 +155,8 @@ def verify_cookie(cookie):
the_uuid, separator, the_signature = cookie.partition(':')
assert len(the_uuid) == 36, "Is session_id a uuid?"
assert separator == ":", "Expected a : here"
- assert the_signature == actual_hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?"
+ assert the_signature == actual_hmac_creation(
+ the_uuid), "Uh-oh, someone tampering with the cookie?"
return the_uuid
@@ -282,7 +290,8 @@ class UserSession:
updated_collection['members'] = updated_traits
updated_collection['num_members'] = len(updated_traits)
- updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+ updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime(
+ '%b %d %Y %I:%M%p')
updated_collections = []
for collection in self.user_collections:
@@ -308,7 +317,8 @@ class UserSession:
updated_collection['members'] = updated_traits
updated_collection['num_members'] = len(updated_traits)
- updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+ updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime(
+ '%b %d %Y %I:%M%p')
updated_collections = []
for collection in self.user_collections:
@@ -355,7 +365,8 @@ def get_cookie():
def set_cookie(response):
if not request.cookies.get(g.cookie_session.cookie_name):
- response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie)
+ response.set_cookie(g.cookie_session.cookie_name,
+ g.cookie_session.cookie)
return response
@@ -390,22 +401,28 @@ class RegisterUser:
self.errors = []
self.user = Bunch()
- self.user.email_address = kw.get('email_address', '').encode("utf-8").strip()
+ self.user.email_address = kw.get(
+ 'email_address', '').encode("utf-8").strip()
if not (5 <= len(self.user.email_address) <= 50):
- self.errors.append('Email Address needs to be between 5 and 50 characters.')
+ self.errors.append(
+ 'Email Address needs to be between 5 and 50 characters.')
else:
- email_exists = get_user_by_unique_column("email_address", self.user.email_address)
+ email_exists = get_user_by_unique_column(
+ "email_address", self.user.email_address)
#email_exists = get_user_by_unique_column(es, "email_address", self.user.email_address)
if email_exists:
self.errors.append('User already exists with that email')
self.user.full_name = kw.get('full_name', '').encode("utf-8").strip()
if not (5 <= len(self.user.full_name) <= 50):
- self.errors.append('Full Name needs to be between 5 and 50 characters.')
+ self.errors.append(
+ 'Full Name needs to be between 5 and 50 characters.')
- self.user.organization = kw.get('organization', '').encode("utf-8").strip()
+ self.user.organization = kw.get(
+ 'organization', '').encode("utf-8").strip()
if self.user.organization and not (5 <= len(self.user.organization) <= 50):
- self.errors.append('Organization needs to be empty or between 5 and 50 characters.')
+ self.errors.append(
+ 'Organization needs to be empty or between 5 and 50 characters.')
password = str(kw.get('password', ''))
if not (6 <= len(password)):
@@ -568,14 +585,16 @@ def password_reset():
if verification_code:
user_email = check_verification_code(verification_code)
if user_email:
- user_details = get_user_by_unique_column('email_address', user_email)
+ user_details = get_user_by_unique_column(
+ 'email_address', user_email)
if user_details:
return render_template(
"new_security/password_reset.html", user_encode=user_details["user_id"])
else:
flash("Invalid code: User no longer exists!", "error")
else:
- flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+ flash(
+ "Invalid code: Password reset code does not exist or might have expired!", "error")
else:
return redirect(url_for("login"))
@@ -648,8 +667,10 @@ def github_oauth2():
"client_secret": GITHUB_CLIENT_SECRET,
"code": code
}
- result = requests.post("https://github.com/login/oauth/access_token", json=data)
- result_dict = {arr[0]: arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]}
+ result = requests.post(
+ "https://github.com/login/oauth/access_token", json=data)
+ result_dict = {arr[0]: arr[1] for arr in [tok.split(
+ "=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]}
github_user = get_github_user_details(result_dict["access_token"])
@@ -696,7 +717,8 @@ def orcid_oauth2():
def get_github_user_details(access_token):
from utility.tools import GITHUB_API_URL
- result = requests.get(GITHUB_API_URL, params={"access_token": access_token})
+ result = requests.get(GITHUB_API_URL, params={
+ "access_token": access_token})
return result.json()
@@ -737,7 +759,8 @@ class LoginUser:
return render_template(
"new_security/login_user.html", external_login=external_login, redis_is_available=is_redis_available())
else:
- user_details = get_user_by_unique_column("email_address", params["email_address"])
+ user_details = get_user_by_unique_column(
+ "email_address", params["email_address"])
#user_details = get_user_by_unique_column(es, "email_address", params["email_address"])
user = None
valid = None
@@ -755,8 +778,10 @@ class LoginUser:
pwfields.iterations,
pwfields.keylength,
pwfields.hashfunc)
- logger.debug("\n\nComparing:\n{}\n{}\n".format(encrypted.password, pwfields.password))
- valid = pbkdf2.safe_str_cmp(encrypted.password, pwfields.password)
+ logger.debug("\n\nComparing:\n{}\n{}\n".format(
+ encrypted.password, pwfields.password))
+ valid = pbkdf2.safe_str_cmp(
+ encrypted.password, pwfields.password)
logger.debug("valid is:", valid)
if valid and not user.confirmed:
@@ -782,7 +807,8 @@ class LoginUser:
else:
if user:
self.unsuccessful_login(user)
- flash("Invalid email-address or password. Please try again.", "alert-danger")
+ flash("Invalid email-address or password. Please try again.",
+ "alert-danger")
response = make_response(redirect(url_for('login')))
return response
@@ -790,14 +816,17 @@ class LoginUser:
def actual_login(self, user, assumed_by=None, import_collections=None):
"""The meat of the logging in process"""
session_id_signed = self.successful_login(user, assumed_by)
- flash("Thank you for logging in {}.".format(user.full_name), "alert-success")
- response = make_response(redirect(url_for('index_page', import_collections=import_collections)))
+ flash("Thank you for logging in {}.".format(
+ user.full_name), "alert-success")
+ response = make_response(
+ redirect(url_for('index_page', import_collections=import_collections)))
if self.remember_me:
max_age = self.remember_time
else:
max_age = None
- response.set_cookie(UserSession.cookie_name, session_id_signed, max_age=max_age)
+ response.set_cookie(UserSession.cookie_name,
+ session_id_signed, max_age=max_age)
return response
def successful_login(self, user, assumed_by=None):
@@ -866,13 +895,15 @@ def forgot_password_submit():
next_page = None
if email_address != "":
logger.debug("Wants to send password E-mail to ", email_address)
- user_details = get_user_by_unique_column("email_address", email_address)
+ user_details = get_user_by_unique_column(
+ "email_address", email_address)
if user_details:
ForgotPasswordEmail(user_details["email_address"])
return render_template("new_security/forgot_password_step2.html",
subject=ForgotPasswordEmail.subject)
else:
- flash("The e-mail entered is not associated with an account.", "alert-danger")
+ flash("The e-mail entered is not associated with an account.",
+ "alert-danger")
return redirect(url_for("forgot_password"))
else:
@@ -959,7 +990,8 @@ def register():
errors = result.errors
if len(errors) == 0:
- flash("Registration successful. You may login with your new account", "alert-info")
+ flash(
+ "Registration successful. You may login with your new account", "alert-info")
return redirect(url_for("login"))
return render_template("new_security/register_user.html", values=params, errors=errors)
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index f0f0d60c..6ccb2e80 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -36,7 +36,8 @@ def get_user_session():
def set_user_session(response):
if hasattr(g, 'user_session'):
if not request.cookies.get(g.user_session.cookie_name):
- response.set_cookie(g.user_session.cookie_name, g.user_session.cookie)
+ response.set_cookie(g.user_session.cookie_name,
+ g.user_session.cookie)
return response
@@ -44,7 +45,8 @@ def verify_cookie(cookie):
the_uuid, separator, the_signature = cookie.partition(':')
assert len(the_uuid) == 36, "Is session_id a uuid?"
assert separator == ":", "Expected a : here"
- assert the_signature == hmac.hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?"
+ assert the_signature == hmac.hmac_creation(
+ the_uuid), "Uh-oh, someone tampering with the cookie?"
return the_uuid
@@ -60,9 +62,11 @@ def create_signed_cookie():
def manage_user():
params = request.form if request.form else request.args
if 'new_full_name' in params:
- set_user_attribute(g.user_session.user_id, 'full_name', params['new_full_name'])
+ set_user_attribute(g.user_session.user_id,
+ 'full_name', params['new_full_name'])
if 'new_organization' in params:
- set_user_attribute(g.user_session.user_id, 'organization', params['new_organization'])
+ set_user_attribute(g.user_session.user_id,
+ 'organization', params['new_organization'])
user_details = get_user_by_unique_column("user_id", g.user_session.user_id)
@@ -108,7 +112,8 @@ class UserSession:
# Grrr...this won't work because of the way flask handles cookies
# Delete the cookie
- flash("Due to inactivity your session has expired. If you'd like please login again.")
+ flash(
+ "Due to inactivity your session has expired. If you'd like please login again.")
return None
else:
self.record = dict(login_time=time.time(),
@@ -178,7 +183,9 @@ class UserSession:
# ZS: Get user's collections if they exist
collections = get_user_collections(self.user_id)
- collections = [item for item in collections if item['name'] != "Your Default Collection"] + [item for item in collections if item['name'] == "Your Default Collection"] # ZS: Ensure Default Collection is last in list
+ collections = [item for item in collections if item['name'] != "Your Default Collection"] + \
+ [item for item in collections if item['name'] ==
+ "Your Default Collection"] # ZS: Ensure Default Collection is last in list
return collections
@property
@@ -234,12 +241,14 @@ class UserSession:
this_collection = self.get_collection_by_id(collection_id)
updated_collection = this_collection
- current_members_minus_new = [member for member in this_collection['members'] if member not in traits_to_add]
+ current_members_minus_new = [
+ member for member in this_collection['members'] if member not in traits_to_add]
updated_traits = traits_to_add + current_members_minus_new
updated_collection['members'] = updated_traits
updated_collection['num_members'] = len(updated_traits)
- updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+ updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime(
+ '%b %d %Y %I:%M%p')
updated_collections = []
for collection in self.user_collections:
@@ -265,7 +274,8 @@ class UserSession:
updated_collection['members'] = updated_traits
updated_collection['num_members'] = len(updated_traits)
- updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+ updated_collection['changed_timestamp'] = datetime.datetime.utcnow().strftime(
+ '%b %d %Y %I:%M%p')
updated_collections = []
for collection in self.user_collections:
--
cgit v1.2.3
From bd702e59d7a426fe351d34367bf824683c655696 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 30 Apr 2021 12:52:55 +0300
Subject: autopep8: Fix W291, W292, W293, W391
---
wqflask/base/mrna_assay_tissue_data.py | 2 +-
wqflask/maintenance/convert_dryad_to_bimbam.py | 2 +-
wqflask/maintenance/convert_geno_to_bimbam.py | 4 +--
.../maintenance/generate_kinship_from_bimbam.py | 8 ++---
wqflask/maintenance/geno_to_json.py | 34 +++++++++---------
wqflask/tests/unit/wqflask/api/test_correlation.py | 4 +--
.../correlation/test_correlation_functions.py | 2 +-
.../marker_regression/test_qtlreaper_mapping.py | 4 +--
.../wqflask/marker_regression/test_rqtl_mapping.py | 7 ----
.../unit/wqflask/snp_browser/test_snp_browser.py | 8 ++---
wqflask/tests/unit/wqflask/test_server_side.py | 4 +--
wqflask/utility/__init__.py | 2 --
wqflask/utility/genofile_parser.py | 1 -
wqflask/wqflask/__init__.py | 2 +-
wqflask/wqflask/api/mapping.py | 2 --
wqflask/wqflask/api/router.py | 14 ++++----
wqflask/wqflask/collect.py | 1 -
.../comparison_bar_chart/comparison_bar_chart.py | 7 ++--
wqflask/wqflask/correlation/corr_scatter_plot.py | 4 +--
wqflask/wqflask/correlation/show_corr_results.py | 1 -
.../wqflask/correlation_matrix/show_corr_matrix.py | 2 +-
wqflask/wqflask/ctl/ctl_analysis.py | 3 +-
wqflask/wqflask/db_info.py | 2 --
wqflask/wqflask/docs.py | 2 +-
wqflask/wqflask/export_traits.py | 4 +--
.../wqflask/external_tools/send_to_webgestalt.py | 2 +-
wqflask/wqflask/heatmap/heatmap.py | 2 +-
wqflask/wqflask/interval_analyst/GeneUtil.py | 24 ++++++-------
.../wqflask/marker_regression/qtlreaper_mapping.py | 10 +++---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 2 +-
wqflask/wqflask/resource_manager.py | 2 +-
wqflask/wqflask/search_results.py | 1 -
wqflask/wqflask/server_side.py | 2 +-
wqflask/wqflask/snp_browser/snp_browser.py | 7 ++--
wqflask/wqflask/user_login.py | 42 +++++++++++-----------
wqflask/wqflask/user_session.py | 2 --
36 files changed, 98 insertions(+), 124 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 9bb29664..882ae911 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -74,7 +74,7 @@ class MrnaAssayTissueData:
def get_symbol_values_pairs(self):
id_list = [self.data[symbol].data_id for symbol in self.data]
-
+
symbol_values_dict = {}
if len(id_list) > 0:
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index e417c280..18fbb8a1 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -52,7 +52,7 @@ def read_dryad_file(filename):
# this_row.append(line.split(" ")[i+2])
# print("row: " + str(i))
# geno_rows.append(this_row)
- #
+ #
# return geno_rows
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index a2ede1f9..c5af1ca6 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -91,7 +91,7 @@ class ConvertGenoFile:
self.markers.append(this_marker.__dict__)
- self.write_to_bimbam()
+ self.write_to_bimbam()
def write_to_bimbam(self):
with open(self.output_files[0], "w") as geno_fh:
@@ -126,7 +126,7 @@ class ConvertGenoFile:
self.sample_list = row_contents[3:]
else:
self.sample_list = row_contents[2:]
-
+
def process_rows(self):
for self.latest_row_pos, row in enumerate(self.input_fh):
self.latest_row_value = row
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index bed634fa..cd39fceb 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -19,7 +19,7 @@ class GenerateKinshipMatrices:
self.group_name = group_name
self.geno_file = geno_file
self.pheno_file = pheno_file
-
+
def generate_kinship(self):
gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \
" -p " + self.pheno_file + \
@@ -56,11 +56,11 @@ class GenerateKinshipMatrices:
print(" Column is:", convertob.latest_col_value)
print(" Row is:", convertob.latest_row_value)
break
-
-
+
+
if __name__ == "__main__":
Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/"""
Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
-
+
# ./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 76a0fc98..27eb6553 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -29,7 +29,7 @@ from pprint import pformat as pf
class EmptyConfigurations(Exception):
pass
-
+
class Marker:
def __init__(self):
self.name = None
@@ -42,20 +42,20 @@ class Marker:
class ConvertGenoFile:
def __init__(self, input_file, output_file):
-
+
self.input_file = input_file
self.output_file = output_file
-
+
self.mb_exists = False
self.cm_exists = False
self.markers = []
-
+
self.latest_row_pos = None
self.latest_col_pos = None
-
+
self.latest_row_value = None
self.latest_col_value = None
-
+
def convert(self):
self.haplotype_notation = {
@@ -64,16 +64,16 @@ class ConvertGenoFile:
'@het': "0.5",
'@unk': "NA"
}
-
+
self.configurations = {}
#self.skipped_cols = 3
-
+
# if self.input_file.endswith(".geno.gz"):
# print("self.input_file: ", self.input_file)
# self.input_fh = gzip.open(self.input_file)
# else:
self.input_fh = open(self.input_file)
-
+
with open(self.output_file, "w") as self.output_fh:
# if self.file_type == "geno":
self.process_csv()
@@ -105,22 +105,22 @@ class ConvertGenoFile:
self.configurations[genotype.upper()])
else:
this_marker.genotypes.append("NA")
-
- #print("this_marker is:", pf(this_marker.__dict__))
+
+ #print("this_marker is:", pf(this_marker.__dict__))
# if this_marker.chr == "14":
self.markers.append(this_marker.__dict__)
with open(self.output_file, 'w') as fh:
json.dump(self.markers, fh, indent=" ", sort_keys=True)
-
+
# print('configurations:', str(configurations))
#self.latest_col_pos = item_count + self.skipped_cols
#self.latest_col_value = item
-
+
# if item_count != 0:
# self.output_fh.write(" ")
# self.output_fh.write(self.configurations[item.upper()])
-
+
# self.output_fh.write("\n")
def process_rows(self):
@@ -176,12 +176,12 @@ class ConvertGenoFile:
print(" Column is:", convertob.latest_col_value)
print(" Row is:", convertob.latest_row_value)
break
-
+
# def process_snps_file(cls, snps_file, new_directory):
# output_file = os.path.join(new_directory, "mouse_families.json")
# print("%s -> %s" % (snps_file, output_file))
# convertob = ConvertGenoFile(input_file, output_file)
-
+
if __name__ == "__main__":
Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
@@ -192,5 +192,5 @@ if __name__ == "__main__":
# convertob.convert()
ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
# ConvertGenoFiles(Geno_Directory)
-
+
#process_csv(Input_File, Output_File)
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index bd99838d..34ffa9ef 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -105,9 +105,9 @@ class TestCorrelations(unittest.TestCase):
target_dataset = AttributeSetter({"group": group})
target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6]
- trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
+ trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
"S3": AttributeSetter(
- {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
+ {"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
"S6": AttributeSetter({"value": 5.0})}
this_trait = AttributeSetter({"data": trait_data})
mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
diff --git a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
index 44d2e0fc..2bbeab1f 100644
--- a/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
+++ b/wqflask/tests/unit/wqflask/correlation/test_correlation_functions.py
@@ -5,7 +5,7 @@ from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_ti
class TestCorrelationFunctions(unittest.TestCase):
-
+
@mock.patch("wqflask.correlation.correlation_functions.MrnaAssayTissueData")
def test_get_trait_symbol_and_tissue_values(self, mock_class):
"""test for getting trait symbol and tissue_values"""
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index c762982b..1198740d 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -8,7 +8,7 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
class TestQtlReaperMapping(unittest.TestCase):
@mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
- def test_gen_pheno_txt_file(self):
+ def test_gen_pheno_txt_file(self):
vals = ["V1", "x", "V4", "V3","x"]
samples = ["S1", "S2", "S3", "S4","S5"]
trait_filename = "trait_file"
@@ -21,5 +21,3 @@ class TestQtlReaperMapping(unittest.TestCase):
'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
filehandler.write.assert_has_calls(write_calls)
-
-
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 6996c275..d69a20d3 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -40,10 +40,3 @@ class TestRqtlMapping(unittest.TestCase):
expected_sanitized_name = "c('f',NA,'r',NA,NA)"
results = sanitize_rqtl_names(vals)
self.assertEqual(expected_sanitized_name, results)
-
-
-
-
-
-
-
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index ce3e7b83..8823e1fc 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -21,9 +21,9 @@ class TestSnpBrowser(unittest.TestCase):
"transcript": "false", "exon": "false", "domain_2": "true", "function": "false", "function_details": "true"}
strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
- 'Domain 1', 'Domain 2', 'Details'],
- ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
- ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
+ 'Domain 1', 'Domain 2', 'Details'],
+ ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
+ ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
'conservation_score', 'domain_1', 'domain_2',
'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
@@ -33,7 +33,7 @@ class TestSnpBrowser(unittest.TestCase):
variant_type="InDel", strains=strains, species="rat", empty_columns=[])
expected_results_with_indel = (
['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
- 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
+ 'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
index 69977146..9d988aea 100644
--- a/wqflask/tests/unit/wqflask/test_server_side.py
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -17,8 +17,8 @@ class TestServerSideTableTests(unittest.TestCase):
def test_get_page(self):
rows_count = 3
table_rows = [
- {'first': 'd', 'second': 4, 'third': 'zz'},
- {'first': 'b', 'second': 2, 'third': 'aa'},
+ {'first': 'd', 'second': 4, 'third': 'zz'},
+ {'first': 'b', 'second': 2, 'third': 'aa'},
{'first': 'c', 'second': 1, 'third': 'ss'},
]
headers = ['first', 'second', 'third']
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index d540c96e..816bc4df 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -33,5 +33,3 @@ class Struct:
def __repr__(self):
return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for
(k, v) in list(self.__dict__.items())))
-
-
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index 09100bd9..c0629b5d 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -98,4 +98,3 @@ class ConvertGenoFile:
print("WARNING:", genotype.upper())
this_marker.genotypes.append("NA")
self.markers.append(this_marker.__dict__)
-
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 712517a3..a2bf3085 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -50,4 +50,4 @@ from wqflask import db_info
from wqflask import user_login
from wqflask import user_session
-import wqflask.views
+import wqflask.views
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index c22b44a9..e4a3fb77 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -140,5 +140,3 @@ def initialize_parameters(start_vars, dataset, this_trait):
mapping_params['perm_check'] = False
return mapping_params
-
-
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index e7dfa4e0..f7d52ca3 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -59,13 +59,13 @@ def get_species_info(species_name, file_format="json"):
WHERE (Name="{0}" OR FullName="{0}" OR SpeciesName="{0}");""".format(species_name))
the_species = results.fetchone()
- species_dict = {
+ species_dict = {
"Id": the_species[0],
"Name": the_species[1],
"FullName": the_species[2],
"TaxonomyId": the_species[3]
}
-
+
return flask.jsonify(species_dict)
@@ -639,7 +639,7 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"):
return flask.jsonify(sample_list)
else:
- return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
+ return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
@app.route("/api/v_{}/trait//".format(version))
@@ -685,7 +685,7 @@ def get_trait_info(dataset_name, trait_name, file_format="json"):
# ZS: Check if the user input the dataset_name as BXDPublish, etc (which is always going to be the group name + "Publish"
if "Publish" in dataset_name:
dataset_name = dataset_name.replace("Publish", "")
-
+
group_id = get_group_id(dataset_name)
pheno_query = """
SELECT
@@ -898,7 +898,7 @@ def get_dataset_trait_ids(dataset_name, start_vars):
data_type = "Publish"
dataset_name = dataset_name.replace("Publish", "")
dataset_id = get_group_id(dataset_name)
-
+
query = """
SELECT
PublishXRef.PhenotypeId, PublishXRef.Id, InbredSet.InbredSetCode
@@ -949,9 +949,9 @@ def get_samplelist(dataset_name):
WHERE StrainXRef.StrainId = Strain.Id AND
StrainXRef.InbredSetId = {}
""".format(group_id)
-
+
results = g.db.execute(query).fetchall()
-
+
samplelist = [result[0] for result in results]
return samplelist
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 1fcf15f0..9fd89524 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -239,4 +239,3 @@ def change_collection_name():
g.user_session.change_collection_name(collection_id, new_name)
return new_name
-
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 0fabb833..d86c8e16 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -45,7 +45,7 @@ class ComparisonBarChart:
# ZS: Getting initial group name before verifying all traits are in the same group in the following loop
this_group = self.trait_list[0][1].group.name
for trait_db in self.trait_list:
-
+
if trait_db[1].group.name != this_group:
self.insufficient_shared_samples = True
break
@@ -53,7 +53,7 @@ class ComparisonBarChart:
this_group = trait_db[1].group.name
this_trait = trait_db[0]
self.traits.append(this_trait)
-
+
this_sample_data = this_trait.data
for sample in this_sample_data:
@@ -79,7 +79,7 @@ class ComparisonBarChart:
self.js_data = dict(traits=[trait.name for trait in self.traits],
samples=self.all_sample_list,
sample_data=self.sample_data,)
-
+
def get_trait_db_obs(self, trait_db_list):
self.trait_list = []
@@ -95,4 +95,3 @@ class ComparisonBarChart:
self.trait_list.append((trait_ob, dataset_ob))
#print("trait_list:", self.trait_list)
-
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index f9a0ea11..4f756f58 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -68,7 +68,7 @@ class CorrScatterPlot:
slope_string = '%.3E' % slope
else:
slope_string = '%.3f' % slope
-
+
x_buffer = (max(vals_1) - min(vals_1)) * 0.1
y_buffer = (max(vals_2) - min(vals_2)) * 0.1
@@ -82,7 +82,7 @@ class CorrScatterPlot:
ry = stats.rankdata(vals_2)
self.rdata = []
self.rdata.append(rx.tolist())
- self.rdata.append(ry.tolist())
+ self.rdata.append(ry.tolist())
srslope, srintercept, srr_value, srp_value, srstd_err = stats.linregress(
rx, ry)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index e75c4a85..8ee24246 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -680,4 +680,3 @@ def get_header_fields(data_type, corr_method):
'Sample p(r)']
return header_fields
-
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index aefb4453..59469428 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -324,7 +324,7 @@ def sortEigenVectors(vector):
A.append(item[0])
B.append(item[1])
sum = reduce(lambda x, y: x + y, A, 0.0)
- A = [x * 100.0 / sum for x in A]
+ A = [x * 100.0 / sum for x in A]
return [A, B]
except:
return []
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 48a82435..f4eafbe7 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -66,7 +66,7 @@ class CTL:
def addNode(self, gt):
node_dict = {'data': {'id': str(gt.name) + ":" + str(gt.dataset.name),
- 'sid': str(gt.name),
+ 'sid': str(gt.name),
'dataset': str(gt.dataset.name),
'label': gt.name,
'symbol': gt.symbol,
@@ -238,4 +238,3 @@ class CTL:
self.render_image(self.results)
sys.stdout.flush()
return(dict(template_vars))
-
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index c7558ed8..8d28fef0 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -135,5 +135,3 @@ def process_query_results(results):
}
return info_ob
-
-
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index fc93248a..0a1a597d 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -20,7 +20,7 @@ class Docs:
self.title = self.entry.capitalize()
self.content = ""
else:
-
+
self.title = result[0]
self.content = result[1].decode("utf-8")
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 5bd54f9d..2c180d49 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -1,6 +1,6 @@
import csv
import xlsxwriter
-import io
+import io
import datetime
import itertools
@@ -20,7 +20,7 @@ def export_search_results_csv(targs):
table_data = json.loads(targs['export_data'])
table_rows = table_data['rows']
-
+
now = datetime.datetime.now()
time_str = now.strftime('%H:%M_%d%B%Y')
if 'file_name' in targs:
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index fd12562f..fcd943ba 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -48,7 +48,7 @@ class SendToWebGestalt:
id_type = "entrezgene"
- self.hidden_vars = {
+ self.hidden_vars = {
'gene_list': "\n".join(gene_id_list),
'id_type': "entrezgene",
'ref_set': "genome",
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index aa11caa8..02eb66e5 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -125,7 +125,7 @@ class Heatmap:
webqtlConfig.GENERATED_IMAGE_DIR,
output_filename)
- os.system(reaper_command)
+ os.system(reaper_command)
reaper_results = parse_reaper_output(output_filename)
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index cadff080..e624a146 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -10,7 +10,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
-
+
# List All Species in the Gene Table
speciesDict = {}
results = g.db.execute("""
@@ -21,7 +21,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
for item in results:
speciesDict[item[0]] = item[1]
-
+
# List current Species and other Species
speciesId = speciesDict[species]
otherSpecies = [[X, speciesDict[X]] for X in list(speciesDict.keys())]
@@ -45,7 +45,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
newdict = {}
for j, item in enumerate(fetchFields):
newdict[item] = result[j]
- # count SNPs if possible
+ # count SNPs if possible
if diffCol and species == 'mouse':
newdict["snpCount"] = g.db.execute("""
SELECT count(*)
@@ -58,17 +58,17 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
(newdict["TxEnd"] - newdict["TxStart"]) / 1000.0
else:
newdict["snpDensity"] = newdict["snpCount"] = 0
-
+
try:
newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart'])
except:
pass
-
+
# load gene from other Species by the same name
for item in otherSpecies:
othSpec, othSpecId = item
newdict2 = {}
-
+
resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields),
othSpecId,
newdict["GeneSymbol"])).fetchone()
@@ -76,8 +76,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
if resultsOther:
for j, item in enumerate(fetchFields):
newdict2[item] = resultsOther[j]
-
- # count SNPs if possible, could be a separate function
+
+ # count SNPs if possible, could be a separate function
if diffCol and othSpec == 'mouse':
newdict2["snpCount"] = g.db.execute("""
SELECT count(*)
@@ -91,17 +91,15 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
(newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0
else:
newdict2["snpDensity"] = newdict2["snpCount"] = 0
-
+
try:
newdict2['GeneLength'] = 1000.0 * \
(newdict2['TxEnd'] - newdict2['TxStart'])
except:
pass
-
+
newdict['%sGene' % othSpec] = newdict2
-
+
GeneList.append(newdict)
return GeneList
-
-
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index f932498f..c51b7a9a 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -34,7 +34,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list = []
if boot_check and num_bootstrap > 0:
- bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" +
+ bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" +
''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
)
@@ -44,8 +44,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list.append(
f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
if num_perm > 0:
- permu_filename = ("{this_dataset.group.name}_PERM_" +
- ''.join(random.choice(string.ascii_uppercase +
+ permu_filename = ("{this_dataset.group.name}_PERM_" +
+ ''.join(random.choice(string.ascii_uppercase +
string.digits) for _ in range(6))
)
opt_list.append("-n " + str(num_perm))
@@ -56,7 +56,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
if manhattan_plot != True:
opt_list.append("--interval 1")
- reaper_command = (REAPER_COMMAND +
+ reaper_command = (REAPER_COMMAND +
' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'),
genofile_name,
@@ -81,7 +81,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
suggestive = permu_vals[int(num_perm * 0.37 - 1)]
significant = permu_vals[int(num_perm * 0.95 - 1)]
- return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals,
+ return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals,
[output_filename, permu_filename, bootstrap_filename])
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 741d6c23..b3c9fddf 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -300,7 +300,7 @@ def add_categorical_covar(cross, covar_as_string, i):
ro.r('the_cross$pheno <- cbind(pheno, ' + \
col_name + ' = newcovar[,' + str(x) + '])')
col_names.append(col_name)
- #logger.info("loop" + str(x) + "done");
+ #logger.info("loop" + str(x) + "done");
logger.info("returning from add_categorical_covar")
return ro.r["the_cross"], col_names
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 36d4cd61..61f3b202 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -142,5 +142,5 @@ def get_group_names(group_masks):
group_name = get_group_info(group_id)['name']
this_mask['name'] = group_name
group_masks_with_names[group_id] = this_mask
-
+
return group_masks_with_names
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 273a97a4..0d2fb2f8 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -343,4 +343,3 @@ def get_aliases(symbol_list, species):
search_terms.append(the_search_term)
return search_terms
-
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 8b3a4faa..8ca3a9eb 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -30,7 +30,7 @@ class ServerSideTable:
self.rows_count = rows_count
self.table_rows = table_rows
self.header_data_names = header_data_names
-
+
self.sort_rows()
self.paginate_rows()
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index e98cfb71..5b7a663c 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -494,10 +494,10 @@ class SnpBrowser:
function_details = function_details + ", Coding Region Unknown"
self.empty_columns['function_details'] = "true"
-
+
#[snp_href, chr, mb_formatted, alleles, snp_source_cell, conservation_score, gene_name_cell, transcript_href, exon, domain_1, domain_2, function, function_details]
- base_color_dict = {"A": "#C33232", "C": "#1569C7", "T": "#CFCF32", "G": "#32C332",
+ base_color_dict = {"A": "#C33232", "C": "#1569C7", "T": "#CFCF32", "G": "#32C332",
"t": "#FF6", "c": "#5CB3FF", "a": "#F66", "g": "#CF9", ":": "#FFFFFF", "-": "#FFFFFF", "?": "#FFFFFF"}
the_bases = []
@@ -735,7 +735,7 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None):
if empty_columns['function_details'] == "false":
empty_field_count += 1
header_fields[0].remove('Details')
-
+
for col in empty_columns.keys():
if empty_columns[col] == "false":
header_data_names.remove(col)
@@ -952,4 +952,3 @@ def check_if_in_gene(species_id, chr, mb):
return [result[0], result[1]]
else:
return ""
-
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 708d43d2..bfaed9c2 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -45,10 +45,10 @@ def encode_password(pass_gen_fields, unencrypted_password):
salt = pass_gen_fields['salt']
else:
salt = bytes(pass_gen_fields['salt'], "utf-8")
- encrypted_password = pbkdf2.pbkdf2_hex(str(unencrypted_password),
+ encrypted_password = pbkdf2.pbkdf2_hex(str(unencrypted_password),
salt,
- pass_gen_fields['iterations'],
- pass_gen_fields['keylength'],
+ pass_gen_fields['iterations'],
+ pass_gen_fields['keylength'],
pass_gen_fields['hashfunc'])
pass_gen_fields.pop("unencrypted_password", None)
@@ -111,7 +111,7 @@ def get_signed_session_id(user):
key = UserSession.user_cookie_name + ":" + session_id
Redis.hmset(key, session)
Redis.expire(key, THREE_DAYS)
-
+
return session_id_signed
@@ -207,7 +207,7 @@ def login():
UserSession.user_cookie_name, session_id_signed, max_age=None)
else:
flash("Something went unexpectedly wrong.", "alert-danger")
- response = make_response(redirect(url_for('index_page')))
+ response = make_response(redirect(url_for('index_page')))
return response
else:
user_details = get_user_by_unique_column(
@@ -276,13 +276,13 @@ def github_oauth2():
user_details = get_user_by_unique_column("github_id", github_user["id"])
if user_details == None:
user_details = {
- "user_id": str(uuid.uuid4()),
- "name": github_user["name"].encode("utf-8") if github_user["name"] else "None",
+ "user_id": str(uuid.uuid4()),
+ "name": github_user["name"].encode("utf-8") if github_user["name"] else "None",
"github_id": github_user["id"],
- "user_url": github_user["html_url"].encode("utf-8"),
- "login_type": "github",
- "organization": "",
- "active": 1,
+ "user_url": github_user["html_url"].encode("utf-8"),
+ "login_type": "github",
+ "organization": "",
+ "active": 1,
"confirmed": 1
}
save_user(user_details, user_details["user_id"])
@@ -308,8 +308,8 @@ def orcid_oauth2():
url = "/n/login"
if code:
data = {
- "client_id": ORCID_CLIENT_ID,
- "client_secret": ORCID_CLIENT_SECRET,
+ "client_id": ORCID_CLIENT_ID,
+ "client_secret": ORCID_CLIENT_SECRET,
"grant_type": "authorization_code",
"redirect_uri": GN2_BRANCH_URL + "n/login/orcid_oauth2",
"code": code
@@ -321,13 +321,13 @@ def orcid_oauth2():
user_details = get_user_by_unique_column("orcid", result_dict["orcid"])
if user_details == None:
user_details = {
- "user_id": str(uuid4()),
- "name": result_dict["name"],
- "orcid": result_dict["orcid"],
- "user_url": "%s/%s" % ("/".join(ORCID_AUTH_URL.split("/")[:-2]), result_dict["orcid"]),
- "login_type": "orcid",
- "organization": "",
- "active": 1,
+ "user_id": str(uuid4()),
+ "name": result_dict["name"],
+ "orcid": result_dict["orcid"],
+ "user_url": "%s/%s" % ("/".join(ORCID_AUTH_URL.split("/")[:-2]), result_dict["orcid"]),
+ "login_type": "orcid",
+ "organization": "",
+ "active": 1,
"confirmed": 1
}
save_user(user_details, user_details["user_id"])
@@ -374,7 +374,7 @@ def send_forgot_password_email(verification_email):
key_prefix = "forgot_password_code"
subject = "GeneNetwork password reset"
fromaddr = "no-reply@genenetwork.org"
-
+
verification_code = str(uuid.uuid4())
key = key_prefix + ":" + verification_code
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 6ccb2e80..963288b3 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -318,5 +318,3 @@ class UserSession:
# And more importantly delete the redis record
Redis.delete(self.redis_key)
self.logged_in = False
-
-
--
cgit v1.2.3
From 90ec57905c8afdbd5e9e8c44dcc369bd0e9c2d1b Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 30 Apr 2021 13:01:02 +0300
Subject: autopep8: Fix W504
---
wqflask/base/GeneralObject.py | 4 +-
wqflask/base/data_set.py | 4 +-
wqflask/base/trait.py | 10 ++--
.../maintenance/generate_probesetfreeze_file.py | 7 ++-
wqflask/tests/unit/base/test_data_set.py | 10 ++--
wqflask/tests/unit/wqflask/api/test_gen_menu.py | 68 +++++++++++-----------
wqflask/utility/svg.py | 24 ++++----
wqflask/wqflask/api/gen_menu.py | 10 ++--
wqflask/wqflask/correlation/show_corr_results.py | 10 ++--
wqflask/wqflask/db_info.py | 34 +++++------
wqflask/wqflask/do_search.py | 12 ++--
.../wqflask/marker_regression/qtlreaper_mapping.py | 14 ++---
wqflask/wqflask/show_trait/SampleList.py | 4 +-
wqflask/wqflask/show_trait/show_trait.py | 4 +-
wqflask/wqflask/user_session.py | 4 +-
wqflask/wqflask/views.py | 12 ++--
16 files changed, 116 insertions(+), 115 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/GeneralObject.py b/wqflask/base/GeneralObject.py
index 249195e2..ce8e60b8 100644
--- a/wqflask/base/GeneralObject.py
+++ b/wqflask/base/GeneralObject.py
@@ -62,5 +62,5 @@ class GeneralObject:
return s
def __eq__(self, other):
- return (len(list(self.__dict__.keys())) ==
- len(list(other.__dict__.keys())))
+ return (len(list(self.__dict__.keys()))
+ == len(list(other.__dict__.keys())))
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 8ec0aaad..5eac695e 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1032,8 +1032,8 @@ class MrnaAssayDataSet(DataSet):
else:
description_display = this_trait.symbol
- if (len(description_display) > 1 and description_display != 'N/A' and
- len(target_string) > 1 and target_string != 'None'):
+ if (len(description_display) > 1 and description_display != 'N/A'
+ and len(target_string) > 1 and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 5574128d..d09cfd40 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -479,9 +479,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
else:
description_display = trait.symbol
- if (str(description_display or "") != "" and
- description_display != 'N/A' and
- str(target_string or "") != "" and target_string != 'None'):
+ if (str(description_display or "") != ""
+ and description_display != 'N/A'
+ and str(target_string or "") != "" and target_string != 'None'):
description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
@@ -575,6 +575,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if str(trait.lrs or "") != "":
trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
else:
- raise KeyError(repr(trait.name) +
- ' information is not found in the database.')
+ raise KeyError(repr(trait.name)
+ + ' information is not found in the database.')
return trait
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index bd9c2ab4..e964c8ed 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -110,9 +110,10 @@ def write_data_matrix_file(strains, probeset_vals, filename):
def main():
- filename = os.path.expanduser("~/gene/wqflask/maintenance/" +
- "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2" +
- "(Oct08)_RankInv_Beta.txt")
+ filename = os.path.expanduser(
+ "~/gene/wqflask/maintenance/"
+ "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2"
+ "(Oct08)_RankInv_Beta.txt")
dataset_name = "Eye_AXBXA_1008_RankInv"
cursor = get_cursor()
diff --git a/wqflask/tests/unit/base/test_data_set.py b/wqflask/tests/unit/base/test_data_set.py
index ee5d6f06..66ad361d 100644
--- a/wqflask/tests/unit/base/test_data_set.py
+++ b/wqflask/tests/unit/base/test_data_set.py
@@ -88,8 +88,8 @@ class TestDataSetTypes(unittest.TestCase):
'"B139_K_1206_R": "ProbeSet", '
'"Test": "ProbeSet"}'))
db_mock.db.execute.assert_called_once_with(
- ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze " +
- "WHERE ProbeSetFreeze.Name = \"Test\" ")
+ ("SELECT ProbeSetFreeze.Id FROM ProbeSetFreeze "
+ + "WHERE ProbeSetFreeze.Name = \"Test\" ")
)
@mock.patch('base.data_set.g')
@@ -145,9 +145,9 @@ class TestDataSetTypes(unittest.TestCase):
'"Test": "Publish"}'))
db_mock.db.execute.assert_called_with(
- ("SELECT PublishFreeze.Name " +
- "FROM PublishFreeze, InbredSet " +
- "WHERE InbredSet.Name = 'Test' AND "
+ ("SELECT PublishFreeze.Name "
+ + "FROM PublishFreeze, InbredSet "
+ + "WHERE InbredSet.Name = 'Test' AND "
"PublishFreeze.InbredSetId = InbredSet.Id")
)
diff --git a/wqflask/tests/unit/wqflask/api/test_gen_menu.py b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
index 57eb1650..fd0fe52e 100644
--- a/wqflask/tests/unit/wqflask/api/test_gen_menu.py
+++ b/wqflask/tests/unit/wqflask/api/test_gen_menu.py
@@ -105,13 +105,13 @@ class TestGenMenu(unittest.TestCase):
for name in ["mouse", "human"]:
db_mock.db.execute.assert_any_call(
("SELECT InbredSet.Name, InbredSet.FullName, " +
- "IFNULL(InbredSet.Family, 'None') " +
- "FROM InbredSet, Species WHERE Species.Name " +
- "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by " +
- "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, " +
- "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, " +
- "InbredSet.FullName) ASC, InbredSet.FullName ASC, " +
- "InbredSet.MenuOrderId ASC").format(name)
+ "IFNULL(InbredSet.Family, 'None') "
+ + "FROM InbredSet, Species WHERE Species.Name "
+ + "= '{}' AND InbredSet.SpeciesId = Species.Id GROUP by "
+ + "InbredSet.Name ORDER BY IFNULL(InbredSet.FamilyOrder, "
+ + "InbredSet.FullName) ASC, IFNULL(InbredSet.Family, "
+ + "InbredSet.FullName) ASC, InbredSet.FullName ASC, "
+ + "InbredSet.MenuOrderId ASC").format(name)
)
@mock.patch('wqflask.api.gen_menu.g')
@@ -172,12 +172,12 @@ class TestGenMenu(unittest.TestCase):
self.assertEqual(build_datasets("Mouse", "BXD", "Phenotypes"),
[['602', "BXDPublish", "BXD Published Phenotypes"]])
db_mock.db.execute.assert_called_with(
- "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, " +
- "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, " +
- "InbredSet WHERE InbredSet.Name = 'BXD' AND " +
- "PublishFreeze.InbredSetId = InbredSet.Id AND " +
- "InfoFiles.InfoPageName = PublishFreeze.Name " +
- "ORDER BY PublishFreeze.CreateTime ASC"
+ "SELECT InfoFiles.GN_AccesionId, PublishFreeze.Name, "
+ + "PublishFreeze.FullName FROM InfoFiles, PublishFreeze, "
+ + "InbredSet WHERE InbredSet.Name = 'BXD' AND "
+ + "PublishFreeze.InbredSetId = InbredSet.Id AND "
+ + "InfoFiles.InfoPageName = PublishFreeze.Name "
+ + "ORDER BY PublishFreeze.CreateTime ASC"
)
self.assertEqual(build_datasets("Mouse", "MDP", "Phenotypes"),
[['602', "BXDPublish", "Mouse Phenome Database"]])
@@ -221,8 +221,8 @@ class TestGenMenu(unittest.TestCase):
"SELECT InfoFiles.GN_AccesionId FROM InfoFiles, "
"GenoFreeze, InbredSet WHERE InbredSet.Name = 'HLC' AND "
"GenoFreeze.InbredSetId = InbredSet.Id AND "
- "InfoFiles.InfoPageName = GenoFreeze.ShortName " +
- "ORDER BY GenoFreeze.CreateTime DESC"
+ "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+ + "ORDER BY GenoFreeze.CreateTime DESC"
)
db_mock.db.execute.return_value.fetchone.return_value = ()
self.assertEqual(build_datasets("Mouse", "HLC", "Genotypes"),
@@ -239,16 +239,16 @@ class TestGenMenu(unittest.TestCase):
"112", 'HC_M2_0606_P', "Hippocampus Consortium M430v2 (Jun06) PDNN"
]])
db_mock.db.execute.assert_called_once_with(
- "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, " +
- "ProbeSetFreeze.FullName FROM ProbeSetFreeze, " +
- "ProbeFreeze, InbredSet, Tissue, Species WHERE " +
- "Species.Name = 'Mouse' AND Species.Id = " +
- "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND " +
- "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND " +
- "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = " +
- "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND " +
- "ProbeSetFreeze.public > 0 " +
- "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC")
+ "SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, "
+ + "ProbeSetFreeze.FullName FROM ProbeSetFreeze, "
+ + "ProbeFreeze, InbredSet, Tissue, Species WHERE "
+ + "Species.Name = 'Mouse' AND Species.Id = "
+ + "InbredSet.SpeciesId AND InbredSet.Name = 'HLC' AND "
+ + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND "
+ + "Tissue.Name = 'mRNA' AND ProbeFreeze.TissueId = "
+ + "Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND "
+ + "ProbeSetFreeze.public > 0 "
+ + "ORDER BY -ProbeSetFreeze.OrderList DESC, ProbeSetFreeze.CreateTime DESC")
@mock.patch('wqflask.api.gen_menu.build_datasets')
@mock.patch('wqflask.api.gen_menu.g')
@@ -266,15 +266,15 @@ class TestGenMenu(unittest.TestCase):
['H', 'H', 'Molecular Traits'],
['R', 'R', 'Molecular Traits']])
db_mock.db.execute.assert_called_once_with(
- "SELECT DISTINCT Tissue.Name " +
- "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, " +
- "Tissue, Species WHERE Species.Name = 'mouse' " +
- "AND Species.Id = InbredSet.SpeciesId AND " +
- "InbredSet.Name = 'random group' AND " +
- "ProbeFreeze.TissueId = Tissue.Id AND " +
- "ProbeFreeze.InbredSetId = InbredSet.Id AND " +
- "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id " +
- "ORDER BY Tissue.Name"
+ "SELECT DISTINCT Tissue.Name "
+ + "FROM ProbeFreeze, ProbeSetFreeze, InbredSet, "
+ + "Tissue, Species WHERE Species.Name = 'mouse' "
+ + "AND Species.Id = InbredSet.SpeciesId AND "
+ + "InbredSet.Name = 'random group' AND "
+ + "ProbeFreeze.TissueId = Tissue.Id AND "
+ + "ProbeFreeze.InbredSetId = InbredSet.Id AND "
+ + "ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+ + "ORDER BY Tissue.Name"
)
@mock.patch('wqflask.api.gen_menu.build_types')
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 8d2e13ab..bc3bc833 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -229,13 +229,13 @@ class pathdata:
def bezier(self, x1, y1, x2, y2, x, y):
"""bezier with xy1 and xy2 to xy absolut"""
- self.path.append('C' + str(x1) + ','+str(y1)+' '+str(x2) +
- ',' + str(y2) + ' '+str(x)+','+str(y))
+ self.path.append('C' + str(x1) + ','+str(y1)+' '+str(x2)
+ + ',' + str(y2) + ' '+str(x)+','+str(y))
def relbezier(self, x1, y1, x2, y2, x, y):
"""bezier with xy1 and xy2 to xy relative"""
- self.path.append('c' + str(x1) + ','+str(y1)+' '+str(x2) +
- ',' + str(y2) + ' '+str(x)+','+str(y))
+ self.path.append('c' + str(x1) + ','+str(y1)+' '+str(x2)
+ + ',' + str(y2) + ' '+str(x)+','+str(y))
def smbezier(self, x2, y2, x, y):
"""smooth bezier with xy2 to xy absolut"""
@@ -267,13 +267,13 @@ class pathdata:
def ellarc(self, rx, ry, xrot, laf, sf, x, y):
"""elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut"""
- self.path.append('A' + str(rx) + ','+str(ry)+' '+str(xrot) +
- ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
+ self.path.append('A' + str(rx) + ','+str(ry)+' '+str(xrot)
+ + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
def relellarc(self, rx, ry, xrot, laf, sf, x, y):
"""elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative"""
- self.path.append('a' + str(rx) + ','+str(ry)+' '+str(xrot) +
- ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
+ self.path.append('a' + str(rx) + ','+str(ry)+' '+str(xrot)
+ + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
def __repr__(self):
return ' '.join(self.path)
@@ -319,11 +319,11 @@ class SVGelement:
f.write('\t' * level)
f.write('<' + self.type)
for attkey in list(self.attributes.keys()):
- f.write(' ' + _escape(str(attkey)) + '=' +
- _quoteattr(str(self.attributes[attkey])))
+ f.write(' ' + _escape(str(attkey)) + '='
+ + _quoteattr(str(self.attributes[attkey])))
if self.namespace:
- f.write(' xmlns="' + _escape(str(self.namespace)) +
- '" xmlns:xlink="http://www.w3.org/1999/xlink"')
+ f.write(' xmlns="' + _escape(str(self.namespace))
+ + '" xmlns:xlink="http://www.w3.org/1999/xlink"')
if self.elements or self.text or self.cdata:
f.write('>')
if self.elements:
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index a64524dd..e65b36e4 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -179,11 +179,11 @@ def build_datasets(species, group, type_name):
elif type_name == "Genotypes":
results = g.db.execute(
("SELECT InfoFiles.GN_AccesionId " +
- "FROM InfoFiles, GenoFreeze, InbredSet " +
- "WHERE InbredSet.Name = '{}' AND " +
- "GenoFreeze.InbredSetId = InbredSet.Id AND " +
- "InfoFiles.InfoPageName = GenoFreeze.ShortName " +
- "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone()
+ "FROM InfoFiles, GenoFreeze, InbredSet "
+ + "WHERE InbredSet.Name = '{}' AND "
+ + "GenoFreeze.InbredSetId = InbredSet.Id AND "
+ + "InfoFiles.InfoPageName = GenoFreeze.ShortName "
+ + "ORDER BY GenoFreeze.CreateTime DESC").format(group)).fetchone()
dataset_id = "None"
if bool(results):
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 8ee24246..e8b7b057 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -96,9 +96,9 @@ class CorrelationResults:
self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
- if ('loc_chr' in start_vars and
- 'min_loc_mb' in start_vars and
- 'max_loc_mb' in start_vars):
+ if ('loc_chr' in start_vars
+ and 'min_loc_mb' in start_vars
+ and 'max_loc_mb' in start_vars):
self.location_type = get_string(start_vars, 'location_type')
self.location_chr = get_string(start_vars, 'loc_chr')
@@ -200,8 +200,8 @@ class CorrelationResults:
if chr_info.name == trait_object.chr:
chr_as_int = order_id
- if (float(self.correlation_data[trait][0]) >= self.p_range_lower and
- float(self.correlation_data[trait][0]) <= self.p_range_upper):
+ if (float(self.correlation_data[trait][0]) >= self.p_range_lower
+ and float(self.correlation_data[trait][0]) <= self.p_range_upper):
if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index 8d28fef0..938c453e 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -23,23 +23,23 @@ class InfoPage:
def get_info(self, create=False):
query_base = ("SELECT InfoPageName, GN_AccesionId, Species.MenuName, Species.TaxonomyId, Tissue.Name, InbredSet.Name, " +
- "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, " +
- "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, " +
- "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, " +
- "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, " +
- "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, " +
- "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, " +
- "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics " +
- "FROM InfoFiles " +
- "LEFT JOIN Species USING (SpeciesId) " +
- "LEFT JOIN Tissue USING (TissueId) " +
- "LEFT JOIN InbredSet USING (InbredSetId) " +
- "LEFT JOIN GeneChip USING (GeneChipId) " +
- "LEFT JOIN AvgMethod USING (AvgMethodId) " +
- "LEFT JOIN Datasets USING (DatasetId) " +
- "LEFT JOIN Investigators USING (InvestigatorId) " +
- "LEFT JOIN Organizations USING (OrganizationId) " +
- "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
+ "GeneChip.GeneChipName, GeneChip.GeoPlatform, AvgMethod.Name, Datasets.DatasetName, Datasets.GeoSeries, "
+ + "Datasets.PublicationTitle, DatasetStatus.DatasetStatusName, Datasets.Summary, Datasets.AboutCases, "
+ + "Datasets.AboutTissue, Datasets.AboutDataProcessing, Datasets.Acknowledgment, Datasets.ExperimentDesign, "
+ + "Datasets.Contributors, Datasets.Citation, Datasets.Notes, Investigators.FirstName, Investigators.LastName, "
+ + "Investigators.Address, Investigators.City, Investigators.State, Investigators.ZipCode, Investigators.Country, "
+ + "Investigators.Phone, Investigators.Email, Investigators.Url, Organizations.OrganizationName, "
+ + "InvestigatorId, DatasetId, DatasetStatusId, Datasets.AboutPlatform, InfoFileTitle, Specifics "
+ + "FROM InfoFiles "
+ + "LEFT JOIN Species USING (SpeciesId) "
+ + "LEFT JOIN Tissue USING (TissueId) "
+ + "LEFT JOIN InbredSet USING (InbredSetId) "
+ + "LEFT JOIN GeneChip USING (GeneChipId) "
+ + "LEFT JOIN AvgMethod USING (AvgMethodId) "
+ + "LEFT JOIN Datasets USING (DatasetId) "
+ + "LEFT JOIN Investigators USING (InvestigatorId) "
+ + "LEFT JOIN Organizations USING (OrganizationId) "
+ + "LEFT JOIN DatasetStatus USING (DatasetStatusId) WHERE ")
if self.gn_accession_id:
final_query = query_base + \
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index e50ff50b..48527785 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -111,8 +111,8 @@ class MrnaAssaySearch(DoSearch):
else:
match_clause = ""
- where_clause = (match_clause +
- """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ where_clause = (match_clause
+ + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
""" % (escape(str(self.dataset.id))))
@@ -134,8 +134,8 @@ class MrnaAssaySearch(DoSearch):
else:
match_clause = ""
- where_clause = (match_clause +
- """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ where_clause = (match_clause
+ + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
""" % (escape(str(self.dataset.id))))
@@ -348,8 +348,8 @@ class GenotypeSearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
if self.search_term[0] == "*":
- query = (self.base_query +
- """WHERE Geno.Id = GenoXRef.GenoId
+ query = (self.base_query
+ + """WHERE Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id))))
else:
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index c51b7a9a..9f9591ad 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -25,8 +25,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
trait_filename = f"{str(this_trait.name)}_{str(this_dataset.name)}_pheno"
gen_pheno_txt_file(samples, vals, trait_filename)
- output_filename = (f"{this_dataset.group.name}_GWA_" +
- ''.join(random.choice(string.ascii_uppercase + string.digits)
+ output_filename = (f"{this_dataset.group.name}_GWA_"
+ + ''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
)
bootstrap_filename = None
@@ -34,8 +34,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list = []
if boot_check and num_bootstrap > 0:
- bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_" +
- ''.join(random.choice(string.ascii_uppercase + string.digits)
+ bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_"
+ + ''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
)
@@ -44,9 +44,9 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list.append(
f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
if num_perm > 0:
- permu_filename = ("{this_dataset.group.name}_PERM_" +
- ''.join(random.choice(string.ascii_uppercase +
- string.digits) for _ in range(6))
+ permu_filename = ("{this_dataset.group.name}_PERM_"
+ + ''.join(random.choice(string.ascii_uppercase
+ + string.digits) for _ in range(6))
)
opt_list.append("-n " + str(num_perm))
opt_list.append(
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 6419335e..3a63c84e 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -57,8 +57,8 @@ class SampleList:
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
sample.extra_info = {}
- if (self.dataset.group.name == 'AXBXA' and
- sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
+ if (self.dataset.group.name == 'AXBXA'
+ and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17')):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 18cadea4..fcebbc4d 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -452,8 +452,8 @@ class ShowTrait:
for sample in list(self.this_trait.data.keys()):
if (self.this_trait.data[sample].name2 != self.this_trait.data[sample].name):
- if ((self.this_trait.data[sample].name2 in primary_sample_names) and
- (self.this_trait.data[sample].name not in primary_sample_names)):
+ if ((self.this_trait.data[sample].name2 in primary_sample_names)
+ and (self.this_trait.data[sample].name not in primary_sample_names)):
primary_sample_names.append(
self.this_trait.data[sample].name)
primary_sample_names.remove(
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 963288b3..3e543445 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -184,8 +184,8 @@ class UserSession:
# ZS: Get user's collections if they exist
collections = get_user_collections(self.user_id)
collections = [item for item in collections if item['name'] != "Your Default Collection"] + \
- [item for item in collections if item['name'] ==
- "Your Default Collection"] # ZS: Ensure Default Collection is last in list
+ [item for item in collections if item['name']
+ == "Your Default Collection"] # ZS: Ensure Default Collection is last in list
return collections
@property
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 2c53012a..f75209ff 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -140,8 +140,8 @@ def handle_bad_request(e):
logger.error(traceback.format_exc())
now = datetime.datetime.utcnow()
time_str = now.strftime('%l:%M%p UTC %b %d, %Y')
- formatted_lines = [request.url +
- " (" + time_str + ")"]+traceback.format_exc().splitlines()
+ formatted_lines = [request.url
+ + " (" + time_str + ")"]+traceback.format_exc().splitlines()
# Handle random animations
# Use a cookie to have one animation on refresh
@@ -518,10 +518,10 @@ def export_perm_data():
["#N_genotypes: " + str(perm_info['n_genotypes'])],
["#Genotype_file: " + perm_info['genofile']],
["#Units_linkage: " + perm_info['units_linkage']],
- ["#Permutation_stratified_by: " +
- ", ".join([str(cofactor) for cofactor in perm_info['strat_cofactors']])],
- ["#RESULTS_1: Suggestive LRS(p=0.63) = " +
- str(np.percentile(np.array(perm_info['perm_data']), 67))],
+ ["#Permutation_stratified_by: "
+ + ", ".join([str(cofactor) for cofactor in perm_info['strat_cofactors']])],
+ ["#RESULTS_1: Suggestive LRS(p=0.63) = "
+ + str(np.percentile(np.array(perm_info['perm_data']), 67))],
["#RESULTS_2: Significant LRS(p=0.05) = " + str(
np.percentile(np.array(perm_info['perm_data']), 95))],
["#RESULTS_3: Highly Significant LRS(p=0.01) = " + str(
--
cgit v1.2.3
From 4e65b73a0f903834f8dbd02d11c49b75d7c935c7 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 30 Apr 2021 13:06:58 +0300
Subject: autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133
---
wqflask/base/data_set.py | 2 +-
wqflask/maintenance/convert_geno_to_bimbam.py | 6 +-
wqflask/maintenance/gen_select_dataset.py | 8 +-
.../maintenance/generate_kinship_from_bimbam.py | 4 +-
wqflask/maintenance/geno_to_json.py | 4 +-
wqflask/maintenance/quantile_normalize.py | 16 +--
wqflask/maintenance/set_resource_defaults.py | 30 ++--
wqflask/tests/unit/base/test_webqtl_case_data.py | 8 +-
wqflask/tests/unit/wqflask/api/test_correlation.py | 4 +-
.../marker_regression/test_gemma_mapping.py | 14 +-
.../marker_regression/test_qtlreaper_mapping.py | 2 +-
.../wqflask/marker_regression/test_rqtl_mapping.py | 2 +-
.../unit/wqflask/snp_browser/test_snp_browser.py | 12 +-
wqflask/tests/unit/wqflask/test_server_side.py | 2 +-
wqflask/utility/Plot.py | 2 +-
wqflask/utility/__init__.py | 2 +-
wqflask/utility/elasticsearch_tools.py | 2 +-
wqflask/utility/genofile_parser.py | 10 +-
wqflask/utility/startup_config.py | 2 +-
wqflask/utility/tools.py | 4 +-
wqflask/utility/webqtlUtil.py | 46 +++---
wqflask/wqflask/api/correlation.py | 2 +-
wqflask/wqflask/api/mapping.py | 14 +-
wqflask/wqflask/api/router.py | 118 ++++++++--------
wqflask/wqflask/collect.py | 14 +-
.../comparison_bar_chart/comparison_bar_chart.py | 6 +-
wqflask/wqflask/correlation/show_corr_results.py | 122 ++++++++--------
.../wqflask/correlation_matrix/show_corr_matrix.py | 4 +-
wqflask/wqflask/ctl/ctl_analysis.py | 18 +--
wqflask/wqflask/do_search.py | 156 ++++++++++-----------
wqflask/wqflask/export_traits.py | 6 +-
wqflask/wqflask/external_tools/send_to_bnw.py | 2 +-
.../wqflask/external_tools/send_to_geneweaver.py | 12 +-
.../wqflask/external_tools/send_to_webgestalt.py | 6 +-
wqflask/wqflask/group_manager.py | 20 +--
wqflask/wqflask/gsearch.py | 46 +++---
wqflask/wqflask/heatmap/heatmap.py | 16 +--
wqflask/wqflask/interval_analyst/GeneUtil.py | 20 +--
wqflask/wqflask/markdown_routes.py | 2 +-
.../marker_regression/display_mapping_results.py | 72 +++++-----
.../wqflask/marker_regression/qtlreaper_mapping.py | 46 +++---
wqflask/wqflask/marker_regression/rqtl_mapping.py | 4 +-
wqflask/wqflask/marker_regression/run_mapping.py | 34 ++---
wqflask/wqflask/model.py | 4 +-
wqflask/wqflask/parser.py | 2 +-
wqflask/wqflask/search_results.py | 10 +-
wqflask/wqflask/server_side.py | 4 +-
wqflask/wqflask/show_trait/SampleList.py | 4 +-
wqflask/wqflask/show_trait/export_trait_data.py | 4 +-
wqflask/wqflask/snp_browser/snp_browser.py | 22 +--
wqflask/wqflask/user_login.py | 34 ++---
wqflask/wqflask/user_manager.py | 2 +-
wqflask/wqflask/user_session.py | 8 +-
wqflask/wqflask/wgcna/wgcna_analysis.py | 2 +-
54 files changed, 509 insertions(+), 509 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 5eac695e..e20f2f98 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -151,7 +151,7 @@ class DatasetType:
"WHERE InbredSet.Name = '%s' AND "
"PublishFreeze.InbredSetId = InbredSet.Id"),
'geno': ("SELECT GenoFreeze.Id FROM GenoFreeze WHERE "
- "GenoFreeze.Name = \"%s\" ")
+ "GenoFreeze.Name = \"%s\" ")
}
dataset_name_mapping = {
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index c5af1ca6..078be529 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -56,7 +56,7 @@ class ConvertGenoFile:
'@pat': "0",
'@het': "0.5",
'@unk': "NA"
- }
+ }
self.configurations = {}
self.input_fh = open(self.input_file)
@@ -171,7 +171,7 @@ class ConvertGenoFile:
snp_output_file = os.path.join(
new_directory, group_name + "_snps.txt")
output_files = [geno_output_file,
- pheno_output_file, snp_output_file]
+ pheno_output_file, snp_output_file]
print("%s -> %s" % (
os.path.join(old_directory, input_file), geno_output_file))
convertob = ConvertGenoFile(input_file, output_files)
@@ -184,7 +184,7 @@ class ConvertGenoFile:
print(" Exception:", why)
print(traceback.print_exc())
print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos,
- convertob.latest_col_pos))
+ convertob.latest_col_pos))
print(" Column is:", convertob.latest_col_value)
print(" Row is:", convertob.latest_row_value)
break
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 484336a6..db65a11f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -62,10 +62,10 @@ def parse_db_uri():
parsed_uri = urllib.parse.urlparse(SQL_URI)
db_conn_info = dict(
- db=parsed_uri.path[1:],
- host=parsed_uri.hostname,
- user=parsed_uri.username,
- passwd=parsed_uri.password)
+ db=parsed_uri.path[1:],
+ host=parsed_uri.hostname,
+ user=parsed_uri.username,
+ passwd=parsed_uri.password)
print(db_conn_info)
return db_conn_info
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index cd39fceb..9f01d094 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -23,7 +23,7 @@ class GenerateKinshipMatrices:
def generate_kinship(self):
gemma_command = "/gnu/store/xhzgjr0jvakxv6h3blj8z496xjig69b0-profile/bin/gemma -g " + self.geno_file + \
" -p " + self.pheno_file + \
- " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
+ " -gk 1 -outdir /home/zas1024/genotype_files/genotype/bimbam/ -o " + self.group_name
print("command:", gemma_command)
os.system(gemma_command)
@@ -52,7 +52,7 @@ class GenerateKinshipMatrices:
print(" Exception:", why)
print(traceback.print_exc())
print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos,
- convertob.latest_col_pos))
+ convertob.latest_col_pos))
print(" Column is:", convertob.latest_col_value)
print(" Row is:", convertob.latest_row_value)
break
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index c74489a8..32e0e34b 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -63,7 +63,7 @@ class ConvertGenoFile:
'@pat': "0",
'@het': "0.5",
'@unk': "NA"
- }
+ }
self.configurations = {}
#self.skipped_cols = 3
@@ -172,7 +172,7 @@ class ConvertGenoFile:
print(" Exception:", why)
print(traceback.print_exc())
print(" Found in row %s at tabular column %s" % (convertob.latest_row_pos,
- convertob.latest_col_pos))
+ convertob.latest_col_pos))
print(" Column is:", convertob.latest_col_value)
print(" Row is:", convertob.latest_row_value)
break
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index ac7689f5..88bb2cb5 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -21,10 +21,10 @@ def parse_db_uri():
parsed_uri = urllib.parse.urlparse(SQL_URI)
db_conn_info = dict(
- db=parsed_uri.path[1:],
- host=parsed_uri.hostname,
- user=parsed_uri.username,
- passwd=parsed_uri.password)
+ db=parsed_uri.path[1:],
+ host=parsed_uri.hostname,
+ user=parsed_uri.username,
+ passwd=parsed_uri.password)
print(db_conn_info)
return db_conn_info
@@ -70,10 +70,10 @@ def set_data(dataset_name):
trait_name = line1.split('\t')[0]
for i, sample in enumerate(sample_names):
this_sample = {
- "name": sample,
- "value": line1.split('\t')[i + 1],
- "qnorm": line2.split('\t')[i + 1]
- }
+ "name": sample,
+ "value": line1.split('\t')[i + 1],
+ "qnorm": line2.split('\t')[i + 1]
+ }
sample_list.append(this_sample)
query = """SELECT Species.SpeciesName, InbredSet.InbredSetName, ProbeSetFreeze.FullName
FROM Species, InbredSet, ProbeSetFreeze, ProbeFreeze, ProbeSetXRef, ProbeSet
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index c6c4f44c..0f472494 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -44,10 +44,10 @@ def parse_db_uri():
parsed_uri = urllib.parse.urlparse(SQL_URI)
db_conn_info = dict(
- db=parsed_uri.path[1:],
- host=parsed_uri.hostname,
- user=parsed_uri.username,
- passwd=parsed_uri.password)
+ db=parsed_uri.path[1:],
+ host=parsed_uri.hostname,
+ user=parsed_uri.username,
+ passwd=parsed_uri.password)
print(db_conn_info)
return db_conn_info
@@ -69,12 +69,12 @@ def insert_probeset_resources(default_owner_id):
resource_ob['type'] = "dataset-probeset"
if resource[2] < 1 and resource[3] > 0:
resource_ob['default_mask'] = {"data": "view",
- "metadata": "view",
- "admin": "not-admin"}
+ "metadata": "view",
+ "admin": "not-admin"}
else:
resource_ob['default_mask'] = {"data": "no-access",
- "metadata": "no-access",
- "admin": "not-admin"}
+ "metadata": "no-access",
+ "admin": "not-admin"}
resource_ob['group_masks'] = {}
add_resource(resource_ob, update=False)
@@ -101,11 +101,11 @@ def insert_publish_resources(default_owner_id):
resource_ob['name'] = str(resource[0])
resource_ob['owner_id'] = default_owner_id
resource_ob['data'] = {"dataset": str(resource[1]),
- "trait": str(resource[0])}
+ "trait": str(resource[0])}
resource_ob['type'] = "dataset-publish"
resource_ob['default_mask'] = {"data": "view",
- "metadata": "view",
- "admin": "not-admin"}
+ "metadata": "view",
+ "admin": "not-admin"}
resource_ob['group_masks'] = {}
@@ -133,12 +133,12 @@ def insert_geno_resources(default_owner_id):
resource_ob['type'] = "dataset-geno"
if resource[2] < 1:
resource_ob['default_mask'] = {"data": "view",
- "metadata": "view",
- "admin": "not-admin"}
+ "metadata": "view",
+ "admin": "not-admin"}
else:
resource_ob['default_mask'] = {"data": "no-access",
- "metadata": "no-access",
- "admin": "not-admin"}
+ "metadata": "no-access",
+ "admin": "not-admin"}
resource_ob['group_masks'] = {}
add_resource(resource_ob, update=False)
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
index cebd41ce..e1555cb4 100644
--- a/wqflask/tests/unit/base/test_webqtl_case_data.py
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
@@ -10,10 +10,10 @@ class TestWebqtlCaseData(unittest.TestCase):
def setUp(self):
self.w = webqtlCaseData(name="Test",
- value=0,
- variance=0.0,
- num_cases=10,
- name2="Test2")
+ value=0,
+ variance=0.0,
+ num_cases=10,
+ name2="Test2")
def test_webqtl_case_data_repr(self):
self.assertEqual(
diff --git a/wqflask/tests/unit/wqflask/api/test_correlation.py b/wqflask/tests/unit/wqflask/api/test_correlation.py
index 34ffa9ef..1089a36f 100644
--- a/wqflask/tests/unit/wqflask/api/test_correlation.py
+++ b/wqflask/tests/unit/wqflask/api/test_correlation.py
@@ -106,9 +106,9 @@ class TestCorrelations(unittest.TestCase):
target_vals = [3.4, 6.2, 4.1, 3.4, 1.2, 5.6]
trait_data = {"S1": AttributeSetter({"value": 2.3}), "S2": AttributeSetter({"value": 1.1}),
- "S3": AttributeSetter(
+ "S3": AttributeSetter(
{"value": 6.3}), "S4": AttributeSetter({"value": 3.6}), "S5": AttributeSetter({"value": 4.1}),
- "S6": AttributeSetter({"value": 5.0})}
+ "S6": AttributeSetter({"value": 5.0})}
this_trait = AttributeSetter({"data": trait_data})
mock_normalize.return_value = ([2.3, 1.1, 6.3, 3.6, 4.1, 5.0],
[3.4, 6.2, 4.1, 3.4, 1.2, 5.6], 6)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index 5cbaf0e0..4003d68f 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -162,13 +162,13 @@ X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
results = parse_loco_output(
this_dataset={}, gwa_output_filename=".xw/")
expected_results = [
- {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85,
- 'additive': 23.3, 'lod_score': 0.07058107428570727},
- {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5,
- 'additive': 24.0, 'lod_score': 0.3010299956639812},
- {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7,
- 'additive': 11.6, 'lod_score': 0.1549019599857432},
- {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
+ {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85,
+ 'additive': 23.3, 'lod_score': 0.07058107428570727},
+ {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5,
+ 'additive': 24.0, 'lod_score': 0.3010299956639812},
+ {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7,
+ 'additive': 11.6, 'lod_score': 0.1549019599857432},
+ {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
self.assertEqual(expected_results, results)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index 47377873..93848a84 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -18,6 +18,6 @@ class TestQtlReaperMapping(unittest.TestCase):
mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w")
filehandler = mock_open()
write_calls = [mock.call('Trait\t'), mock.call(
- 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
+ 'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
filehandler.write.assert_has_calls(write_calls)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index e518ec22..68686e27 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -21,7 +21,7 @@ class TestRqtlMapping(unittest.TestCase):
"""test for getting trait data_type return True"""
query_value = """SELECT value FROM TraitMetadata WHERE type='trait_data_type'"""
mock_db.db.execute.return_value.fetchone.return_value = [
- """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
+ """{"type":"trait_data_type","name":"T1","traid_id":"fer434f"}"""]
results = get_trait_data_type("traid_id")
mock_db.db.execute.assert_called_with(query_value)
self.assertEqual(results, "fer434f")
diff --git a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
index 8823e1fc..89442c47 100644
--- a/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
+++ b/wqflask/tests/unit/wqflask/snp_browser/test_snp_browser.py
@@ -22,10 +22,10 @@ class TestSnpBrowser(unittest.TestCase):
strains = {"mouse": ["S1", "S2", "S3", "S4", "S5"], "rat": []}
expected_results = ([['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'ConScore',
'Domain 1', 'Domain 2', 'Details'],
- ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
- ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
- 'conservation_score', 'domain_1', 'domain_2',
- 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
+ ['S1', 'S2', 'S3', 'S4', 'S5']], 5,
+ ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles',
+ 'conservation_score', 'domain_1', 'domain_2',
+ 'function_details', 'S1', 'S2', 'S3', 'S4', 'S5'])
results_with_snp = get_header_list(
variant_type="SNP", strains=strains, species="Mouse", empty_columns=empty_columns)
@@ -34,8 +34,8 @@ class TestSnpBrowser(unittest.TestCase):
expected_results_with_indel = (
['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start',
'Mb End', 'Strand', 'Size', 'Sequence', 'Source'], 0,
- ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
- 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
+ ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
+ 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name'])
self.assertEqual(expected_results, results_with_snp)
self.assertEqual(expected_results_with_indel, results_with_indel)
diff --git a/wqflask/tests/unit/wqflask/test_server_side.py b/wqflask/tests/unit/wqflask/test_server_side.py
index 9d988aea..be7ca2df 100644
--- a/wqflask/tests/unit/wqflask/test_server_side.py
+++ b/wqflask/tests/unit/wqflask/test_server_side.py
@@ -23,7 +23,7 @@ class TestServerSideTableTests(unittest.TestCase):
]
headers = ['first', 'second', 'third']
request_args = {'sEcho': '1', 'iSortCol_0': '1', 'iSortingCols': '1',
- 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
+ 'sSortDir_0': 'asc', 'iDisplayStart': '0', 'iDisplayLength': '3'}
test_page = ServerSideTable(
rows_count, table_rows, headers, request_args).get_page()
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index f61e3b88..37a8a1a5 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -206,7 +206,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
im_drawer.text(
text=strY,
xy=(xLeftOffset - im_drawer.textsize(strY,
- font=scaleFont)[0] - 6, yc + 5),
+ font=scaleFont)[0] - 6, yc + 5),
font=scaleFont)
y += (yTop - yLow) / stepY
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index 6c8cd546..25273fa0 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -32,4 +32,4 @@ class Struct:
def __repr__(self):
return '{%s}' % str(', '.join('%s : %s' % (k, repr(v)) for
- (k, v) in list(self.__dict__.items())))
+ (k, v) in list(self.__dict__.items())))
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 55907dd5..e56c22eb 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -50,7 +50,7 @@ from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
def test_elasticsearch_connection():
es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + \
- ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True)
+ ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True)
if not es.ping():
logger.warning("Elasticsearch is DOWN")
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index eb545478..86d9823e 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -37,10 +37,10 @@ class ConvertGenoFile:
self.input_fh = open(input_file)
print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!")
self.haplotype_notation = {
- '@mat': "1",
- '@pat': "2",
- '@het': "-999",
- '@unk': "-999"
+ '@mat': "1",
+ '@pat': "2",
+ '@het': "-999",
+ '@unk': "-999"
}
self.configurations = {}
@@ -93,7 +93,7 @@ class ConvertGenoFile:
for item_count, genotype in enumerate(genotypes):
if genotype.upper().strip() in self.configurations:
this_marker.genotypes.append(
- self.configurations[genotype.upper().strip()])
+ self.configurations[genotype.upper().strip()])
else:
print("WARNING:", genotype.upper())
this_marker.genotypes.append("NA")
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 05f8a2b0..6ef759e0 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -39,4 +39,4 @@ def app_config():
# es.test_elasticsearch_connection()
print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" %
- (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL"))))
+ (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL"))))
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 4f09176a..e28abb48 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -295,8 +295,8 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
ORCID_AUTH_URL = None
if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \
- ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + \
- "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
+ ORCID_CLIENT_ID + "&client_secret=" + ORCID_CLIENT_SECRET + \
+ "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index f355a865..0cb71567 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -35,29 +35,29 @@ from base import webqtlConfig
# NL, 07/27/2010. moved from webqtlForm.py
# Dict of Parents and F1 information, In the order of [F1, Mat, Pat]
ParInfo = {
-'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'],
-'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
-'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'C57BL-6JxC57BL-6NJF2': ['', '', 'C57BL/6J', 'C57BL/6NJ'],
-'BXD300': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'B6BTBRF2': ['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
-'BHHBF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
-'BHF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
-'B6D2F2': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'BDF2-1999': ['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
-'BDF2-2005': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'CTB6F2': ['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
-'CXB': ['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
-'AXBXA': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
-'AXB': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
-'BXA': ['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
-'LXS': ['LSF1', 'SLF1', 'ISS', 'ILS'],
-'HXBBXH': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
-'BayXSha': ['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
-'ColXBur': ['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
-'ColXCvi': ['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
-'SXM': ['SMF1', 'MSF1', 'Steptoe', 'Morex'],
-'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
+ 'BXH': ['BHF1', 'HBF1', 'C57BL/6J', 'C3H/HeJ'],
+ 'AKXD': ['AKF1', 'KAF1', 'AKR/J', 'DBA/2J'],
+ 'BXD': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+ 'C57BL-6JxC57BL-6NJF2': ['', '', 'C57BL/6J', 'C57BL/6NJ'],
+ 'BXD300': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+ 'B6BTBRF2': ['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
+ 'BHHBF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
+ 'BHF2': ['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
+ 'B6D2F2': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+ 'BDF2-1999': ['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
+ 'BDF2-2005': ['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
+ 'CTB6F2': ['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
+ 'CXB': ['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
+ 'AXBXA': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
+ 'AXB': ['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
+ 'BXA': ['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
+ 'LXS': ['LSF1', 'SLF1', 'ISS', 'ILS'],
+ 'HXBBXH': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
+ 'BayXSha': ['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
+ 'ColXBur': ['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
+ 'ColXCvi': ['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
+ 'SXM': ['SMF1', 'MSF1', 'Steptoe', 'Morex'],
+ 'HRDP': ['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
}
#########################################
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index 52026a82..870f3275 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -88,7 +88,7 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
corr_results = do_literature_correlation_for_all_traits(
this_trait, this_dataset, trait_geneid_dict, corr_params)
sorted_results = collections.OrderedDict(sorted(list(corr_results.items()),
- key=lambda t: -abs(t[1][1])))
+ key=lambda t: -abs(t[1][1])))
else:
for target_trait, target_vals in list(target_dataset.trait_data.items()):
result = get_sample_r_and_p_values(
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index e4a3fb77..cbef96eb 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -53,15 +53,15 @@ def do_mapping_for_api(start_vars):
header_row = ["name", "chr", "cM", "lod_score"]
if mapping_params['num_perm'] > 0:
_sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'],
- mapping_params['perm_check'], mapping_params['num_perm'],
- mapping_params['do_control'], mapping_params[
- 'control_marker'],
- mapping_params['manhattan_plot'], mapping_params['pair_scan'])
+ mapping_params['perm_check'], mapping_params['num_perm'],
+ mapping_params['do_control'], mapping_params[
+ 'control_marker'],
+ mapping_params['manhattan_plot'], mapping_params['pair_scan'])
else:
result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'],
- mapping_params['perm_check'], mapping_params['num_perm'],
- mapping_params['do_control'], mapping_params['control_marker'],
- mapping_params['manhattan_plot'], mapping_params['pair_scan'])
+ mapping_params['perm_check'], mapping_params['num_perm'],
+ mapping_params['do_control'], mapping_params['control_marker'],
+ mapping_params['manhattan_plot'], mapping_params['pair_scan'])
if mapping_params['limit_to']:
result_markers = result_markers[:mapping_params['limit_to']]
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index f7d52ca3..9d3446db 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -41,10 +41,10 @@ def get_species_list():
species_list = []
for species in the_species:
species_dict = {
- "Id": species[0],
- "Name": species[1],
- "FullName": species[2],
- "TaxonomyId": species[3]
+ "Id": species[0],
+ "Name": species[1],
+ "FullName": species[2],
+ "TaxonomyId": species[3]
}
species_list.append(species_dict)
@@ -60,10 +60,10 @@ def get_species_info(species_name, file_format="json"):
the_species = results.fetchone()
species_dict = {
- "Id": the_species[0],
- "Name": the_species[1],
- "FullName": the_species[2],
- "TaxonomyId": the_species[3]
+ "Id": the_species[0],
+ "Name": the_species[1],
+ "FullName": the_species[2],
+ "TaxonomyId": the_species[3]
}
return flask.jsonify(species_dict)
@@ -92,12 +92,12 @@ def get_groups_list(species_name=None):
groups_list = []
for group in the_groups:
group_dict = {
- "Id": group[0],
- "SpeciesId": group[1],
- "DisplayName": group[2],
- "Name": group[3],
- "FullName": group[4],
- "public": group[5],
+ "Id": group[0],
+ "SpeciesId": group[1],
+ "DisplayName": group[2],
+ "Name": group[3],
+ "FullName": group[4],
+ "public": group[5],
"MappingMethodId": group[6],
"GeneticType": group[7]
}
@@ -137,12 +137,12 @@ def get_group_info(group_name, species_name=None, file_format="json"):
group = results.fetchone()
if group:
group_dict = {
- "Id": group[0],
- "SpeciesId": group[1],
- "DisplayName": group[2],
- "Name": group[3],
- "FullName": group[4],
- "public": group[5],
+ "Id": group[0],
+ "SpeciesId": group[1],
+ "DisplayName": group[2],
+ "Name": group[3],
+ "FullName": group[4],
+ "public": group[5],
"MappingMethodId": group[6],
"GeneticType": group[7]
}
@@ -186,12 +186,12 @@ def get_datasets_for_group(group_name, species_name=None):
datasets_list = []
for dataset in the_datasets:
dataset_dict = {
- "Id": dataset[0],
- "ProbeFreezeId": dataset[1],
- "AvgID": dataset[2],
- "Short_Abbreviation": dataset[3],
- "Long_Abbreviation": dataset[4],
- "FullName": dataset[5],
+ "Id": dataset[0],
+ "ProbeFreezeId": dataset[1],
+ "AvgID": dataset[2],
+ "Short_Abbreviation": dataset[3],
+ "Long_Abbreviation": dataset[4],
+ "FullName": dataset[5],
"ShortName": dataset[6],
"CreateTime": dataset[7],
"public": dataset[8],
@@ -243,12 +243,12 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
if dataset:
dataset_dict = {
- "dataset_type": "mRNA expression",
- "id": dataset[0],
- "name": dataset[1],
- "full_name": dataset[2],
- "short_name": dataset[3],
- "data_scale": dataset[4],
+ "dataset_type": "mRNA expression",
+ "id": dataset[0],
+ "name": dataset[1],
+ "full_name": dataset[2],
+ "short_name": dataset[3],
+ "data_scale": dataset[4],
"tissue_id": dataset[5],
"tissue": dataset[6],
"public": dataset[7],
@@ -280,25 +280,25 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
if dataset:
if dataset[5]:
dataset_dict = {
- "dataset_type": "phenotype",
- "id": dataset[0],
- "name": dataset[1],
- "description": dataset[2],
- "pubmed_id": dataset[5],
- "title": dataset[6],
+ "dataset_type": "phenotype",
+ "id": dataset[0],
+ "name": dataset[1],
+ "description": dataset[2],
+ "pubmed_id": dataset[5],
+ "title": dataset[6],
"year": dataset[7]
}
elif dataset[4]:
dataset_dict = {
- "dataset_type": "phenotype",
- "id": dataset[0],
- "name": dataset[3],
- "description": dataset[4]
+ "dataset_type": "phenotype",
+ "id": dataset[0],
+ "name": dataset[3],
+ "description": dataset[4]
}
else:
dataset_dict = {
- "dataset_type": "phenotype",
- "id": dataset[0]
+ "dataset_type": "phenotype",
+ "id": dataset[0]
}
datasets_list.append(dataset_dict)
@@ -364,7 +364,7 @@ def fetch_traits(dataset_name, file_format="json"):
"""
field_list = ["Id", "Name", "Symbol", "Description", "Chr", "Mb",
- "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"]
+ "Aliases", "Mean", "SE", "Locus", "LRS", "P-Value", "Additive", "h2"]
elif data_type == "Geno":
query = """
SELECT
@@ -382,7 +382,7 @@ def fetch_traits(dataset_name, file_format="json"):
"""
field_list = ["Id", "Name", "Marker_Name",
- "Chr", "Mb", "Sequence", "Source"]
+ "Chr", "Mb", "Sequence", "Source"]
else:
query = """
SELECT
@@ -399,7 +399,7 @@ def fetch_traits(dataset_name, file_format="json"):
"""
field_list = ["Id", "PhenotypeId", "PublicationId",
- "Locus", "LRS", "Additive", "Sequence"]
+ "Locus", "LRS", "Additive", "Sequence"]
if 'limit_to' in request.args:
limit_number = request.args['limit_to']
@@ -579,10 +579,10 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"):
sample_list = []
for sample in sample_data:
sample_dict = {
- "sample_name": sample[0],
- "sample_name_2": sample[1],
- "value": sample[2],
- "data_id": sample[3],
+ "sample_name": sample[0],
+ "sample_name_2": sample[1],
+ "value": sample[2],
+ "data_id": sample[3],
}
if sample[4]:
sample_dict["se"] = sample[4]
@@ -626,10 +626,10 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"):
sample_list = []
for sample in sample_data:
sample_dict = {
- "sample_name": sample[0],
- "sample_name_2": sample[1],
- "value": sample[2],
- "data_id": sample[3]
+ "sample_name": sample[0],
+ "sample_name_2": sample[1],
+ "value": sample[2],
+ "data_id": sample[3]
}
if sample[4]:
sample_dict["se"] = sample[4]
@@ -796,9 +796,9 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
config_file = [filename + ".json", json.dumps(yaml_file)]
#config_file = [filename + ".yaml", open("{0}/{1}.yaml".format(flat_files("genotype/rqtl2"), group_name))]
geno_file = [filename + "_geno.csv",
- open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))]
+ open("{0}/{1}_geno.csv".format(flat_files("genotype/rqtl2"), group_name))]
gmap_file = [filename + "_gmap.csv",
- open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))]
+ open("{0}/{1}_gmap.csv".format(flat_files("genotype/rqtl2"), group_name))]
if dataset_name:
phenotypes = requests.get(
"http://gn2.genenetwork.org/api/v_pre1/sample_data/" + dataset_name)
@@ -828,7 +828,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
if limit_num and i >= limit_num:
break
output_lines.append([line.strip()
- for line in line.split(",")])
+ for line in line.split(",")])
i += 1
csv_writer = csv.writer(si, delimiter=",")
@@ -914,7 +914,7 @@ def get_dataset_trait_ids(dataset_name, start_vars):
trait_ids = [result[0] for result in results]
trait_names = [str(result[2]) + "_" + str(result[1])
- for result in results]
+ for result in results]
return trait_ids, trait_names, data_type, dataset_id
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index b06d84ff..58518639 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -75,14 +75,14 @@ def collections_add():
if 'traits' in request.args:
traits = request.args['traits']
return render_template("collections/add.html",
- traits=traits,
- collections=collections,
+ traits=traits,
+ collections=collections,
)
else:
hash = request.args['hash']
return render_template("collections/add.html",
- hash=hash,
- collections=collections,
+ hash=hash,
+ collections=collections,
)
@@ -145,8 +145,8 @@ def list_collections():
user_collections = list(g.user_session.user_collections)
return render_template("collections/list.html",
- params=params,
- collections=user_collections,
+ params=params,
+ collections=user_collections,
)
@@ -225,7 +225,7 @@ def view_collection():
return json.dumps(json_version)
else:
return render_template("collections/view.html",
- **collection_info
+ **collection_info
)
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index d86c8e16..cb88eb53 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -35,7 +35,7 @@ class ComparisonBarChart:
def __init__(self, start_vars):
trait_db_list = [trait.strip()
- for trait in start_vars['trait_list'].split(',')]
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
@@ -90,8 +90,8 @@ class ComparisonBarChart:
#print("dataset_name:", dataset_name)
dataset_ob = data_set.create_dataset(dataset_name)
trait_ob = create_trait(dataset=dataset_ob,
- name=trait_name,
- cellid=None)
+ name=trait_name,
+ cellid=None)
self.trait_list.append((trait_ob, dataset_ob))
#print("trait_list:", self.trait_list)
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index e8b7b057..aa39bc5c 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -82,8 +82,8 @@ class CorrelationResults:
dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group'])
self.trait_id = start_vars['trait_id']
self.this_trait = create_trait(dataset=self.dataset,
- name=self.trait_id,
- cellid=None)
+ name=self.trait_id,
+ cellid=None)
else:
helper_functions.get_species_dataset_trait(self, start_vars)
@@ -98,7 +98,7 @@ class CorrelationResults:
if ('loc_chr' in start_vars
and 'min_loc_mb' in start_vars
- and 'max_loc_mb' in start_vars):
+ and 'max_loc_mb' in start_vars):
self.location_type = get_string(start_vars, 'location_type')
self.location_chr = get_string(start_vars, 'loc_chr')
@@ -129,7 +129,7 @@ class CorrelationResults:
if corr_samples_group != 'samples_primary':
if corr_samples_group == 'samples_other':
primary_samples = [x for x in primary_samples if x not in (
- self.dataset.group.parlist + self.dataset.group.f1list)]
+ self.dataset.group.parlist + self.dataset.group.f1list)]
self.process_samples(start_vars, list(
self.this_trait.data.keys()), primary_samples)
@@ -201,7 +201,7 @@ class CorrelationResults:
chr_as_int = order_id
if (float(self.correlation_data[trait][0]) >= self.p_range_lower
- and float(self.correlation_data[trait][0]) <= self.p_range_upper):
+ and float(self.correlation_data[trait][0]) <= self.p_range_upper):
if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
@@ -221,8 +221,8 @@ class CorrelationResults:
continue
(trait_object.sample_r,
- trait_object.sample_p,
- trait_object.num_overlap) = self.correlation_data[trait]
+ trait_object.sample_p,
+ trait_object.num_overlap) = self.correlation_data[trait]
# Set some sane defaults
trait_object.tissue_corr = 0
@@ -277,7 +277,7 @@ class CorrelationResults:
trait.symbol for trait in self.correlation_results if trait.symbol]
corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
- symbol_list=gene_symbol_list)
+ symbol_list=gene_symbol_list)
for trait in self.correlation_results:
if trait.symbol and trait.symbol.lower() in corr_result_tissue_vals_dict:
@@ -285,8 +285,8 @@ class CorrelationResults:
)]
result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
- this_trait_tissue_values,
- self.corr_method)
+ this_trait_tissue_values,
+ self.corr_method)
trait.tissue_corr = result[0]
trait.tissue_pvalue = result[2]
@@ -302,7 +302,7 @@ class CorrelationResults:
#print("trait_gene_symbols: ", pf(trait_gene_symbols.values()))
corr_result_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(
- symbol_list=list(self.trait_symbol_dict.values()))
+ symbol_list=list(self.trait_symbol_dict.values()))
#print("corr_result_tissue_vals: ", pf(corr_result_tissue_vals_dict))
@@ -315,13 +315,13 @@ class CorrelationResults:
)]
result = correlation_functions.cal_zero_order_corr_for_tiss(primary_trait_tissue_values,
- this_trait_tissue_values,
- self.corr_method)
+ this_trait_tissue_values,
+ self.corr_method)
tissue_corr_data[trait] = [symbol, result[0], result[2]]
tissue_corr_data = collections.OrderedDict(sorted(list(tissue_corr_data.items()),
- key=lambda t: -abs(t[1][1])))
+ key=lambda t: -abs(t[1][1])))
return tissue_corr_data
@@ -397,7 +397,7 @@ class CorrelationResults:
lit_corr_data[trait] = [gene_id, 0]
lit_corr_data = collections.OrderedDict(sorted(list(lit_corr_data.items()),
- key=lambda t: -abs(t[1][1])))
+ key=lambda t: -abs(t[1][1])))
return lit_corr_data
@@ -603,12 +603,12 @@ def get_header_fields(data_type, corr_method):
if data_type == "ProbeSet":
if corr_method == "spearman":
header_fields = ['Index',
- 'Record',
- 'Symbol',
- 'Description',
- 'Location',
- 'Mean',
- 'Sample rho',
+ 'Record',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean',
+ 'Sample rho',
'N',
'Sample p(rho)',
'Lit rho',
@@ -619,12 +619,12 @@ def get_header_fields(data_type, corr_method):
'Additive Effect']
else:
header_fields = ['Index',
- 'Record',
- 'Symbol',
- 'Description',
- 'Location',
- 'Mean',
- 'Sample r',
+ 'Record',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean',
+ 'Sample r',
'N',
'Sample p(r)',
'Lit r',
@@ -636,47 +636,47 @@ def get_header_fields(data_type, corr_method):
elif data_type == "Publish":
if corr_method == "spearman":
header_fields = ['Index',
- 'Record',
- 'Abbreviation',
- 'Description',
- 'Mean',
- 'Authors',
- 'Year',
- 'Sample rho',
- 'N',
- 'Sample p(rho)',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
+ 'Record',
+ 'Abbreviation',
+ 'Description',
+ 'Mean',
+ 'Authors',
+ 'Year',
+ 'Sample rho',
+ 'N',
+ 'Sample p(rho)',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect']
else:
header_fields = ['Index',
- 'Record',
- 'Abbreviation',
- 'Description',
- 'Mean',
- 'Authors',
- 'Year',
- 'Sample r',
- 'N',
- 'Sample p(r)',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
+ 'Record',
+ 'Abbreviation',
+ 'Description',
+ 'Mean',
+ 'Authors',
+ 'Year',
+ 'Sample r',
+ 'N',
+ 'Sample p(r)',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect']
else:
if corr_method == "spearman":
header_fields = ['Index',
- 'ID',
- 'Location',
- 'Sample rho',
- 'N',
- 'Sample p(rho)']
+ 'ID',
+ 'Location',
+ 'Sample rho',
+ 'N',
+ 'Sample p(rho)']
else:
header_fields = ['Index',
- 'ID',
- 'Location',
- 'Sample r',
- 'N',
- 'Sample p(r)']
+ 'ID',
+ 'Location',
+ 'Sample r',
+ 'N',
+ 'Sample p(r)']
return header_fields
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index c04b17be..c1bf3daa 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -45,7 +45,7 @@ class CorrelationMatrix:
def __init__(self, start_vars):
trait_db_list = [trait.strip()
- for trait in start_vars['trait_list'].split(',')]
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
@@ -215,7 +215,7 @@ class CorrelationMatrix:
temp_dataset.group.get_samplelist()
for i, pca_trait in enumerate(pca_traits):
trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \
- this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
+ this_group_name + "_" + datetime.datetime.now().strftime("%m%d%H%M%S")
this_vals_string = ""
position = 0
for sample in temp_dataset.group.all_samples_ordered():
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 820e81bc..a0fb34d8 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -66,12 +66,12 @@ class CTL:
def addNode(self, gt):
node_dict = {'data': {'id': str(gt.name) + ":" + str(gt.dataset.name),
- 'sid': str(gt.name),
- 'dataset': str(gt.dataset.name),
- 'label': gt.name,
- 'symbol': gt.symbol,
- 'geneid': gt.geneid,
- 'omim': gt.omim}}
+ 'sid': str(gt.name),
+ 'dataset': str(gt.dataset.name),
+ 'label': gt.name,
+ 'symbol': gt.symbol,
+ 'geneid': gt.geneid,
+ 'omim': gt.omim}}
self.nodes_list.append(node_dict)
def addEdge(self, gtS, gtT, significant, x):
@@ -87,7 +87,7 @@ class CTL:
def run_analysis(self, requestform):
logger.info("Starting CTL analysis on dataset")
self.trait_db_list = [trait.strip()
- for trait in requestform['trait_list'].split(',')]
+ for trait in requestform['trait_list'].split(',')]
self.trait_db_list = [x for x in self.trait_db_list if x]
logger.debug("strategy:", requestform.get("strategy"))
@@ -179,9 +179,9 @@ class CTL:
for trait in self.trait_db_list:
# Create the QTL like CTL plots
self.results['imgurl' + \
- str(n)] = webqtlUtil.genRandStr("CTL_") + ".png"
+ str(n)] = webqtlUtil.genRandStr("CTL_") + ".png"
self.results['imgloc' + str(n)] = GENERATED_IMAGE_DIR + \
- self.results['imgurl' + str(n)]
+ self.results['imgurl' + str(n)]
r_png(self.results['imgloc' + str(n)],
width=1000, height=600, type='cairo-png')
self.r_plotCTLobject(
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 48527785..761ae326 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -112,7 +112,7 @@ class MrnaAssaySearch(DoSearch):
match_clause = ""
where_clause = (match_clause
- + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
""" % (escape(str(self.dataset.id))))
@@ -135,7 +135,7 @@ class MrnaAssaySearch(DoSearch):
match_clause = ""
where_clause = (match_clause
- + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ + """ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
""" % (escape(str(self.dataset.id))))
@@ -147,14 +147,14 @@ class MrnaAssaySearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
query = (self.base_query +
- """%s
+ """%s
WHERE %s
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
ORDER BY ProbeSet.symbol ASC
""" % (escape(from_clause),
- where_clause,
- escape(str(self.dataset.id))))
+ where_clause,
+ escape(str(self.dataset.id))))
return query
def run_combined(self, from_clause='', where_clause=''):
@@ -166,14 +166,14 @@ class MrnaAssaySearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
query = (self.base_query +
- """%s
+ """%s
WHERE %s
and ProbeSet.Id = ProbeSetXRef.ProbeSetId
and ProbeSetXRef.ProbeSetFreezeId = %s
ORDER BY ProbeSet.symbol ASC
""" % (escape(from_clause),
- where_clause,
- escape(str(self.dataset.id))))
+ where_clause,
+ escape(str(self.dataset.id))))
return self.execute(query)
@@ -199,15 +199,15 @@ class PhenotypeSearch(DoSearch):
FROM Phenotype, PublishFreeze, Publication, PublishXRef """
search_fields = ('Phenotype.Post_publication_description',
- 'Phenotype.Pre_publication_description',
- 'Phenotype.Pre_publication_abbreviation',
- 'Phenotype.Post_publication_abbreviation',
- 'Phenotype.Lab_code',
- 'Publication.PubMed_ID',
- 'Publication.Abstract',
- 'Publication.Title',
- 'Publication.Authors',
- 'PublishXRef.Id')
+ 'Phenotype.Pre_publication_description',
+ 'Phenotype.Pre_publication_abbreviation',
+ 'Phenotype.Post_publication_abbreviation',
+ 'Phenotype.Lab_code',
+ 'Publication.PubMed_ID',
+ 'Publication.Abstract',
+ 'Publication.Title',
+ 'Publication.Authors',
+ 'PublishXRef.Id')
header_fields = ['Index',
'Record',
@@ -250,28 +250,28 @@ class PhenotypeSearch(DoSearch):
if self.search_term[0] == "*":
query = (self.base_query +
- """%s
+ """%s
WHERE PublishXRef.InbredSetId = %s
and PublishXRef.PhenotypeId = Phenotype.Id
and PublishXRef.PublicationId = Publication.Id
and PublishFreeze.Id = %s
ORDER BY PublishXRef.Id""" % (
- from_clause,
- escape(str(self.dataset.group.id)),
- escape(str(self.dataset.id))))
+ from_clause,
+ escape(str(self.dataset.group.id)),
+ escape(str(self.dataset.id))))
else:
query = (self.base_query +
- """%s
+ """%s
WHERE %s
and PublishXRef.InbredSetId = %s
and PublishXRef.PhenotypeId = Phenotype.Id
and PublishXRef.PublicationId = Publication.Id
and PublishFreeze.Id = %s
ORDER BY PublishXRef.Id""" % (
- from_clause,
- where_clause,
- escape(str(self.dataset.group.id)),
- escape(str(self.dataset.id))))
+ from_clause,
+ where_clause,
+ escape(str(self.dataset.group.id)),
+ escape(str(self.dataset.id))))
return query
@@ -283,16 +283,16 @@ class PhenotypeSearch(DoSearch):
from_clause = self.normalize_spaces(from_clause)
query = (self.base_query +
- """%s
+ """%s
WHERE %s
PublishXRef.InbredSetId = %s and
PublishXRef.PhenotypeId = Phenotype.Id and
PublishXRef.PublicationId = Publication.Id and
PublishFreeze.Id = %s""" % (
- from_clause,
- where_clause,
- escape(str(self.dataset.group.id)),
- escape(str(self.dataset.id))))
+ from_clause,
+ where_clause,
+ escape(str(self.dataset.group.id)),
+ escape(str(self.dataset.id))))
return self.execute(query)
@@ -336,7 +336,7 @@ class GenotypeSearch(DoSearch):
for field in self.search_fields:
where_clause.append('''%s REGEXP "%s"''' % ("%s.%s" % self.mescape(self.dataset.type,
field),
- self.search_term))
+ self.search_term))
logger.debug("hello ;where_clause is:", pf(where_clause))
where_clause = "(%s) " % ' OR '.join(where_clause)
@@ -349,16 +349,16 @@ class GenotypeSearch(DoSearch):
if self.search_term[0] == "*":
query = (self.base_query
- + """WHERE Geno.Id = GenoXRef.GenoId
+ + """WHERE Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
and GenoFreeze.Id = %s""" % (escape(str(self.dataset.id))))
else:
query = (self.base_query +
- """WHERE %s
+ """WHERE %s
and Geno.Id = GenoXRef.GenoId
and GenoXRef.GenoFreezeId = GenoFreeze.Id
and GenoFreeze.Id = %s""" % (where_clause,
- escape(str(self.dataset.id))))
+ escape(str(self.dataset.id))))
return query
@@ -526,7 +526,7 @@ class LrsSearch(DoSearch):
where_clause += """ and %sXRef.Locus = Geno.name and
Geno.SpeciesId = %s
""" % self.mescape(self.dataset.type,
- self.species_id)
+ self.species_id)
else:
# Deal with >, <, >=, and <=
logger.debug("self.search_term is:", self.search_term)
@@ -535,8 +535,8 @@ class LrsSearch(DoSearch):
lrs_val = lrs_val * 4.61
where_clause = """ %sXRef.LRS %s %s """ % self.mescape(self.dataset.type,
- self.search_operator,
- self.search_term[0])
+ self.search_operator,
+ self.search_term[0])
return where_clause
@@ -618,18 +618,18 @@ class CisTransLrsSearch(DoSearch):
sub_clause = """ %sXRef.LRS > %s and
%sXRef.LRS < %s and """ % (
- escape(self.dataset.type),
- escape(str(min(lrs_min, lrs_max))),
- escape(self.dataset.type),
- escape(str(max(lrs_min, lrs_max)))
- )
+ escape(self.dataset.type),
+ escape(str(min(lrs_min, lrs_max))),
+ escape(self.dataset.type),
+ escape(str(max(lrs_min, lrs_max)))
+ )
else:
# Deal with >, <, >=, and <=
sub_clause = """ %sXRef.LRS %s %s and """ % (
- escape(self.dataset.type),
- escape(self.search_operator),
- escape(self.search_term[0])
- )
+ escape(self.dataset.type),
+ escape(self.search_operator),
+ escape(self.search_term[0])
+ )
if cis_trans == "cis":
where_clause = sub_clause + """
@@ -637,27 +637,27 @@ class CisTransLrsSearch(DoSearch):
%sXRef.Locus = Geno.name and
Geno.SpeciesId = %s and
%s.Chr = Geno.Chr""" % (
- escape(self.dataset.type),
- the_operator,
- escape(str(self.mb_buffer)),
- escape(self.dataset.type),
- escape(str(self.species_id)),
- escape(self.dataset.type)
- )
+ escape(self.dataset.type),
+ the_operator,
+ escape(str(self.mb_buffer)),
+ escape(self.dataset.type),
+ escape(str(self.species_id)),
+ escape(self.dataset.type)
+ )
else:
if chromosome:
location_clause = "(%s.Chr = '%s' and %s.Chr = Geno.Chr and ABS(%s.Mb-Geno.Mb) %s %s) or (%s.Chr != Geno.Chr and Geno.Chr = '%s')" % (escape(self.dataset.type),
- chromosome,
- escape(
+ chromosome,
+ escape(
self.dataset.type),
- escape(
+ escape(
self.dataset.type),
- the_operator,
- escape(
+ the_operator,
+ escape(
str(self.mb_buffer)),
- escape(
+ escape(
self.dataset.type),
- chromosome)
+ chromosome)
else:
location_clause = "(ABS(%s.Mb-Geno.Mb) %s %s and %s.Chr = Geno.Chr) or (%s.Chr != Geno.Chr)" % (escape(
self.dataset.type), the_operator, escape(str(self.mb_buffer)), escape(self.dataset.type), escape(self.dataset.type))
@@ -665,10 +665,10 @@ class CisTransLrsSearch(DoSearch):
%sXRef.Locus = Geno.name and
Geno.SpeciesId = %s and
(%s)""" % (
- escape(self.dataset.type),
- escape(str(self.species_id)),
- location_clause
- )
+ escape(self.dataset.type),
+ escape(str(self.species_id)),
+ location_clause
+ )
return where_clause
@@ -752,15 +752,15 @@ class MeanSearch(MrnaAssaySearch):
where_clause = """ %sXRef.mean > %s and
%sXRef.mean < %s """ % self.mescape(self.dataset.type,
- min(self.mean_min,
- self.mean_max),
- self.dataset.type,
- max(self.mean_min, self.mean_max))
+ min(self.mean_min,
+ self.mean_max),
+ self.dataset.type,
+ max(self.mean_min, self.mean_max))
else:
# Deal with >, <, >=, and <=
where_clause = """ %sXRef.mean %s %s """ % self.mescape(self.dataset.type,
- self.search_operator,
- self.search_term[0])
+ self.search_operator,
+ self.search_term[0])
return where_clause
@@ -893,17 +893,17 @@ class PvalueSearch(MrnaAssaySearch):
self.pvalue_min, self.pvalue_max = self.search_term[:2]
self.where_clause = """ %sXRef.pValue > %s and %sXRef.pValue < %s
""" % self.mescape(
- self.dataset.type,
- min(self.pvalue_min, self.pvalue_max),
- self.dataset.type,
- max(self.pvalue_min, self.pvalue_max))
+ self.dataset.type,
+ min(self.pvalue_min, self.pvalue_max),
+ self.dataset.type,
+ max(self.pvalue_min, self.pvalue_max))
else:
# Deal with >, <, >=, and <=
self.where_clause = """ %sXRef.pValue %s %s
""" % self.mescape(
- self.dataset.type,
- self.search_operator,
- self.search_term[0])
+ self.dataset.type,
+ self.search_operator,
+ self.search_term[0])
logger.debug("where_clause is:", pf(self.where_clause))
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 2c180d49..a22d6acc 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -60,7 +60,7 @@ def export_search_results_csv(targs):
trait_list.append(trait_ob)
table_headers = ['Index', 'URL', 'Species', 'Group', 'Dataset', 'Record ID', 'Symbol', 'Description', 'ProbeTarget', 'PubMed_ID', 'Chr', 'Mb', 'Alias', 'Gene_ID', 'Homologene_ID', 'UniGene_ID',
- 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression']
+ 'Strand_Probe', 'Probe_set_specificity', 'Probe_set_BLAT_score', 'Probe_set_BLAT_Mb_start', 'Probe_set_BLAT_Mb_end', 'QTL_Chr', 'QTL_Mb', 'Locus_at_Peak', 'Max_LRS', 'P_value_of_MAX', 'Mean_Expression']
traits_by_group = sort_traits_by_group(trait_list)
@@ -93,7 +93,7 @@ def export_search_results_csv(targs):
row_contents = [
i + 1,
"https://genenetwork.org/show_trait?trait_id=" + \
- str(trait.name) + "&dataset=" + str(trait.dataset.name),
+ str(trait.name) + "&dataset=" + str(trait.dataset.name),
trait.dataset.group.species,
trait.dataset.group.name,
trait.dataset.name,
@@ -124,7 +124,7 @@ def export_search_results_csv(targs):
for sample in trait.dataset.group.samplelist:
if sample in trait.data:
row_contents += [trait.data[sample].value,
- trait.data[sample].variance]
+ trait.data[sample].variance]
else:
row_contents += ["x", "x"]
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index 3c0f2ca7..c1b14ede 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -28,7 +28,7 @@ logger = utility.logger.getLogger(__name__)
class SendToBNW:
def __init__(self, start_vars):
trait_db_list = [trait.strip()
- for trait in start_vars['trait_list'].split(',')]
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
trait_samples_list = []
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 8af9bee9..9a4f7150 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -33,7 +33,7 @@ logger = utility.logger.getLogger(__name__)
class SendToGeneWeaver:
def __init__(self, start_vars):
trait_db_list = [trait.strip()
- for trait in start_vars['trait_list'].split(',')]
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
self.chip_name = test_chip(self.trait_list)
@@ -54,11 +54,11 @@ class SendToGeneWeaver:
trait_name_list = get_trait_name_list(self.trait_list)
self.hidden_vars = {
- 'client': "genenetwork",
- 'species': species_name,
- 'idtype': self.chip_name,
- 'list': ",".join(trait_name_list),
- }
+ 'client': "genenetwork",
+ 'species': species_name,
+ 'idtype': self.chip_name,
+ 'list': ",".join(trait_name_list),
+ }
def get_trait_name_list(trait_list):
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index fcd943ba..6e74f4fe 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -33,7 +33,7 @@ logger = utility.logger.getLogger(__name__)
class SendToWebGestalt:
def __init__(self, start_vars):
trait_db_list = [trait.strip()
- for trait in start_vars['trait_list'].split(',')]
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
self.chip_name = test_chip(self.trait_list)
@@ -49,7 +49,7 @@ class SendToWebGestalt:
id_type = "entrezgene"
self.hidden_vars = {
- 'gene_list': "\n".join(gene_id_list),
+ 'gene_list': "\n".join(gene_id_list),
'id_type': "entrezgene",
'ref_set': "genome",
'enriched_database_category': "geneontology",
@@ -59,7 +59,7 @@ class SendToWebGestalt:
'enrich_method': "ORA",
'fdr_method': "BH",
'min_num': "2"
- }
+ }
species = self.trait_list[0][1].group.species
if species == "rat":
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index 995915a9..b7e7e38a 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -8,7 +8,7 @@ from wqflask import app
from wqflask.user_login import send_verification_email, send_invitation_email, basic_info, set_password
from utility.redis_tools import get_user_groups, get_group_info, save_user, create_group, delete_group, add_users_to_group, remove_users_from_group, \
- change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column, get_resources, get_resource_info
+ change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column, get_resources, get_resource_info
from utility.logger import getLogger
logger = getLogger(__name__)
@@ -78,9 +78,9 @@ def remove_users():
member_ids_to_remove = request.form['selected_member_ids']
remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(
- ":"), group_id, user_type="admins")
+ ":"), group_id, user_type="admins")
remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(
- ":"), group_id, user_type="members")
+ ":"), group_id, user_type="members")
return redirect(url_for('view_group', id=group_id))
@@ -133,7 +133,7 @@ def add_or_edit_group():
#send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
create_group(list(admin_user_ids), list(
- member_user_ids), params['group_name'])
+ member_user_ids), params['group_name'])
return redirect(url_for('manage_groups'))
else:
return render_template("admin/create_group.html")
@@ -159,13 +159,13 @@ def send_group_invites(group_id, user_email_list=[], user_type="members"):
key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group")
else:
temp_password = ''.join(random.choice(
- string.ascii_uppercase + string.digits) for _ in range(6))
+ string.ascii_uppercase + string.digits) for _ in range(6))
user_details = {
- 'user_id': str(uuid.uuid4()),
- 'email_address': user_email,
- 'registration_info': basic_info(),
- 'password': set_password(temp_password),
- 'confirmed': 0
+ 'user_id': str(uuid.uuid4()),
+ 'email_address': user_email,
+ 'registration_info': basic_info(),
+ 'password': set_password(temp_password),
+ 'confirmed': 0
}
save_user(user_details, user_details['user_id'])
send_invitation_email(user_email, temp_password)
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index f02da27c..fb8bdc55 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -124,7 +124,7 @@ class GSearch:
if this_trait['locus_chr'] != None and this_trait['locus_mb'] != None:
max_lrs_text = "Chr" + \
str(this_trait['locus_chr']) + \
- ": " + str(this_trait['locus_mb'])
+ ": " + str(this_trait['locus_mb'])
this_trait['max_lrs_text'] = max_lrs_text
trait_list.append(this_trait)
@@ -133,18 +133,18 @@ class GSearch:
self.trait_list = json.dumps(trait_list)
self.header_fields = ['Index',
- 'Record',
- 'Species',
- 'Group',
- 'Tissue',
- 'Dataset',
- 'Symbol',
- 'Description',
- 'Location',
- 'Mean',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
+ 'Record',
+ 'Species',
+ 'Group',
+ 'Tissue',
+ 'Dataset',
+ 'Symbol',
+ 'Description',
+ 'Location',
+ 'Mean',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect']
elif self.type == "phenotype":
search_term = self.terms
@@ -251,7 +251,7 @@ class GSearch:
if trait_ob.locus_chr != "" and trait_ob.locus_mb != "":
this_trait['max_lrs_text'] = "Chr" + \
str(trait_ob.locus_chr) + \
- ": " + str(trait_ob.locus_mb)
+ ": " + str(trait_ob.locus_mb)
except:
this_trait['max_lrs_text'] = "N/A"
@@ -261,12 +261,12 @@ class GSearch:
self.trait_list = json.dumps(trait_list)
self.header_fields = ['Index',
- 'Species',
- 'Group',
- 'Record',
- 'Description',
- 'Authors',
- 'Year',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
+ 'Species',
+ 'Group',
+ 'Record',
+ 'Description',
+ 'Authors',
+ 'Year',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect']
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 02eb66e5..001bab3b 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -19,7 +19,7 @@ class Heatmap:
def __init__(self, start_vars, temp_uuid):
trait_db_list = [trait.strip()
- for trait in start_vars['trait_list'].split(',')]
+ for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
self.temp_uuid = temp_uuid
@@ -35,7 +35,7 @@ class Heatmap:
self.species = species.TheSpecies(dataset=self.trait_list[0][1])
for key in list(self.species.chromosomes.chromosomes.keys()):
chrnames.append([self.species.chromosomes.chromosomes[key].name,
- self.species.chromosomes.chromosomes[key].mb_length])
+ self.species.chromosomes.chromosomes[key].mb_length])
for trait_db in self.trait_list:
@@ -111,7 +111,7 @@ class Heatmap:
trimmed_values.append(values[i])
trait_filename = str(this_trait.name) + "_" + \
- str(self.dataset.name) + "_pheno"
+ str(self.dataset.name) + "_pheno"
gen_pheno_txt_file(trimmed_samples, trimmed_values, trait_filename)
output_filename = self.dataset.group.name + "_GWA_" + \
@@ -119,11 +119,11 @@ class Heatmap:
for _ in range(6))
reaper_command = REAPER_COMMAND + ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt -n 1000 -o {4}{5}.txt'.format(flat_files('genotype'),
- genofile_name,
- TEMPDIR,
- trait_filename,
- webqtlConfig.GENERATED_IMAGE_DIR,
- output_filename)
+ genofile_name,
+ TEMPDIR,
+ trait_filename,
+ webqtlConfig.GENERATED_IMAGE_DIR,
+ output_filename)
os.system(reaper_command)
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 2f1c142c..04980281 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -8,8 +8,8 @@ from flask import Flask, g
def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
- 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
- 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
+ 'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
+ 'exonCount', 'exonStarts', 'exonEnds', 'cdsStart', 'cdsEnd']
# List All Species in the Gene Table
speciesDict = {}
@@ -34,9 +34,9 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
((TxStart > %f and TxStart <= %f) OR (TxEnd > %f and TxEnd <= %f))
ORDER BY txStart
""" % (", ".join(fetchFields),
- speciesId, chrName,
- startMb, endMb,
- startMb, endMb)).fetchall()
+ speciesId, chrName,
+ startMb, endMb,
+ startMb, endMb)).fetchall()
GeneList = []
@@ -55,7 +55,7 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
StrainId1 = %d AND StrainId2 = %d
""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0]
newdict["snpDensity"] = newdict["snpCount"] / \
- (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0
+ (newdict["TxEnd"] - newdict["TxStart"]) / 1000.0
else:
newdict["snpDensity"] = newdict["snpCount"] = 0
@@ -70,8 +70,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
newdict2 = {}
resultsOther = g.db.execute("SELECT %s FROM GeneList WHERE SpeciesId = %d AND geneSymbol= '%s' LIMIT 1" % (", ".join(fetchFields),
- othSpecId,
- newdict["GeneSymbol"])).fetchone()
+ othSpecId,
+ newdict["GeneSymbol"])).fetchone()
if resultsOther:
for j, item in enumerate(fetchFields):
@@ -88,13 +88,13 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
""" % (chrName, newdict["TxStart"], newdict["TxEnd"], diffCol[0], diffCol[1])).fetchone()[0]
newdict2["snpDensity"] = newdict2["snpCount"] / \
- (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0
+ (newdict2["TxEnd"] - newdict2["TxStart"]) / 1000.0
else:
newdict2["snpDensity"] = newdict2["snpCount"] = 0
try:
newdict2['GeneLength'] = 1000.0 * \
- (newdict2['TxEnd'] - newdict2['TxStart'])
+ (newdict2['TxEnd'] - newdict2['TxStart'])
except:
pass
diff --git a/wqflask/wqflask/markdown_routes.py b/wqflask/wqflask/markdown_routes.py
index ebf75807..c27ff143 100644
--- a/wqflask/wqflask/markdown_routes.py
+++ b/wqflask/wqflask/markdown_routes.py
@@ -103,7 +103,7 @@ def environments():
@environments_blueprint.route('/svg-dependency-graph')
def svg_graph():
directory, file_name, _ = get_file_from_python_search_path(
- "wqflask/dependency-graph.svg").partition("dependency-graph.svg")
+ "wqflask/dependency-graph.svg").partition("dependency-graph.svg")
return send_from_directory(directory, file_name)
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index c68e0fde..f3b1b1fc 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -629,7 +629,7 @@ class DisplayMappingResults:
submit=HtmlGenWrapper.create_input_tag(type_='hidden'))
hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+ \
- "Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
+ "Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
for key in hddn.keys():
showLocusForm.append(HtmlGenWrapper.create_input_tag(
name=key, value=hddn[key], type_='hidden'))
@@ -889,7 +889,7 @@ class DisplayMappingResults:
bootY = yZero - bootHeightThresh * item / highestPercent
im_drawer.line(
xy=((canvas.size[0] - bootOffset + 4, bootY),
- (canvas.size[0] - bootOffset, bootY)),
+ (canvas.size[0] - bootOffset, bootY)),
fill=BLACK)
im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, bootY+TEXT_Y_DISPLACEMENT),
text='%2.1f' % item, font=bootScaleFont, fill=BLACK)
@@ -983,7 +983,7 @@ class DisplayMappingResults:
break
if locPixel >= 0 and self.plotScale == 'physic':
traitPixel = ((locPixel, yZero), (locPixel - 7,
- yZero + 14), (locPixel + 7, yZero + 14))
+ yZero + 14), (locPixel + 7, yZero + 14))
draw_open_polygon(canvas, xy=traitPixel, outline=BLACK,
fill=self.TRANSCRIPT_LOCATION_COLOR)
@@ -1029,7 +1029,7 @@ class DisplayMappingResults:
SNPCounts[i - xLeftOffset] * SNP_HEIGHT_MODIFIER / maxCount)
im_drawer.line(
xy=((i, drawSNPLocationY + (snpDensity) * zoom),
- (i, drawSNPLocationY - (snpDensity) * zoom)),
+ (i, drawSNPLocationY - (snpDensity) * zoom)),
fill=self.SNP_COLOR, width=1)
def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset=(40, 120, 80, 10), zoom=1):
@@ -1356,7 +1356,7 @@ class DisplayMappingResults:
# always apply colors now, even if SNP Track not checked - Zach 11/24/2010
densities = [1.0000000000000001e-05, 0.094094033555233408,
- 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
+ 0.3306166377816987, 0.88246026851027781, 2.6690084029581951, 4.1, 61.0]
if SNPdensity < densities[0]:
myColor = BLACK
elif SNPdensity < densities[1]:
@@ -1462,13 +1462,13 @@ class DisplayMappingResults:
xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH,
geneYLocation),
(geneStartPix + xCoord,
- geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)),
+ geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)),
fill=arrowColor, width=1)
im_drawer.line(
xy=((geneStartPix + xCoord + self.EACH_GENE_ARROW_WIDTH,
geneYLocation + self.EACH_GENE_HEIGHT * zoom),
(geneStartPix + xCoord,
- geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)),
+ geneYLocation + (self.EACH_GENE_HEIGHT / 2) * zoom)),
fill=arrowColor, width=1)
# draw the blocks for the exon regions
@@ -1476,7 +1476,7 @@ class DisplayMappingResults:
exonStartPix = (
exonStarts[i] - startMb) * plotXScale + xLeftOffset
exonEndPix = (exonEnds[i] - startMb) * \
- plotXScale + xLeftOffset
+ plotXScale + xLeftOffset
if (exonStartPix < xLeftOffset):
exonStartPix = xLeftOffset
if (exonEndPix < xLeftOffset):
@@ -1493,7 +1493,7 @@ class DisplayMappingResults:
# draw gray blocks for 3' and 5' UTR blocks
if cdsStart and cdsEnd:
utrStartPix = (txStart - startMb) * \
- plotXScale + xLeftOffset
+ plotXScale + xLeftOffset
utrEndPix = (cdsStart - startMb) * plotXScale + xLeftOffset
if (utrStartPix < xLeftOffset):
utrStartPix = xLeftOffset
@@ -1741,9 +1741,9 @@ class DisplayMappingResults:
mylineColor = self.HAPLOTYPE_RECOMBINATION
im_drawer.line(
xy=((plotRight,
- geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
(drawEnd,
- geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
+ geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
if lastGene == 0:
@@ -1869,7 +1869,7 @@ class DisplayMappingResults:
fill=self.CLICKABLE_WEBQTL_REGION_COLOR)
im_drawer.line(
xy=((xBrowse1, paddingTop), (xBrowse1,
- (paddingTop + self.BAND_HEIGHT))),
+ (paddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
@@ -1895,7 +1895,7 @@ class DisplayMappingResults:
fill=self.CLICKABLE_PHENOGEN_REGION_COLOR)
im_drawer.line(
xy=((xBrowse1, phenogenPaddingTop), (xBrowse1,
- (phenogenPaddingTop + self.BAND_HEIGHT))),
+ (phenogenPaddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
UCSC_COORDS = "%d, %d, %d, %d" % (
@@ -2051,7 +2051,7 @@ class DisplayMappingResults:
fill=xAxisLabelColor)
else:
im_drawer.line(xy=((Xc, yZero),
- (Xc, yZero + xMinorTickHeight)),
+ (Xc, yZero + xMinorTickHeight)),
fill=xAxisTickMarkColor,
width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
@@ -2159,17 +2159,17 @@ class DisplayMappingResults:
if differ:
im_drawer.line(
xy=((startPosX + Lpos, yZero), (xLeftOffset + offsetA,\
- yZero + 25)),
+ yZero + 25)),
fill=lineColor)
im_drawer.line(
xy=((xLeftOffset + offsetA, yZero + 25), (xLeftOffset+offsetA,\
- yZero + 40 + Zorder*(LRectWidth+3))),
+ yZero + 40 + Zorder*(LRectWidth+3))),
fill=lineColor)
rectColor = ORANGE
else:
im_drawer.line(
xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)-3), (\
- xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3))),
+ xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3))),
fill=lineColor)
rectColor = DEEPPINK
im_drawer.rectangle(
@@ -2178,7 +2178,7 @@ class DisplayMappingResults:
yZero + 40 + Zorder*(LRectWidth+3)+LRectWidth)),
outline=rectColor, fill=rectColor, width=0)
COORDS = "%d,%d,%d,%d" % (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
- xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth)
+ xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth)
HREF = "/show_trait?trait_id=%s&dataset=%s" % (
Lname, self.dataset.group.name + "Geno")
#HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
@@ -2230,7 +2230,7 @@ class DisplayMappingResults:
if self.lrsMax <= 0: # sliding scale
if "lrs_value" in self.qtlresults[0]:
LRS_LOD_Max = max([result['lrs_value']
- for result in self.qtlresults])
+ for result in self.qtlresults])
if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
LRS_LOD_Max = LRS_LOD_Max / self.LODFACTOR
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
@@ -2248,7 +2248,7 @@ class DisplayMappingResults:
pass
else:
LRS_LOD_Max = max([result['lod_score']
- for result in self.qtlresults])
+ for result in self.qtlresults])
if self.LRS_LOD == "LRS":
LRS_LOD_Max = LRS_LOD_Max * self.LODFACTOR
if self.permChecked and self.nperm > 0 and not self.multipleInterval:
@@ -2390,7 +2390,7 @@ class DisplayMappingResults:
)
im_drawer.line(
xy=((start_pos_x + self.SUGGESTIVE_WIDTH / 1.5, significantY),
- (rightEdge, significantY)),
+ (rightEdge, significantY)),
fill=self.SIGNIFICANT_COLOR,
width=self.SIGNIFICANT_WIDTH * zoom
# , clipX=(xLeftOffset, xLeftOffset + plotWidth-2)
@@ -2440,7 +2440,7 @@ class DisplayMappingResults:
else:
if self.additiveChecked:
additiveMax = max([abs(X['additive'])
- for X in self.qtlresults])
+ for X in self.qtlresults])
lrsEdgeWidth = 3
if zoom == 2:
@@ -2484,7 +2484,7 @@ class DisplayMappingResults:
Xcm = Xc
else:
Xcm = (yZero - Yc0) / \
- ((Yc - Yc0) / (Xc - Xc0)) + Xc0
+ ((Yc - Yc0) / (Xc - Xc0)) + Xc0
if Yc0 < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xcm, yZero)),
@@ -2583,12 +2583,12 @@ class DisplayMappingResults:
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR)
Yc = yZero - webqtlConfig.MAXLRS * \
LRSHeightThresh / \
- (LRS_LOD_Max * self.LODFACTOR)
+ (LRS_LOD_Max * self.LODFACTOR)
else:
#Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/(LRSAxisList[-1]*self.LODFACTOR)
Yc = yZero - \
qtlresult['lrs_value'] * LRSHeightThresh / \
- (LRS_LOD_Max * self.LODFACTOR)
+ (LRS_LOD_Max * self.LODFACTOR)
else:
if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1]
@@ -2597,7 +2597,7 @@ class DisplayMappingResults:
#Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSAxisList[-1]
Yc = yZero - \
qtlresult['lrs_value'] * \
- LRSHeightThresh / LRS_LOD_Max
+ LRSHeightThresh / LRS_LOD_Max
else:
if qtlresult['lod_score'] > 100 or qtlresult['lod_score'] == 'inf':
#Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSAxisList[-1]
@@ -2607,12 +2607,12 @@ class DisplayMappingResults:
#Yc = yZero - qtlresult['lod_score']*self.LODFACTOR*LRSHeightThresh/LRSAxisList[-1]
Yc = yZero - \
qtlresult['lod_score'] * self.LODFACTOR * \
- LRSHeightThresh / LRS_LOD_Max
+ LRSHeightThresh / LRS_LOD_Max
else:
#Yc = yZero - qtlresult['lod_score']*LRSHeightThresh/LRSAxisList[-1]
Yc = yZero - \
qtlresult['lod_score'] * \
- LRSHeightThresh / LRS_LOD_Max
+ LRSHeightThresh / LRS_LOD_Max
if self.manhattan_plot == True:
if self.color_scheme == "single":
@@ -2665,7 +2665,7 @@ class DisplayMappingResults:
Xcm = Xc
else:
Xcm = (yZero - Yc0) / \
- ((Yc - Yc0) / (Xc - Xc0)) + Xc0
+ ((Yc - Yc0) / (Xc - Xc0)) + Xc0
if Yc0 < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xcm, yZero)),
@@ -2731,7 +2731,7 @@ class DisplayMappingResults:
Xcm = Xc
else:
Xcm = (yZero - Yc0) / \
- ((Yc - Yc0) / (Xc - Xc0)) + Xc0
+ ((Yc - Yc0) / (Xc - Xc0)) + Xc0
if Yc0 < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xcm, yZero)),
@@ -2947,12 +2947,12 @@ class DisplayMappingResults:
if self.dataset.group.species == "mouse":
if refGene:
gene_table_header_list = ["Index",
- "Symbol",
- "Mb Start",
- "Length (Kb)",
- "SNP Count",
- "SNP Density",
- "Avg Expr",
+ "Symbol",
+ "Mb Start",
+ "Length (Kb)",
+ "SNP Count",
+ "SNP Density",
+ "Avg Expr",
"Human Chr",
"Mb Start (hg19)",
"Literature Correlation",
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 9f9591ad..5d16abde 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -26,18 +26,18 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
gen_pheno_txt_file(samples, vals, trait_filename)
output_filename = (f"{this_dataset.group.name}_GWA_"
- + ''.join(random.choice(string.ascii_uppercase + string.digits)
- for _ in range(6))
- )
+ + ''.join(random.choice(string.ascii_uppercase + string.digits)
+ for _ in range(6))
+ )
bootstrap_filename = None
permu_filename = None
opt_list = []
if boot_check and num_bootstrap > 0:
bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_"
- + ''.join(random.choice(string.ascii_uppercase + string.digits)
- for _ in range(6))
- )
+ + ''.join(random.choice(string.ascii_uppercase + string.digits)
+ for _ in range(6))
+ )
opt_list.append("-b")
opt_list.append(f"--n_bootstrap {str(num_bootstrap)}")
@@ -45,8 +45,8 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
f"--bootstrap_output {webqtlConfig.GENERATED_IMAGE_DIR}{bootstrap_filename}.txt")
if num_perm > 0:
permu_filename = ("{this_dataset.group.name}_PERM_"
- + ''.join(random.choice(string.ascii_uppercase
- + string.digits) for _ in range(6))
+ + ''.join(random.choice(string.ascii_uppercase
+ + string.digits) for _ in range(6))
)
opt_list.append("-n " + str(num_perm))
opt_list.append(
@@ -57,15 +57,15 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
opt_list.append("--interval 1")
reaper_command = (REAPER_COMMAND +
- ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'),
+ ' --geno {0}/{1}.geno --traits {2}/gn2/{3}.txt {4} -o {5}{6}.txt'.format(flat_files('genotype'),
- genofile_name,
- TEMPDIR,
- trait_filename,
- " ".join(
- opt_list),
- webqtlConfig.GENERATED_IMAGE_DIR,
- output_filename))
+ genofile_name,
+ TEMPDIR,
+ trait_filename,
+ " ".join(
+ opt_list),
+ webqtlConfig.GENERATED_IMAGE_DIR,
+ output_filename))
logger.debug("reaper_command:" + reaper_command)
os.system(reaper_command)
@@ -82,7 +82,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
significant = permu_vals[int(num_perm * 0.95 - 1)]
return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals,
- [output_filename, permu_filename, bootstrap_filename])
+ [output_filename, permu_filename, bootstrap_filename])
def gen_pheno_txt_file(samples, vals, trait_filename):
@@ -231,17 +231,17 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
control_geno.append(control_geno2[_idx])
bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
- trait=trimmed_values,
- control=control_geno,
- nboot=num_bootstrap)
+ trait=trimmed_values,
+ control=control_geno,
+ nboot=num_bootstrap)
else:
reaper_results = genotype.regression(strains=trimmed_samples,
trait=trimmed_values)
if bootCheck:
bootstrap_results = genotype.bootstrap(strains=trimmed_samples,
- trait=trimmed_values,
- nboot=num_bootstrap)
+ trait=trimmed_values,
+ nboot=num_bootstrap)
json_data['chr'] = []
json_data['pos'] = []
@@ -265,7 +265,7 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
# if self.additive:
# self.json_data['additive'].append(qtl.additive)
locus = {"name": reaper_locus.name, "chr": reaper_locus.chr,
- "cM": reaper_locus.cM, "Mb": reaper_locus.Mb}
+ "cM": reaper_locus.cM, "Mb": reaper_locus.Mb}
qtl = {"lrs_value": qtl.lrs, "chr": converted_chr, "Mb": reaper_locus.Mb,
"cM": reaper_locus.cM, "name": reaper_locus.name, "additive": qtl.additive, "dominance": qtl.dominance}
qtl_results.append(qtl)
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 32dbad1f..cf8cf514 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -411,7 +411,7 @@ def process_pair_scan_results(result):
result = result[1]
output = [tuple([result[j][i] for j in range(result.ncol)])
- for i in range(result.nrow)]
+ for i in range(result.nrow)]
for i, line in enumerate(result.iter_row()):
marker = {}
@@ -441,7 +441,7 @@ def process_rqtl_perm_results(num_perm, results):
def process_rqtl_results(result, species_name):
qtl_results = []
output = [tuple([result[j][i] for j in range(result.ncol)])
- for i in range(result.nrow)]
+ for i in range(result.nrow)]
for i, line in enumerate(result.iter_row()):
marker = {}
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 041f4348..81e0a03f 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -289,18 +289,18 @@ class RunMapping:
",")
results, self.perm_output, self.suggestive, self.significant, self.bootstrap_results, self.output_files = qtlreaper_mapping.run_reaper(self.this_trait,
- self.dataset,
- self.samples,
- self.vals,
- self.json_data,
- self.num_perm,
- self.bootCheck,
- self.num_bootstrap,
- self.do_control,
- self.control_marker,
- self.manhattan_plot,
- self.first_run,
- self.output_files)
+ self.dataset,
+ self.samples,
+ self.vals,
+ self.json_data,
+ self.num_perm,
+ self.bootCheck,
+ self.num_bootstrap,
+ self.do_control,
+ self.control_marker,
+ self.manhattan_plot,
+ self.first_run,
+ self.output_files)
else:
results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.run_original_reaper(self.this_trait,
self.dataset,
@@ -371,7 +371,7 @@ class RunMapping:
ps=this_ps,
url="/show_trait?trait_id=" + \
marker['name'] + "&dataset=" + \
- self.dataset.group.name + "Geno"
+ self.dataset.group.name + "Geno"
)
if self.geno_db_exists == "True":
@@ -382,7 +382,7 @@ class RunMapping:
pos=this_ps,
url="/show_trait?trait_id=" + \
marker['name'] + "&dataset=" + \
- self.dataset.group.name + "Geno"
+ self.dataset.group.name + "Geno"
)
else:
annot_marker = dict(
@@ -409,11 +409,11 @@ class RunMapping:
if 'Mb' in marker.keys():
marker['display_pos'] = "Chr" + \
str(marker['chr']) + ": " + \
- "{:.6f}".format(marker['Mb'])
+ "{:.6f}".format(marker['Mb'])
elif 'cM' in marker.keys():
marker['display_pos'] = "Chr" + \
str(marker['chr']) + ": " + \
- "{:.3f}".format(marker['cM'])
+ "{:.3f}".format(marker['cM'])
else:
marker['display_pos'] = "N/A"
self.qtl_results.append(marker)
@@ -776,7 +776,7 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
perm_strata_strings.append(combined_string)
d = dict([(y, x + 1)
- for x, y in enumerate(sorted(set(perm_strata_strings)))])
+ for x, y in enumerate(sorted(set(perm_strata_strings)))])
list_to_numbers = [d[x] for x in perm_strata_strings]
perm_strata = list_to_numbers
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 55b0278a..822900cc 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -45,8 +45,8 @@ class User(Base):
)
user_collections = relationship("UserCollection",
- order_by="asc(UserCollection.name)",
- lazy='dynamic',
+ order_by="asc(UserCollection.name)",
+ lazy='dynamic',
)
def display_num_collections(self):
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index 6b836e20..bd1c4407 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -34,7 +34,7 @@ def parse(pstring):
(\w+\s*[=:\>\<][\w\*]+) | # wiki=bar, GO:foobar, etc
(".*?") | ('.*?') | # terms in quotes, i.e. "brain weight"
([\w\*\?]+)) # shh, brain, etc """, pstring,
- flags=re.VERBOSE)
+ flags=re.VERBOSE)
pstring = [item.strip() for item in pstring if item and item.strip()]
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 2e1cb992..fc48959e 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -173,10 +173,10 @@ class SearchResultPage:
if self.dataset.type == "ProbeSet":
self.header_data_names = ['index', 'display_name', 'symbol', 'description',
- 'location', 'mean', 'lrs_score', 'lrs_location', 'additive']
+ 'location', 'mean', 'lrs_score', 'lrs_location', 'additive']
elif self.dataset.type == "Publish":
self.header_data_names = ['index', 'display_name', 'description', 'mean',
- 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive']
+ 'authors', 'pubmed_text', 'lrs_score', 'lrs_location', 'additive']
elif self.dataset.type == "Geno":
self.header_data_names = ['index', 'display_name', 'location']
@@ -273,9 +273,9 @@ class SearchResultPage:
if search_ob:
search_class = getattr(do_search, search_ob)
the_search = search_class(search_term,
- search_operator,
- self.dataset,
- search_type['key']
+ search_operator,
+ self.dataset,
+ search_type['key']
)
return the_search
else:
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 8ca3a9eb..7f68efad 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -49,8 +49,8 @@ class ServerSideTable:
column_name = self.header_data_names[column_number - 1]
sort_direction = self.request_values['sSortDir_' + str(i)]
self.table_rows = sorted(self.table_rows,
- key=lambda x: x[column_name],
- reverse=is_reverse(sort_direction))
+ key=lambda x: x[column_name],
+ reverse=is_reverse(sort_direction))
def paginate_rows(self):
"""
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 3a63c84e..f9d30dba 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -75,7 +75,7 @@ class SampleList:
if self.dataset.group.species == "mouse":
if len(sample.extra_attributes['rrid'].split(":")) > 1:
the_rrid = sample.extra_attributes['rrid'].split(":")[
- 1]
+ 1]
sample.extra_attributes['rrid'] = [
sample.extra_attributes['rrid']]
sample.extra_attributes['rrid'].append(
@@ -83,7 +83,7 @@ class SampleList:
elif self.dataset.group.species == "rat":
if len(str(sample.extra_attributes['rrid'])):
the_rrid = sample.extra_attributes['rrid'].split("_")[
- 1]
+ 1]
sample.extra_attributes['rrid'] = [
sample.extra_attributes['rrid']]
sample.extra_attributes['rrid'].append(
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 81e7903b..7fabc3f6 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -41,7 +41,7 @@ def get_export_metadata(trait_id, dataset_name):
if dataset.type == "Publish":
metadata.append(["Phenotype ID: " + trait_id])
metadata.append(["Phenotype URL: " + "http://genenetwork.org/show_trait?trait_id=" + \
- trait_id + "&dataset=" + dataset_name])
+ trait_id + "&dataset=" + dataset_name])
metadata.append(["Group: " + dataset.group.name])
metadata.append(
["Phenotype: " + this_trait.description_display.replace(",", "\",\"")])
@@ -56,7 +56,7 @@ def get_export_metadata(trait_id, dataset_name):
else:
metadata.append(["Record ID: " + trait_id])
metadata.append(["Trait URL: " + "http://genenetwork.org/show_trait?trait_id=" + \
- trait_id + "&dataset=" + dataset_name])
+ trait_id + "&dataset=" + dataset_name])
if this_trait.symbol:
metadata.append(["Symbol: " + this_trait.symbol])
metadata.append(["Dataset: " + dataset.name])
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 5b7a663c..42fe339e 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -294,7 +294,7 @@ class SnpBrowser:
effect_info_dict = get_effect_info(effect_list)
coding_domain_list = ['Start Gained', 'Start Lost',
- 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
+ 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
intron_domain_list = ['Splice Site', 'Nonsplice Site']
for key in effect_info_dict:
@@ -320,7 +320,7 @@ class SnpBrowser:
if self.redundant == "false" or last_mb != mb: # filter redundant
if self.include_record(domain, function, snp_source, conservation_score):
info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain,
- function, function_details, snp_source, conservation_score, snp_id]
+ function, function_details, snp_source, conservation_score, snp_id]
info_list.extend(self.allele_list)
filtered_results.append(info_list)
last_mb = mb
@@ -351,7 +351,7 @@ class SnpBrowser:
if self.redundant == "false" or last_mb != mb:
if self.include_record(domain, function, snp_source, conservation_score):
info_list = [snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain,
- function, function_details, snp_source, conservation_score, snp_id]
+ function, function_details, snp_source, conservation_score, snp_id]
info_list.extend(self.allele_list)
filtered_results.append(info_list)
last_mb = mb
@@ -366,7 +366,7 @@ class SnpBrowser:
domain = conservation_score = snp_id = snp_name = rs = flank_3 = flank_5 = ncbi = function = ""
if self.include_record(domain, function, source_name, conservation_score):
filtered_results.append([indel_name, indel_chr, indel_mb_start, indel_mb_end,
- indel_strand, indel_type, indel_size, indel_sequence, source_name])
+ indel_strand, indel_type, indel_size, indel_sequence, source_name])
last_mb = indel_mb_start
else:
@@ -703,9 +703,9 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None):
header_data_names = []
if variant_type == "SNP":
header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore',
- 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
+ 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
header_data_names = ['index', 'snp_name', 'chr', 'mb_formatted', 'alleles', 'snp_source', 'conservation_score',
- 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details']
+ 'gene_name', 'transcript', 'exon', 'domain_1', 'domain_2', 'function', 'function_details']
header_fields.append(strain_list)
header_data_names += strain_list
@@ -742,9 +742,9 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None):
elif variant_type == "InDel":
header_fields = ['Index', 'ID', 'Type', 'InDel Chr',
- 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
+ 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
header_data_names = ['index', 'indel_name', 'indel_type', 'indel_chr', 'indel_mb_s',
- 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']
+ 'indel_mb_e', 'indel_strand', 'indel_size', 'indel_sequence', 'source_name']
return header_fields, empty_field_count, header_data_names
@@ -758,9 +758,9 @@ def get_effect_details_by_category(effect_name=None, effect_value=None):
tmp_list = []
gene_group_list = ['Upstream', 'Downstream',
- 'Splice Site', 'Nonsplice Site', '3\' UTR']
+ 'Splice Site', 'Nonsplice Site', '3\' UTR']
biotype_group_list = ['Unknown Effect In Exon', 'Start Gained',
- 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
+ 'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
new_codon_group_list = ['Start Gained']
codon_effect_group_list = [
'Start Lost', 'Stop Gained', 'Stop Lost', 'Nonsynonymous', 'Synonymous']
@@ -913,7 +913,7 @@ def get_gene_id_name_dict(species_id, gene_name_list):
if len(gene_name_list) == 0:
return ""
gene_name_str_list = ["'" + gene_name + \
- "'" for gene_name in gene_name_list]
+ "'" for gene_name in gene_name_list]
gene_name_str = ",".join(gene_name_str_list)
query = """
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 725e7c9e..0d5f1f3e 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -59,12 +59,12 @@ def encode_password(pass_gen_fields, unencrypted_password):
def set_password(password):
pass_gen_fields = {
- "unencrypted_password": password,
- "algorithm": "pbkdf2",
- "hashfunc": "sha256",
- "salt": base64.b64encode(os.urandom(32)),
- "iterations": 100000,
- "keylength": 32,
+ "unencrypted_password": password,
+ "algorithm": "pbkdf2",
+ "hashfunc": "sha256",
+ "salt": base64.b64encode(os.urandom(32)),
+ "iterations": 100000,
+ "keylength": 32,
"created_timestamp": timestamp()
}
@@ -89,18 +89,18 @@ def get_signed_session_id(user):
if 'github_id' in user:
session = dict(login_time=time.time(),
- user_type="github",
- user_id=user['user_id'],
- github_id=user['github_id'],
- user_name=user['name'],
- user_url=user['user_url'])
+ user_type="github",
+ user_id=user['user_id'],
+ github_id=user['github_id'],
+ user_name=user['name'],
+ user_url=user['user_url'])
elif 'orcid' in user:
session = dict(login_time=time.time(),
- user_type="orcid",
- user_id=user['user_id'],
- github_id=user['orcid'],
- user_name=user['name'],
- user_url=user['user_url'])
+ user_type="orcid",
+ user_id=user['user_id'],
+ github_id=user['orcid'],
+ user_name=user['name'],
+ user_url=user['user_url'])
else:
session = dict(login_time=time.time(),
user_type="gn2",
@@ -269,7 +269,7 @@ def github_oauth2():
result = requests.post(
"https://github.com/login/oauth/access_token", json=data)
result_dict = {arr[0]: arr[1]
- for arr in [tok.split("=") for tok in result.text.split("&")]}
+ for arr in [tok.split("=") for tok in result.text.split("&")]}
github_user = get_github_user_details(result_dict["access_token"])
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 9ebec405..fb26bfb1 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -475,7 +475,7 @@ def set_password(password, user):
pwfields.encrypt_time = enc_password.encrypt_time
user.password = json.dumps(pwfields.__dict__,
- sort_keys=True,
+ sort_keys=True,
)
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 3e543445..67e2e158 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -105,8 +105,8 @@ class UserSession:
if user_cookie:
self.logged_in = False
self.record = dict(login_time=time.time(),
- user_type="anon",
- user_id=str(uuid.uuid4()))
+ user_type="anon",
+ user_id=str(uuid.uuid4()))
Redis.hmset(self.redis_key, self.record)
Redis.expire(self.redis_key, THIRTY_DAYS)
@@ -117,8 +117,8 @@ class UserSession:
return None
else:
self.record = dict(login_time=time.time(),
- user_type="anon",
- user_id=str(uuid.uuid4()))
+ user_type="anon",
+ user_id=str(uuid.uuid4()))
Redis.hmset(self.redis_key, self.record)
Redis.expire(self.redis_key, THIRTY_DAYS)
else:
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index 21516b30..f96892a0 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -70,7 +70,7 @@ class WGCNA:
self.trait_db_list = [trait.strip()
for trait in requestform['trait_list'].split(',')]
print(("Retrieved phenotype data from database",
- requestform['trait_list']))
+ requestform['trait_list']))
helper_functions.get_trait_db_obs(self, self.trait_db_list)
# self.input contains the phenotype values we need to send to R
--
cgit v1.2.3
From 99f8bdbb70e4e00df6671c3f20db4857ffa96d6f Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 30 Apr 2021 13:15:10 +0300
Subject: autopep8: Run autopep8 100 times with target rules
Rules used are:
E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242,
E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306,
E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121,
E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
---
wqflask/base/webqtlConfig.py | 2 +-
wqflask/maintenance/quantile_normalize.py | 2 +-
.../marker_regression/test_qtlreaper_mapping.py | 7 +-
.../wqflask/marker_regression/test_rqtl_mapping.py | 4 +-
wqflask/utility/Plot.py | 5 +-
wqflask/utility/elasticsearch_tools.py | 2 +-
wqflask/utility/svg.py | 50 ++++-----
wqflask/wqflask/api/mapping.py | 3 +-
wqflask/wqflask/api/router.py | 30 +++---
wqflask/wqflask/collect.py | 8 +-
wqflask/wqflask/correlation/corr_scatter_plot.py | 4 +-
wqflask/wqflask/correlation/show_corr_results.py | 34 +++---
.../wqflask/correlation_matrix/show_corr_matrix.py | 2 +-
wqflask/wqflask/ctl/ctl_analysis.py | 2 +-
wqflask/wqflask/group_manager.py | 8 +-
wqflask/wqflask/interval_analyst/GeneUtil.py | 3 +-
.../marker_regression/display_mapping_results.py | 120 ++++++++++-----------
wqflask/wqflask/marker_regression/gemma_mapping.py | 2 +-
.../wqflask/marker_regression/qtlreaper_mapping.py | 9 +-
wqflask/wqflask/marker_regression/rqtl_mapping.py | 10 +-
wqflask/wqflask/marker_regression/run_mapping.py | 3 +-
wqflask/wqflask/model.py | 4 +-
wqflask/wqflask/resource_manager.py | 2 +-
wqflask/wqflask/search_results.py | 2 +-
wqflask/wqflask/snp_browser/snp_browser.py | 4 +-
wqflask/wqflask/user_login.py | 6 +-
wqflask/wqflask/user_manager.py | 6 +-
wqflask/wqflask/views.py | 2 +-
28 files changed, 172 insertions(+), 164 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 872b52eb..39947158 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -15,7 +15,7 @@ from utility.tools import valid_path, mk_dir, assert_dir, assert_writable_dir, f
DEBUG = 1
# USER privilege
-USERDICT = {'guest': 1, 'user': 2, 'admin': 3, 'root':4}
+USERDICT = {'guest': 1, 'user': 2, 'admin': 3, 'root': 4}
# Set privileges
SUPER_PRIVILEGES = {'data': 'edit', 'metadata': 'edit', 'admin': 'edit-admins'}
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 88bb2cb5..0cc963e5 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -123,7 +123,7 @@ if __name__ == '__main__':
success, _ = bulk(es, set_data(sys.argv[1]))
response = es.search(
- index="traits", doc_type="trait", body = {
+ index="traits", doc_type="trait", body={
"query": {"match": {"name": "ENSMUSG00000028982"}}
}
)
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index 93848a84..8b4337ec 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -9,13 +9,14 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
class TestQtlReaperMapping(unittest.TestCase):
@mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
def test_gen_pheno_txt_file(self):
- vals = ["V1", "x", "V4", "V3","x"]
- samples = ["S1", "S2", "S3", "S4","S5"]
+ vals = ["V1", "x", "V4", "V3", "x"]
+ samples = ["S1", "S2", "S3", "S4", "S5"]
trait_filename = "trait_file"
with mock.patch("builtins.open", mock.mock_open())as mock_open:
gen_pheno_txt_file(samples=samples, vals=vals,
trait_filename=trait_filename)
- mock_open.assert_called_once_with("/home/user/data/gn2/trait_file.txt", "w")
+ mock_open.assert_called_once_with(
+ "/home/user/data/gn2/trait_file.txt", "w")
filehandler = mock_open()
write_calls = [mock.call('Trait\t'), mock.call(
'S1\tS3\tS4\n'), mock.call('T1\t'), mock.call('V1\tV4\tV3')]
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 68686e27..91d2c587 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -28,7 +28,7 @@ class TestRqtlMapping(unittest.TestCase):
def test_sanitize_rqtl_phenotype(self):
"""test for sanitizing rqtl phenotype"""
- vals = ['f', "x", "r", "x","x"]
+ vals = ['f', "x", "r", "x", "x"]
results = sanitize_rqtl_phenotype(vals)
expected_phenotype_string = 'c(f,NA,r,NA,NA)'
@@ -36,7 +36,7 @@ class TestRqtlMapping(unittest.TestCase):
def test_sanitize_rqtl_names(self):
"""test for sanitzing rqtl names"""
- vals = ['f', "x", "r", "x","x"]
+ vals = ['f', "x", "r", "x", "x"]
expected_sanitized_name = "c('f',NA,'r',NA,NA)"
results = sanitize_rqtl_names(vals)
self.assertEqual(expected_sanitized_name, results)
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 37a8a1a5..9b2c6735 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -188,7 +188,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
for i in range(int(stepX) + 1):
xc = xLeftOffset + (x - xLow) * xScale
im_drawer.line(
- xy=((xc, yTopOffset + plotHeight), (xc, yTopOffset + plotHeight + 5)),
+ xy=((xc, yTopOffset + plotHeight),
+ (xc, yTopOffset + plotHeight + 5)),
fill=axesColor)
strX = cformat(d=x, rank=0)
im_drawer.text(
@@ -217,7 +218,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
text=XLabel,
xy=(xLeftOffset + (
plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0,
- yTopOffset + plotHeight + yBottomOffset-10),
+ yTopOffset + plotHeight + yBottomOffset - 10),
font=labelFont, fill=labelColor)
if YLabel:
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index e56c22eb..eae3ba03 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -105,7 +105,7 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
item_details = None
try:
response = es.search(
- index=index, doc_type=doc_type, body = {
+ index=index, doc_type=doc_type, body={
"query": {"match": {column_name: column_value}}
})
if len(response["hits"]["hits"]) > 0:
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index bc3bc833..eddb97da 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -229,13 +229,13 @@ class pathdata:
def bezier(self, x1, y1, x2, y2, x, y):
"""bezier with xy1 and xy2 to xy absolut"""
- self.path.append('C' + str(x1) + ','+str(y1)+' '+str(x2)
- + ',' + str(y2) + ' '+str(x)+','+str(y))
+ self.path.append('C' + str(x1) + ',' + str(y1) + ' ' + str(x2)
+ + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
def relbezier(self, x1, y1, x2, y2, x, y):
"""bezier with xy1 and xy2 to xy relative"""
- self.path.append('c' + str(x1) + ','+str(y1)+' '+str(x2)
- + ',' + str(y2) + ' '+str(x)+','+str(y))
+ self.path.append('c' + str(x1) + ',' + str(y1) + ' ' + str(x2)
+ + ',' + str(y2) + ' ' + str(x) + ',' + str(y))
def smbezier(self, x2, y2, x, y):
"""smooth bezier with xy2 to xy absolut"""
@@ -267,13 +267,13 @@ class pathdata:
def ellarc(self, rx, ry, xrot, laf, sf, x, y):
"""elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy absolut"""
- self.path.append('A' + str(rx) + ','+str(ry)+' '+str(xrot)
- + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
+ self.path.append('A' + str(rx) + ',' + str(ry) + ' ' + str(xrot)
+ + ' ' + str(laf) + ' ' + str(sf) + ' ' + str(x) + ' ' + str(y))
def relellarc(self, rx, ry, xrot, laf, sf, x, y):
"""elliptival arc with rx and ry rotating with xrot using large-arc-flag and sweep-flag to xy relative"""
- self.path.append('a' + str(rx) + ','+str(ry)+' '+str(xrot)
- + ' ' + str(laf) + ' '+str(sf)+' '+str(x)+' '+str(y))
+ self.path.append('a' + str(rx) + ',' + str(ry) + ' ' + str(xrot)
+ + ' ' + str(laf) + ' ' + str(sf) + ' ' + str(x) + ' ' + str(y))
def __repr__(self):
return ' '.join(self.path)
@@ -471,7 +471,7 @@ class ellipse(SVGelement):
an ellipse is defined as a center and a x and y radius.
"""
- def __init__(self, cx=None, cy=None, rx=None, ry=None,fill=None,stroke=None,stroke_width=None,**args):
+ def __init__(self, cx=None, cy=None, rx=None, ry=None, fill=None, stroke=None, stroke_width=None, **args):
if rx == None or ry == None:
raise ValueError('both rx and ry are required')
@@ -494,7 +494,7 @@ class circle(SVGelement):
The circle creates an element using a x, y and radius values eg
"""
- def __init__(self, cx=None, cy=None, r=None, fill=None,stroke=None,stroke_width=None,**args):
+ def __init__(self, cx=None, cy=None, r=None, fill=None, stroke=None, stroke_width=None, **args):
if r == None:
raise ValueError('r is required')
SVGelement.__init__(self, 'circle', {'r': r}, **args)
@@ -527,7 +527,7 @@ class line(SVGelement):
A line is defined by a begin x,y pair and an end x,y pair
"""
- def __init__(self, x1=None, y1=None, x2=None, y2=None,stroke=None,stroke_width=None,**args):
+ def __init__(self, x1=None, y1=None, x2=None, y2=None, stroke=None, stroke_width=None, **args):
SVGelement.__init__(self, 'line', **args)
if x1 != None:
self.attributes['x1'] = x1
@@ -549,7 +549,7 @@ class polyline(SVGelement):
a polyline is defined by a list of xy pairs
"""
- def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
+ def __init__(self, points, fill=None, stroke=None, stroke_width=None, **args):
SVGelement.__init__(self, 'polyline', {
'points': _xypointlist(points)}, **args)
if fill != None:
@@ -566,7 +566,7 @@ class polygon(SVGelement):
a polygon is defined by a list of xy pairs
"""
- def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
+ def __init__(self, points, fill=None, stroke=None, stroke_width=None, **args):
SVGelement.__init__(
self, 'polygon', {'points': _xypointlist(points)}, **args)
if fill != None:
@@ -583,7 +583,7 @@ class path(SVGelement):
a path is defined by a path object and optional width, stroke and fillcolor
"""
- def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None,id=None,**args):
+ def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None, id=None, **args):
SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args)
if stroke != None:
self.attributes['stroke'] = stroke
@@ -601,7 +601,7 @@ class text(SVGelement):
a text element can bge used for displaying text on the screen
"""
- def __init__(self, x=None, y=None, text=None, font_size=None,font_family=None,text_anchor=None,**args):
+ def __init__(self, x=None, y=None, text=None, font_size=None, font_family=None, text_anchor=None, **args):
SVGelement.__init__(self, 'text', **args)
if x != None:
self.attributes['x'] = x
@@ -637,7 +637,7 @@ class pattern(SVGelement):
in x and y to cover the areas to be painted.
"""
- def __init__(self, x=None, y=None, width=None, height=None,patternUnits=None,**args):
+ def __init__(self, x=None, y=None, width=None, height=None, patternUnits=None, **args):
SVGelement.__init__(self, 'pattern', **args)
if x != None:
self.attributes['x'] = x
@@ -684,7 +684,7 @@ class lineargradient(SVGelement):
stop elements van be added to define the gradient colors.
"""
- def __init__(self, x1=None, y1=None, x2=None, y2=None,id=None,**args):
+ def __init__(self, x1=None, y1=None, x2=None, y2=None, id=None, **args):
SVGelement.__init__(self, 'linearGradient', **args)
if x1 != None:
self.attributes['x1'] = x1
@@ -705,7 +705,7 @@ class radialgradient(SVGelement):
stop elements van be added to define the gradient colors.
"""
- def __init__(self, cx=None, cy=None, r=None, fx=None,fy=None,id=None,**args):
+ def __init__(self, cx=None, cy=None, r=None, fx=None, fy=None, id=None, **args):
SVGelement.__init__(self, 'radialGradient', **args)
if cx != None:
self.attributes['cx'] = cx
@@ -749,11 +749,11 @@ class image(SVGelement):
adds an image to the drawing. Supported formats are .png, .jpg and .svg.
"""
- def __init__(self, url, x=None, y=None, width=None,height=None,**args):
+ def __init__(self, url, x=None, y=None, width=None, height=None, **args):
if width == None or height == None:
raise ValueError('both height and width are required')
SVGelement.__init__(
- self, 'image', {'xlink:href': url, 'width': width, 'height':height}, **args)
+ self, 'image', {'xlink:href': url, 'width': width, 'height': height}, **args)
if x != None:
self.attributes['x'] = x
if y != None:
@@ -777,7 +777,7 @@ class marker(SVGelement):
add an element to it which should be used as a marker.
"""
- def __init__(self, id=None, viewBox=None, refx=None, refy=None,markerWidth=None,markerHeight=None,**args):
+ def __init__(self, id=None, viewBox=None, refx=None, refy=None, markerWidth=None, markerHeight=None, **args):
SVGelement.__init__(self, 'marker', **args)
if id != None:
self.attributes['id'] = id
@@ -851,7 +851,7 @@ class use(SVGelement):
references a symbol by linking to its id and its position, height and width
"""
- def __init__(self, link, x=None, y=None, width=None,height=None,**args):
+ def __init__(self, link, x=None, y=None, width=None, height=None, **args):
SVGelement.__init__(self, 'use', {'xlink:href': link}, **args)
if x != None:
self.attributes['x'] = x
@@ -904,7 +904,7 @@ class animate(SVGelement):
animates an attribute.
"""
- def __init__(self, attribute, fr=None, to=None, dur=None,**args):
+ def __init__(self, attribute, fr=None, to=None, dur=None, **args):
SVGelement.__init__(
self, 'animate', {'attributeName': attribute}, **args)
if fr != None:
@@ -935,7 +935,7 @@ class animateTransform(SVGelement):
transform an element from and to a value.
"""
- def __init__(self, type=None, fr=None, to=None, dur=None,**args):
+ def __init__(self, type=None, fr=None, to=None, dur=None, **args):
SVGelement.__init__(self, 'animateTransform', {
'attributeName': 'transform'}, **args)
# As far as I know the attributeName is always transform
@@ -955,7 +955,7 @@ class animateColor(SVGelement):
Animates the color of a element
"""
- def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args):
+ def __init__(self, attribute, type=None, fr=None, to=None, dur=None, **args):
SVGelement.__init__(self, 'animateColor', {
'attributeName': attribute}, **args)
if type != None:
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index cbef96eb..f8b0d8bd 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -53,7 +53,8 @@ def do_mapping_for_api(start_vars):
header_row = ["name", "chr", "cM", "lod_score"]
if mapping_params['num_perm'] > 0:
_sperm_output, _suggestive, _significant, result_markers = rqtl_mapping.run_rqtl_geno(vals, dataset, mapping_params['rqtl_method'], mapping_params['rqtl_model'],
- mapping_params['perm_check'], mapping_params['num_perm'],
+ mapping_params['perm_check'], mapping_params[
+ 'num_perm'],
mapping_params['do_control'], mapping_params[
'control_marker'],
mapping_params['manhattan_plot'], mapping_params['pair_scan'])
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 9d3446db..aec74c9e 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -98,8 +98,8 @@ def get_groups_list(species_name=None):
"Name": group[3],
"FullName": group[4],
"public": group[5],
- "MappingMethodId": group[6],
- "GeneticType": group[7]
+ "MappingMethodId": group[6],
+ "GeneticType": group[7]
}
groups_list.append(group_dict)
@@ -143,8 +143,8 @@ def get_group_info(group_name, species_name=None, file_format="json"):
"Name": group[3],
"FullName": group[4],
"public": group[5],
- "MappingMethodId": group[6],
- "GeneticType": group[7]
+ "MappingMethodId": group[6],
+ "GeneticType": group[7]
}
return flask.jsonify(group_dict)
@@ -192,11 +192,11 @@ def get_datasets_for_group(group_name, species_name=None):
"Short_Abbreviation": dataset[3],
"Long_Abbreviation": dataset[4],
"FullName": dataset[5],
- "ShortName": dataset[6],
- "CreateTime": dataset[7],
- "public": dataset[8],
- "confidentiality": dataset[9],
- "DataScale": dataset[10]
+ "ShortName": dataset[6],
+ "CreateTime": dataset[7],
+ "public": dataset[8],
+ "confidentiality": dataset[9],
+ "DataScale": dataset[10]
}
datasets_list.append(dataset_dict)
@@ -249,10 +249,10 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
"full_name": dataset[2],
"short_name": dataset[3],
"data_scale": dataset[4],
- "tissue_id": dataset[5],
- "tissue": dataset[6],
- "public": dataset[7],
- "confidential": dataset[8]
+ "tissue_id": dataset[5],
+ "tissue": dataset[6],
+ "public": dataset[7],
+ "confidential": dataset[8]
}
datasets_list.append(dataset_dict)
@@ -286,7 +286,7 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
"description": dataset[2],
"pubmed_id": dataset[5],
"title": dataset[6],
- "year": dataset[7]
+ "year": dataset[7]
}
elif dataset[4]:
dataset_dict = {
@@ -777,7 +777,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
i += 1
csv_writer = csv.writer(
- si, delimiter="\t", escapechar="\\", quoting = csv.QUOTE_NONE)
+ si, delimiter="\t", escapechar="\\", quoting=csv.QUOTE_NONE)
else:
return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
elif file_format == "rqtl2":
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 58518639..01274ba9 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -77,13 +77,13 @@ def collections_add():
return render_template("collections/add.html",
traits=traits,
collections=collections,
- )
+ )
else:
hash = request.args['hash']
return render_template("collections/add.html",
hash=hash,
collections=collections,
- )
+ )
@app.route("/collections/new")
@@ -147,7 +147,7 @@ def list_collections():
return render_template("collections/list.html",
params=params,
collections=user_collections,
- )
+ )
@app.route("/collections/remove", methods=('POST',))
@@ -226,7 +226,7 @@ def view_collection():
else:
return render_template("collections/view.html",
**collection_info
- )
+ )
@app.route("/collections/change_name", methods=('POST',))
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 4f756f58..cafb9265 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -18,12 +18,12 @@ class CorrScatterPlot:
def __init__(self, params):
if "Temp" in params['dataset_1']:
self.dataset_1 = data_set.create_dataset(
- dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_1'].split("_")[1])
+ dataset_name="Temp", dataset_type="Temp", group_name=params['dataset_1'].split("_")[1])
else:
self.dataset_1 = data_set.create_dataset(params['dataset_1'])
if "Temp" in params['dataset_2']:
self.dataset_2 = data_set.create_dataset(
- dataset_name="Temp", dataset_type="Temp", group_name = params['dataset_2'].split("_")[1])
+ dataset_name="Temp", dataset_type="Temp", group_name=params['dataset_2'].split("_")[1])
else:
self.dataset_2 = data_set.create_dataset(params['dataset_2'])
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index aa39bc5c..9b0b6118 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -79,7 +79,7 @@ class CorrelationResults:
with Bench("Doing correlations"):
if start_vars['dataset'] == "Temp":
self.dataset = data_set.create_dataset(
- dataset_name="Temp", dataset_type="Temp", group_name = start_vars['group'])
+ dataset_name="Temp", dataset_type="Temp", group_name=start_vars['group'])
self.trait_id = start_vars['trait_id']
self.this_trait = create_trait(dataset=self.dataset,
name=self.trait_id,
@@ -609,14 +609,14 @@ def get_header_fields(data_type, corr_method):
'Location',
'Mean',
'Sample rho',
- 'N',
- 'Sample p(rho)',
- 'Lit rho',
- 'Tissue rho',
- 'Tissue p(rho)',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
+ 'N',
+ 'Sample p(rho)',
+ 'Lit rho',
+ 'Tissue rho',
+ 'Tissue p(rho)',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect']
else:
header_fields = ['Index',
'Record',
@@ -625,14 +625,14 @@ def get_header_fields(data_type, corr_method):
'Location',
'Mean',
'Sample r',
- 'N',
- 'Sample p(r)',
- 'Lit r',
- 'Tissue r',
- 'Tissue p(r)',
- 'Max LRS',
- 'Max LRS Location',
- 'Additive Effect']
+ 'N',
+ 'Sample p(r)',
+ 'Lit r',
+ 'Tissue r',
+ 'Tissue p(r)',
+ 'Max LRS',
+ 'Max LRS Location',
+ 'Additive Effect']
elif data_type == "Publish":
if corr_method == "spearman":
header_fields = ['Index',
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index c1bf3daa..3a54a218 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -211,7 +211,7 @@ class CorrelationMatrix:
this_group_name = self.trait_list[0][1].group.name
temp_dataset = data_set.create_dataset(
- dataset_name="Temp", dataset_type="Temp", group_name = this_group_name)
+ dataset_name="Temp", dataset_type="Temp", group_name=this_group_name)
temp_dataset.group.get_samplelist()
for i, pca_trait in enumerate(pca_traits):
trait_id = "PCA" + str(i + 1) + "_" + temp_dataset.group.species + "_" + \
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index a0fb34d8..bb928ec5 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -154,7 +154,7 @@ class CTL:
# Perform the CTL scan
res = self.r_CTLscan(rGeno, rPheno, strategy=strategy,
- nperm=nperm, parametric = parametric, nthreads=6)
+ nperm=nperm, parametric=parametric, nthreads=6)
# Get significant interactions
significant = self.r_CTLsignificant(res, significance=significance)
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index b7e7e38a..04a100ba 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -120,14 +120,16 @@ def add_or_edit_group():
if "admin_emails_to_add" in params:
admin_emails = params['admin_emails_to_add'].split(",")
for email in admin_emails:
- user_details = get_user_by_unique_column("email_address", email)
+ user_details = get_user_by_unique_column(
+ "email_address", email)
if user_details:
admin_user_ids.add(user_details['user_id'])
#send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins")
if "member_emails_to_add" in params:
member_emails = params['member_emails_to_add'].split(",")
for email in member_emails:
- user_details = get_user_by_unique_column("email_address", email)
+ user_details = get_user_by_unique_column(
+ "email_address", email)
if user_details:
member_user_ids.add(user_details['user_id'])
#send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
@@ -156,7 +158,7 @@ def send_group_invites(group_id, user_email_list=[], user_type="members"):
continue
else:
send_verification_email(user_details, template_name="email/group_verification.txt",
- key_prefix="verification_code", subject = "You've been invited to join a GeneNetwork user group")
+ key_prefix="verification_code", subject="You've been invited to join a GeneNetwork user group")
else:
temp_password = ''.join(random.choice(
string.ascii_uppercase + string.digits) for _ in range(6))
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 04980281..5e86ae31 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -60,7 +60,8 @@ def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
newdict["snpDensity"] = newdict["snpCount"] = 0
try:
- newdict['GeneLength'] = 1000.0 * (newdict['TxEnd'] - newdict['TxStart'])
+ newdict['GeneLength'] = 1000.0 * \
+ (newdict['TxEnd'] - newdict['TxStart'])
except:
pass
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index f3b1b1fc..5bf8822a 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -591,7 +591,7 @@ class DisplayMappingResults:
intCanvas = Image.new("RGBA", size=(self.graphWidth, self.graphHeight))
with Bench("Drawing Plot"):
gifmap = self.plotIntMapping(
- intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm)
+ intCanvas, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm)
self.gifmap = gifmap.__str__()
@@ -610,7 +610,7 @@ class DisplayMappingResults:
intCanvasX2 = Image.new("RGBA", size=(
self.graphWidth * 2, self.graphHeight * 2))
gifmapX2 = self.plotIntMapping(
- intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm= showLocusForm, zoom=2)
+ intCanvasX2, startMb=self.startMb, endMb=self.endMb, showLocusForm=showLocusForm, zoom=2)
intCanvasX2.save(
"{}.png".format(
os.path.join(webqtlConfig.GENERATED_IMAGE_DIR,
@@ -628,8 +628,8 @@ class DisplayMappingResults:
name=showLocusForm,
submit=HtmlGenWrapper.create_input_tag(type_='hidden'))
- hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet+ \
- "Geno",'CellID':'_', 'RISet':fd.RISet, 'incparentsf1':'ON'}
+ hddn = {'FormID': 'showDatabase', 'ProbeSetID': '_', 'database': fd.RISet + \
+ "Geno", 'CellID': '_', 'RISet': fd.RISet, 'incparentsf1': 'ON'}
for key in hddn.keys():
showLocusForm.append(HtmlGenWrapper.create_input_tag(
name=key, value=hddn[key], type_='hidden'))
@@ -651,7 +651,7 @@ class DisplayMappingResults:
btminfo.append(
'Mapping using genotype data as a trait will result in infinity LRS at one locus. In order to display the result properly, all LRSs higher than 100 are capped at 100.')
- def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb= None, endMb = None, showLocusForm = ""):
+ def plotIntMapping(self, canvas, offset=(80, 120, 90, 100), zoom=1, startMb=None, endMb=None, showLocusForm=""):
im_drawer = ImageDraw.Draw(canvas)
# calculating margins
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -730,7 +730,7 @@ class DisplayMappingResults:
zoom=zoom, startMb=startMb, endMb=endMb)
if self.SNPChecked:
self.drawSNPTrackNew(
- canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb = endMb)
+ canvas, offset=newoffset, zoom=2 * zoom, startMb=startMb, endMb=endMb)
# BEGIN HaplotypeAnalyst
if self.haplotypeAnalystChecked:
self.drawHaplotypeBand(
@@ -758,7 +758,7 @@ class DisplayMappingResults:
return gifmap
- def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+ def drawBootStrapResult(self, canvas, nboot, drawAreaHeight, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -873,14 +873,14 @@ class DisplayMappingResults:
font=VERDANA_FILE, size=13 * fontZoom)
im_drawer.rectangle(
xy=((canvas.size[0] - bootOffset, yZero - bootHeightThresh),
- (canvas.size[0] - bootOffset - 15*zoom, yZero)),
+ (canvas.size[0] - bootOffset - 15 * zoom, yZero)),
fill=YELLOW, outline=BLACK)
im_drawer.line(
xy=((canvas.size[0] - bootOffset + 4, yZero),
(canvas.size[0] - bootOffset, yZero)),
fill=BLACK)
TEXT_Y_DISPLACEMENT = -8
- im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, yZero+TEXT_Y_DISPLACEMENT), text='0%',
+ im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, yZero + TEXT_Y_DISPLACEMENT), text='0%',
font=bootScaleFont, fill=BLACK)
for item in bootScale:
@@ -891,7 +891,7 @@ class DisplayMappingResults:
xy=((canvas.size[0] - bootOffset + 4, bootY),
(canvas.size[0] - bootOffset, bootY)),
fill=BLACK)
- im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, bootY+TEXT_Y_DISPLACEMENT),
+ im_drawer.text(xy=(canvas.size[0] - bootOffset + 10, bootY + TEXT_Y_DISPLACEMENT),
text='%2.1f' % item, font=bootScaleFont, fill=BLACK)
if self.legendChecked:
@@ -910,7 +910,7 @@ class DisplayMappingResults:
text='Frequency of the Peak LRS',
font=smallLabelFont, fill=BLACK)
- def drawProbeSetPosition(self, canvas, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+ def drawProbeSetPosition(self, canvas, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
im_drawer = ImageDraw.Draw(canvas)
if len(self.traitList) != 1:
return
@@ -987,7 +987,7 @@ class DisplayMappingResults:
draw_open_polygon(canvas, xy=traitPixel, outline=BLACK,
fill=self.TRANSCRIPT_LOCATION_COLOR)
- def drawSNPTrackNew(self, canvas, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+ def drawSNPTrackNew(self, canvas, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1 or not self.diffCol:
return
@@ -1059,7 +1059,7 @@ class DisplayMappingResults:
im_drawer.rectangle(
xy=((rightShift, yPaddingTop + kstep * 15),
- (rectWidth + rightShift, yPaddingTop + 10+kstep*15)),
+ (rectWidth + rightShift, yPaddingTop + 10 + kstep * 15)),
fill=thisLRSColor, outline=BLACK)
im_drawer.text(
text=name, xy=(rectWidth + 2 + rightShift,
@@ -1303,7 +1303,7 @@ class DisplayMappingResults:
text=string4, xy=(xLeftOffset, y_constant * fontZoom),
font=labelFont, fill=labelColor)
- def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+ def drawGeneBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
return
@@ -1434,7 +1434,7 @@ class DisplayMappingResults:
xy=(
(geneStartPix, geneYLocation + \
self.EACH_GENE_HEIGHT / 2 * zoom),
- (geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 *zoom)),
+ (geneEndPix, geneYLocation + self.EACH_GENE_HEIGHT / 2 * zoom)),
fill=outlineColor, width=1)
# draw the arrows
@@ -1558,7 +1558,7 @@ class DisplayMappingResults:
target="_blank"))
# BEGIN HaplotypeAnalyst
- def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+ def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
if self.plotScale != 'physic' or self.selectedChr == -1 or not self.geneCol:
return
@@ -1630,7 +1630,7 @@ class DisplayMappingResults:
geneStartPix = xLeftOffset + plotXScale * \
(float(txStart) - startMb) - 0
geneEndPix = xLeftOffset + plotXScale * \
- (float(txEnd) - startMb) + 0
+ (float(txEnd) - startMb) + 0
if oldgeneEndPix >= xLeftOffset:
drawStart = oldgeneEndPix + 4
@@ -1707,19 +1707,19 @@ class DisplayMappingResults:
im_drawer.line(
xy=((drawStart,
- geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
(drawEnd,
- geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
- fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
+ geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom)),
+ fill=mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
fillColor = BLACK
outlineColor = BLACK
if lastGene == 0:
im_drawer.rectangle(
xy=((geneStartPix,
- geneYLocation + 2 * ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
(geneEndPix,
- geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)),
+ geneYLocation + 2 * ind * self.EACH_GENE_HEIGHT + 2 * self.EACH_GENE_HEIGHT * zoom)),
outline=outlineColor, fill=fillColor)
COORDS = "%d, %d, %d, %d" % (
@@ -1741,10 +1741,10 @@ class DisplayMappingResults:
mylineColor = self.HAPLOTYPE_RECOMBINATION
im_drawer.line(
xy=((plotRight,
- geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
(drawEnd,
- geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
- fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
+ geneYLocation + 7 + 2 * ind * self.EACH_GENE_HEIGHT * zoom)),
+ fill=mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
if lastGene == 0:
draw_rotated_text(
@@ -1752,7 +1752,7 @@ class DisplayMappingResults:
font=ImageFont.truetype(font=VERDANA_FILE,
size=12),
xy=(geneStartPix,
- geneYLocation + 17 + 2*maxind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 17 + 2 * maxind * self.EACH_GENE_HEIGHT * zoom),
fill=BLACK, angle=-90)
oldgeneEndPix = geneEndPix
@@ -1778,21 +1778,21 @@ class DisplayMappingResults:
im_drawer.text(
text="%s" % (samplelist[j]),
xy=((xLeftOffset + plotWidth + 10),
- geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 11 + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
font=ImageFont.truetype(
font=VERDANA_FILE, size=12),
fill=BLACK)
im_drawer.text(
text="%2.2f" % (expr),
xy=((xLeftOffset + plotWidth + 60),
- geneYLocation + 11 + 2*ind*self.EACH_GENE_HEIGHT*zoom),
+ geneYLocation + 11 + 2 * ind * self.EACH_GENE_HEIGHT * zoom),
font=ImageFont.truetype(
font=VERDANA_FILE, size=12),
fill=BLACK)
# END HaplotypeAnalyst
- def drawClickBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+ def drawClickBand(self, canvas, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
im_drawer = ImageDraw.Draw(canvas)
if self.plotScale != 'physic' or self.selectedChr == -1:
return
@@ -1817,8 +1817,8 @@ class DisplayMappingResults:
numBasesCurrentlyOnScreen = self.kONE_MILLION * \
abs(startMb - endMb) # Number of bases on screen now
- flankingWidthInBases = int (
- min((float(numBasesCurrentlyOnScreen) / 2.0), (5*self.kONE_MILLION)))
+ flankingWidthInBases = int(
+ min((float(numBasesCurrentlyOnScreen) / 2.0), (5 * self.kONE_MILLION)))
webqtlZoomWidth = numBasesCurrentlyOnScreen / 16.0
# Flanking width should be such that we either zoom in to a 10 million base region, or we show the clicked region at the same scale as we are currently seeing.
@@ -1990,7 +1990,7 @@ class DisplayMappingResults:
# end of drawBrowserClickableRegions
pass
- def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+ def drawXAxis(self, canvas, drawAreaHeight, gifmap, plotXScale, showLocusForm, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -2087,7 +2087,7 @@ class DisplayMappingResults:
xy=(
xLeftOffset + (plotWidth - im_drawer.textsize(
"Megabases", font=megabaseLabelFont)[0]) / 2,
- strYLoc + MBLabelFont.font.height + 10*(zoom%2)),
+ strYLoc + MBLabelFont.font.height + 10 * (zoom % 2)),
font=megabaseLabelFont, fill=BLACK)
pass
else:
@@ -2110,7 +2110,7 @@ class DisplayMappingResults:
thisChr.append(
[_locus.name, _locus.cM - Locus0CM])
else:
- for j in (0, nLoci / 4, nLoci / 2, nLoci*3/4, -1):
+ for j in (0, nLoci / 4, nLoci / 2, nLoci * 3 / 4, -1):
while _chr[j].name == ' - ':
j += 1
if _chr[j].cM != preLpos:
@@ -2162,23 +2162,23 @@ class DisplayMappingResults:
yZero + 25)),
fill=lineColor)
im_drawer.line(
- xy=((xLeftOffset + offsetA, yZero + 25), (xLeftOffset+offsetA,\
- yZero + 40 + Zorder*(LRectWidth+3))),
+ xy=((xLeftOffset + offsetA, yZero + 25), (xLeftOffset + offsetA,\
+ yZero + 40 + Zorder * (LRectWidth + 3))),
fill=lineColor)
rectColor = ORANGE
else:
im_drawer.line(
- xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)-3), (\
- xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3))),
+ xy=((xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3) - 3), (\
+ xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3))),
fill=lineColor)
rectColor = DEEPPINK
im_drawer.rectangle(
- xy=((xLeftOffset + offsetA, yZero + 40+Zorder*(LRectWidth+3)),
+ xy=((xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3)),
(xLeftOffset + offsetA - LRectHeight,
- yZero + 40 + Zorder*(LRectWidth+3)+LRectWidth)),
+ yZero + 40 + Zorder * (LRectWidth + 3) + LRectWidth)),
outline=rectColor, fill=rectColor, width=0)
- COORDS = "%d,%d,%d,%d" % (xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
- xLeftOffset + offsetA, yZero +40+Zorder*(LRectWidth+3)+LRectWidth)
+ COORDS = "%d,%d,%d,%d" % (xLeftOffset + offsetA - LRectHeight, yZero + 40 + Zorder * (LRectWidth + 3),\
+ xLeftOffset + offsetA, yZero + 40 + Zorder * (LRectWidth + 3) + LRectWidth)
HREF = "/show_trait?trait_id=%s&dataset=%s" % (
Lname, self.dataset.group.name + "Geno")
#HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
@@ -2203,13 +2203,13 @@ class DisplayMappingResults:
text="Centimorgans",
xy=(xLeftOffset + (plotWidth - im_drawer.textsize(
"Centimorgans", font=centimorganLabelFont)[0]) / 2,
- strYLoc + MBLabelFont.font.height + 10 * (zoom %2)),
+ strYLoc + MBLabelFont.font.height + 10 * (zoom % 2)),
font=centimorganLabelFont, fill=BLACK)
im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset + plotWidth, yZero)),
fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
- def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
+ def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb=None, endMb=None):
im_drawer = ImageDraw.Draw(canvas)
xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
@@ -2364,7 +2364,7 @@ class DisplayMappingResults:
TEXT_Y_DISPLACEMENT = -10
im_drawer.text(
text=scaleStr,
- xy=(xLeftOffset - 4 - im_drawer.textsize(scaleStr, font=LRSScaleFont)[0]-5,
+ xy=(xLeftOffset - 4 - im_drawer.textsize(scaleStr, font=LRSScaleFont)[0] - 5,
yLRS + TEXT_Y_DISPLACEMENT),
font=LRSScaleFont, fill=self.LRS_COLOR)
@@ -2479,7 +2479,7 @@ class DisplayMappingResults:
if k > 0:
Xc0, Yc0 = AdditiveCoordXY[k - 1]
Xc, Yc = aPoint
- if (Yc0 - yZero) * (Yc-yZero) < 0:
+ if (Yc0 - yZero) * (Yc - yZero) < 0:
if Xc == Xc0: # genotype , locus distance is 0
Xcm = Xc
else:
@@ -2509,7 +2509,7 @@ class DisplayMappingResults:
fill=plusColor, width=lineWidth
# , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
- elif (Yc0 - yZero) * (Yc-yZero) > 0:
+ elif (Yc0 - yZero) * (Yc - yZero) > 0:
if Yc < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xc, Yc)),
@@ -2660,7 +2660,7 @@ class DisplayMappingResults:
if k > 0:
Xc0, Yc0 = AdditiveCoordXY[k - 1]
Xc, Yc = aPoint
- if (Yc0 - yZero) * (Yc-yZero) < 0:
+ if (Yc0 - yZero) * (Yc - yZero) < 0:
if Xc == Xc0: # genotype , locus distance is 0
Xcm = Xc
else:
@@ -2689,7 +2689,7 @@ class DisplayMappingResults:
fill=plusColor, width=lineWidth
# , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
- elif (Yc0 - yZero) * (Yc-yZero) > 0:
+ elif (Yc0 - yZero) * (Yc - yZero) > 0:
if Yc < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xc, Yc)), fill=plusColor,
@@ -2726,7 +2726,7 @@ class DisplayMappingResults:
if k > 0:
Xc0, Yc0 = DominanceCoordXY[k - 1]
Xc, Yc = aPoint
- if (Yc0 - yZero) * (Yc-yZero) < 0:
+ if (Yc0 - yZero) * (Yc - yZero) < 0:
if Xc == Xc0: # genotype , locus distance is 0
Xcm = Xc
else:
@@ -2754,7 +2754,7 @@ class DisplayMappingResults:
fill=plusColor, width=lineWidth
# , clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
- elif (Yc0 - yZero) * (Yc-yZero) > 0:
+ elif (Yc0 - yZero) * (Yc - yZero) > 0:
if Yc < yZero:
im_drawer.line(
xy=((Xc0, Yc0), (Xc, Yc)),
@@ -2805,8 +2805,8 @@ class DisplayMappingResults:
scaleStr = "%2.3f" % item
im_drawer.text(
text=scaleStr,
- xy= (xLeftOffset + plotWidth + 6,
- additiveY + TEXT_Y_DISPLACEMENT),
+ xy=(xLeftOffset + plotWidth + 6,
+ additiveY + TEXT_Y_DISPLACEMENT),
font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE)
im_drawer.line(
@@ -2818,7 +2818,7 @@ class DisplayMappingResults:
xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30 * (zoom - 1))),
fill=self.LRS_COLOR, width=1 * zoom) # the blue line running up the y axis
- def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb= None, endMb = None):
+ def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb=None, endMb=None):
# conditions
# multiple Chromosome view
# single Chromosome Physical
@@ -2953,10 +2953,10 @@ class DisplayMappingResults:
"SNP Count",
"SNP Density",
"Avg Expr",
- "Human Chr",
- "Mb Start (hg19)",
- "Literature Correlation",
- "Gene Description"]
+ "Human Chr",
+ "Mb Start (hg19)",
+ "Literature Correlation",
+ "Gene Description"]
else:
gene_table_header_list = ["",
"Index",
@@ -3073,12 +3073,12 @@ class DisplayMappingResults:
geneIdString,
theGO["GeneSymbol"],
target="_blank")
- ),
+ ),
str(HtmlGenWrapper.create_link_tag(
mouseStartString,
"{:.6f}".format(txStart),
target="_blank")
- ),
+ ),
str(HtmlGenWrapper.create_link_tag(
"javascript:rangeView('{}', {:f}, {:f})".format(
str(chr_as_int),
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 289f1d5c..f88c5ac8 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -150,7 +150,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
if dataset_name == "Temp":
temp_group = trait_name.split("_")[2]
dataset_ob = create_dataset(
- dataset_name="Temp", dataset_type="Temp", group_name = temp_group)
+ dataset_name="Temp", dataset_type="Temp", group_name=temp_group)
else:
dataset_ob = create_dataset(covariate.split(":")[1])
trait_ob = create_trait(dataset=dataset_ob,
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 5d16abde..4d6715ba 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -2,7 +2,8 @@ import os
import math
import string
import random
-import json, re
+import json
+import re
from base import webqtlConfig
from base.trait import GeneralTrait
@@ -28,7 +29,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
output_filename = (f"{this_dataset.group.name}_GWA_"
+ ''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
- )
+ )
bootstrap_filename = None
permu_filename = None
@@ -37,7 +38,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
bootstrap_filename = (f"{this_dataset.group.name}_BOOTSTRAP_"
+ ''.join(random.choice(string.ascii_uppercase + string.digits)
for _ in range(6))
- )
+ )
opt_list.append("-b")
opt_list.append(f"--n_bootstrap {str(num_bootstrap)}")
@@ -47,7 +48,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
permu_filename = ("{this_dataset.group.name}_PERM_"
+ ''.join(random.choice(string.ascii_uppercase
+ string.digits) for _ in range(6))
- )
+ )
opt_list.append("-n " + str(num_perm))
opt_list.append(
"--permu_output " + webqtlConfig.GENERATED_IMAGE_DIR + permu_filename + ".txt")
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index cf8cf514..1fa3dffe 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -110,7 +110,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
if do_control == "true":
logger.info("Using covariate")
result_data_frame = scantwo(
- cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster = 16)
+ cross_object, pheno="the_pheno", addcovar=covars, model=model, method=method, n_cluster=16)
else:
logger.info("No covariates")
result_data_frame = scantwo(
@@ -140,14 +140,14 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
cross_object, strata_ob = add_perm_strata(
cross_object, perm_strata_list)
if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(
- num_perm), perm_strata = strata_ob, model=model, method=method)
+ perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm=int(
+ num_perm), perm_strata=strata_ob, model=model, method=method)
else:
perm_data_frame = scanone(
- cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata = strata_ob, model=model, method=method)
+ cross_object, pheno_col="the_pheno", n_perm=num_perm, perm_strata=strata_ob, model=model, method=method)
else:
if do_control == "true" or cofactors != "":
- perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm = int(
+ perm_data_frame = scanone(cross_object, pheno_col="the_pheno", addcovar=covars, n_perm=int(
num_perm), model=model, method=method)
else:
perm_data_frame = scanone(
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 81e0a03f..32ccec48 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -67,7 +67,8 @@ class RunMapping:
if 'genofile' in start_vars:
if start_vars['genofile'] != "":
self.genofile_string = start_vars['genofile']
- self.dataset.group.genofile = self.genofile_string.split(":")[0]
+ self.dataset.group.genofile = self.genofile_string.split(":")[
+ 0]
genofile_samplelist = get_genofile_samplelist(self.dataset)
all_samples_ordered = self.dataset.group.all_samples_ordered()
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 822900cc..a222b87c 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -36,7 +36,7 @@ class User(Base):
# json detailing when they became a superuser, otherwise empty
superuser = Column(Text)
- # if not superuser
+ # if not superuser
logins = relationship("Login",
order_by="desc(Login.timestamp)",
@@ -47,7 +47,7 @@ class User(Base):
user_collections = relationship("UserCollection",
order_by="asc(UserCollection.name)",
lazy='dynamic',
- )
+ )
def display_num_collections(self):
"""
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 61f3b202..b28c1b04 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -116,7 +116,7 @@ def add_group_to_resource():
group_id = request.form['selected_group']
resource_info = get_resource_info(resource_id)
default_privileges = resource_info['default_mask']
- return render_template("admin/set_group_privileges.html", resource_id=resource_id, group_id=group_id, default_privileges = default_privileges)
+ return render_template("admin/set_group_privileges.html", resource_id=resource_id, group_id=group_id, default_privileges=default_privileges)
elif all(key in request.form for key in ('data_privilege', 'metadata_privilege', 'admin_privilege')):
group_id = request.form['group_id']
group_name = get_group_info(group_id)['name']
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index fc48959e..3cbda3dd 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -276,7 +276,7 @@ class SearchResultPage:
search_operator,
self.dataset,
search_type['key']
- )
+ )
return the_search
else:
return None
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 42fe339e..c4d0e135 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -28,10 +28,10 @@ class SnpBrowser:
if self.limit_strains == "true":
self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(
- variant_type=self.variant_type, strains=self.chosen_strains, empty_columns = self.empty_columns)
+ variant_type=self.variant_type, strains=self.chosen_strains, empty_columns=self.empty_columns)
else:
self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(
- variant_type=self.variant_type, strains=self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
+ variant_type=self.variant_type, strains=self.strain_lists, species=self.species_name, empty_columns=self.empty_columns)
def initialize_parameters(self, start_vars):
if 'first_run' in start_vars:
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 0d5f1f3e..ff77982f 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -65,7 +65,7 @@ def set_password(password):
"salt": base64.b64encode(os.urandom(32)),
"iterations": 100000,
"keylength": 32,
- "created_timestamp": timestamp()
+ "created_timestamp": timestamp()
}
assert len(password) >= 6, "Password shouldn't be shorter than 6 characters"
@@ -132,7 +132,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
logger.info("Successfully sent email to " + toaddr)
-def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject = "GeneNetwork e-mail verification"):
+def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject="GeneNetwork e-mail verification"):
verification_code = str(uuid.uuid4())
key = key_prefix + ":" + verification_code
@@ -147,7 +147,7 @@ def send_verification_email(user_details, template_name="email/user_verification
return {"recipient": recipient, "subject": subject, "body": body}
-def send_invitation_email(user_email, temp_password, template_name="email/user_invitation.txt", subject= "You've been added to a GeneNetwork user group"):
+def send_invitation_email(user_email, temp_password, template_name="email/user_invitation.txt", subject="You've been added to a GeneNetwork user group"):
recipient = user_email
body = render_template(template_name, temp_password)
send_email(recipient, subject, body)
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index fb26bfb1..cf84ea73 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -476,7 +476,7 @@ def set_password(password, user):
user.password = json.dumps(pwfields.__dict__,
sort_keys=True,
- )
+ )
class VerificationEmail:
@@ -677,7 +677,7 @@ def github_oauth2():
user_details = get_user_by_unique_column("github_id", github_user["id"])
if user_details == None:
user_details = {
- "user_id": str(uuid.uuid4()), "name": github_user["name"].encode("utf-8"), "github_id": github_user["id"], "user_url": github_user["html_url"].encode("utf-8") , "login_type": "github" , "organization": "" , "active": 1 , "confirmed": 1
+ "user_id": str(uuid.uuid4()), "name": github_user["name"].encode("utf-8"), "github_id": github_user["id"], "user_url": github_user["html_url"].encode("utf-8"), "login_type": "github", "organization": "", "active": 1, "confirmed": 1
}
save_user(user_details, user_details["user_id"])
@@ -705,7 +705,7 @@ def orcid_oauth2():
user_details = {
"user_id": str(uuid4()), "name": result_dict["name"], "orcid": result_dict["orcid"], "user_url": "%s/%s" % (
"/".join(ORCID_AUTH_URL.split("/")[:-2]),
- result_dict["orcid"]), "login_type": "orcid", "organization": "", "active": 1 , "confirmed": 1
+ result_dict["orcid"]), "login_type": "orcid", "organization": "", "active": 1, "confirmed": 1
}
save_user(user_details, user_details["user_id"])
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index f75209ff..f9b8f310 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -141,7 +141,7 @@ def handle_bad_request(e):
now = datetime.datetime.utcnow()
time_str = now.strftime('%l:%M%p UTC %b %d, %Y')
formatted_lines = [request.url
- + " (" + time_str + ")"]+traceback.format_exc().splitlines()
+ + " (" + time_str + ")"] + traceback.format_exc().splitlines()
# Handle random animations
# Use a cookie to have one animation on refresh
--
cgit v1.2.3
From 7e6886d7f65307519b8d26ec43a04f8d674fc4b6 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 4 May 2021 23:27:34 +0300
Subject: base: species: Format SQL queries
---
wqflask/base/species.py | 31 +++++++++++++------------------
1 file changed, 13 insertions(+), 18 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index e3c29916..c3f4a9ab 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -32,28 +32,23 @@ class Chromosomes:
def __init__(self, dataset=None, species=None):
self.chromosomes = collections.OrderedDict()
if species != None:
- query = """
- Select
- Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species
- where
- Chr_Length.SpeciesId = Species.SpeciesId AND
- Species.Name = '%s'
- Order by OrderId
- """ % species.capitalize()
+ query = (
+ "SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
+ "FROM Chr_Length, Species WHERE "
+ "Chr_Length.SpeciesId = Species.SpeciesId AND "
+ "Species.Name = "
+ "'%s' ORDER BY OrderId" % species.capitalize()
+ )
else:
self.dataset = dataset
-
- query = """
- Select
- Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
- where
- Chr_Length.SpeciesId = InbredSet.SpeciesId AND
- InbredSet.Name = '%s'
- Order by OrderId
- """ % self.dataset.group.name
+ query = (
+ "SELECT Chr_Length.Name, Chr_Length.OrderId, "
+ "Length FROM Chr_Length, InbredSet WHERE "
+ "Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
+ "InbredSet.Name = "
+ "'%s' ORDER BY OrderId" % self.dataset.group.name)
logger.sql(query)
results = g.db.execute(query).fetchall()
-
for item in results:
self.chromosomes[item.OrderId] = IndChromosome(
item.Name, item.Length)
--
cgit v1.2.3
From 5e19a8a505dc7b8fa77fcc836892d1982c6ae36d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 4 May 2021 23:28:40 +0300
Subject: base: species: Remove unused import
---
wqflask/base/species.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index c3f4a9ab..3ec7556d 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -1,6 +1,6 @@
import collections
-from flask import Flask, g
+from flask import g
from utility.logger import getLogger
--
cgit v1.2.3
From 453455b8bc6557c35ad279a208235f0b44aa251e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 4 May 2021 23:34:32 +0300
Subject: base: species: Rewrite TheSpecies class using a dataclass
---
wqflask/base/species.py | 15 +++++++++++----
1 file changed, 11 insertions(+), 4 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 3ec7556d..3865f450 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -1,5 +1,7 @@
import collections
+from dataclasses import dataclass
+from typing import Optional, Dict
from flask import g
@@ -7,13 +9,18 @@ from utility.logger import getLogger
logger = getLogger(__name__)
+@dataclass
class TheSpecies:
- def __init__(self, dataset=None, species_name=None):
- if species_name != None:
- self.name = species_name
+ """Data related to species."""
+ dataset: Optional[Dict] = None
+ species_name: Optional[str] = None
+
+ def __post_init__(self):
+ if self.species_name is not None:
+ self.name = self.species_name
self.chromosomes = Chromosomes(species=self.name)
else:
- self.dataset = dataset
+ self.dataset = self.dataset
self.chromosomes = Chromosomes(dataset=self.dataset)
--
cgit v1.2.3
From 151cbec41a9466f8f716f24ae85c7a5b09919e01 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 4 May 2021 23:35:38 +0300
Subject: base: trait: Remove logging information
The log adds unnecessary noise in addition to creating unwanted
side-effects.
---
wqflask/base/species.py | 5 -----
1 file changed, 5 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 3865f450..ce646538 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -5,10 +5,6 @@ from typing import Optional, Dict
from flask import g
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-
@dataclass
class TheSpecies:
"""Data related to species."""
@@ -54,7 +50,6 @@ class Chromosomes:
"Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
"InbredSet.Name = "
"'%s' ORDER BY OrderId" % self.dataset.group.name)
- logger.sql(query)
results = g.db.execute(query).fetchall()
for item in results:
self.chromosomes[item.OrderId] = IndChromosome(
--
cgit v1.2.3
From 7c6a60d62389fa945f5a7264cde31cf00ddf9fc4 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 4 May 2021 23:46:00 +0300
Subject: base: species: Rewrite IndChromosome using a dataclass
---
wqflask/base/species.py | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index ce646538..628bcc56 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -20,14 +20,15 @@ class TheSpecies:
self.chromosomes = Chromosomes(dataset=self.dataset)
+@dataclass
class IndChromosome:
- def __init__(self, name, length):
- self.name = name
- self.length = length
+ """Data related to IndChromosome"""
+ name: str
+ length: int
@property
def mb_length(self):
- """Chromosome length in megabases"""
+ """Chromosome length in mega-bases"""
return self.length / 1000000
--
cgit v1.2.3
From f2c3528cc81d228a62dfd9e362d0a1202412b098 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 4 May 2021 23:46:45 +0300
Subject: base: species: Rewrite Chromosomes using a dataclass
---
wqflask/base/species.py | 18 +++++++++++-------
1 file changed, 11 insertions(+), 7 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 628bcc56..db1975d4 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -1,6 +1,6 @@
-import collections
-
+from collections import OrderedDict
from dataclasses import dataclass
+from dataclasses import InitVar
from typing import Optional, Dict
from flask import g
@@ -32,17 +32,21 @@ class IndChromosome:
return self.length / 1000000
+@dataclass
class Chromosomes:
- def __init__(self, dataset=None, species=None):
- self.chromosomes = collections.OrderedDict()
- if species != None:
+ """Data related to a chromosome"""
+ dataset: InitVar[Dict] = None
+ species: Optional[str] = None
+
+ def __post_init__(self, dataset):
+ self.chromosomes = OrderedDict()
+ if self.species is not None:
query = (
"SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
"FROM Chr_Length, Species WHERE "
"Chr_Length.SpeciesId = Species.SpeciesId AND "
"Species.Name = "
- "'%s' ORDER BY OrderId" % species.capitalize()
- )
+ "'%s' ORDER BY OrderId" % self.species.capitalize())
else:
self.dataset = dataset
query = (
--
cgit v1.2.3
From 941680d5266159fc5c9f2a65131bf283bd1cef1d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 4 May 2021 23:55:58 +0300
Subject: base: chromosomes: Fetch the chromosomes lazily
---
wqflask/base/species.py | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index db1975d4..430bb675 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -39,7 +39,13 @@ class Chromosomes:
species: Optional[str] = None
def __post_init__(self, dataset):
- self.chromosomes = OrderedDict()
+ if self.species is None:
+ self.dataset = dataset
+
+ @property
+ def chromosomes(self):
+ """Lazily fetch the chromosomes"""
+ chromosomes = OrderedDict()
if self.species is not None:
query = (
"SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
@@ -48,7 +54,6 @@ class Chromosomes:
"Species.Name = "
"'%s' ORDER BY OrderId" % self.species.capitalize())
else:
- self.dataset = dataset
query = (
"SELECT Chr_Length.Name, Chr_Length.OrderId, "
"Length FROM Chr_Length, InbredSet WHERE "
@@ -57,5 +62,6 @@ class Chromosomes:
"'%s' ORDER BY OrderId" % self.dataset.group.name)
results = g.db.execute(query).fetchall()
for item in results:
- self.chromosomes[item.OrderId] = IndChromosome(
+ chromosomes[item.OrderId] = IndChromosome(
item.Name, item.Length)
+ return chromosomes
--
cgit v1.2.3
From dad8ae99812555fbb3d7e680f146c98de3322a57 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 5 May 2021 12:32:53 +0300
Subject: base: species: Remove redundant assignment
---
wqflask/base/species.py | 1 -
1 file changed, 1 deletion(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 430bb675..f303aabb 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -16,7 +16,6 @@ class TheSpecies:
self.name = self.species_name
self.chromosomes = Chromosomes(species=self.name)
else:
- self.dataset = self.dataset
self.chromosomes = Chromosomes(dataset=self.dataset)
--
cgit v1.2.3
From 27538980f93c1d72b0b2d76151312f3fbce4c9a5 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 10 May 2021 08:24:42 +0300
Subject: add previous endpoint for correlation
---
wqflask/base/data_set.py | 37 -------------------------------------
wqflask/wqflask/views.py | 13 ++++++++-----
2 files changed, 8 insertions(+), 42 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 468c4da0..d0f5e6f2 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -655,42 +655,7 @@ class DataSet(object):
"Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
- def fetch_probe_trait_data(self, sample_list=None):
- if sample_list:
- self.samplelist = sample_list
- else:
- self.samplelist = self.group.samplelist
-
- if self.group.parlist != None and self.group.f1list != None:
- if (self.group.parlist + self.group.f1list) in self.samplelist:
- self.samplelist += self.group.parlist + self.group.f1list
-
- query = """
- SELECT Strain.Name, Strain.Id FROM Strain, Species
- WHERE Strain.Name IN {}
- and Strain.SpeciesId=Species.Id
- and Species.name = '{}'
- """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
- logger.sql(query)
- results = dict(g.db.execute(query).fetchall())
- sample_ids = [results[item] for item in self.samplelist]
-
- query = """SELECT * from ProbeSetData WHERE Id in ( SELECT ProbeSetXRef.DataId FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze) WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id and ProbeSetFreeze.Name = 'HC_M2_0606_P' and ProbeSet.Id = ProbeSetXRef.ProbeSetId order by ProbeSet.Id ) and StrainId in ({})""".format(
- ",".join(str(sample_id) for sample_id in sample_ids))
- results = g.db.execute(query).fetchall()
-
- # with conn:
- # cursor = conn.cursor()
- # cursor.execute(query)
- # results = cursor.fetchall()
- trait_data = {}
- for trait_id, StrainId, value in results:
- if trait_id in trait_data:
- trait_data[trait_id].append(value)
- else:
- trait_data[trait_id] = [value]
- self.trait_data = trait_data
def get_trait_data(self, sample_list=None):
if sample_list:
@@ -711,7 +676,6 @@ class DataSet(object):
logger.sql(query)
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
- print("the number of sample ids are", len(sample_ids))
# MySQL limits the number of tables that can be used in a join to 61,
# so we break the sample ids into smaller chunks
@@ -762,7 +726,6 @@ class DataSet(object):
trait_sample_data.append(results)
trait_count = len(trait_sample_data[0])
- print("the trait count is >>>", trait_count)
self.trait_data = collections.defaultdict(list)
# put all of the separate data together into a dictionary where the keys are
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b042a211..19779651 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -881,11 +881,14 @@ def network_graph_page():
def corr_compute_page():
logger.info("In corr_compute, request.form is:", pf(request.form))
logger.info(request.url)
- import time
- initial_time = time.time()
- correlation_results = compute_correlation(request.form)
- print(">>>>Time taken by this endpoint",time.time()-initial_time)
- return render_template("test_correlation_page.html",correlation_results=correlation_results)
+ template_vars = show_corr_results.CorrelationResults(request.form)
+ return render_template("correlation_page.html", **template_vars.__dict__)
+
+ # to test the new correlation api uncomment these lines
+
+ # correlation_results = compute_correlation(request.form)
+ # print(">>>>Time taken by this endpoint",time.time()-initial_time)
+ # return render_template("test_correlation_page.html",correlation_results=correlation_results)
@app.route("/corr_matrix", methods=('POST',))
def corr_matrix_page():
--
cgit v1.2.3
From 4f06f22071898171cb7bbc12f5dfd42b05dc3208 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 21:58:00 +0000
Subject: Added function as_dict to data_set.py for situations where we don't
want to pass around the whole dataset object
---
wqflask/base/data_set.py | 12 ++++++++++++
1 file changed, 12 insertions(+)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 75ddf278..dc338971 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -559,6 +559,7 @@ class DataSet:
self.fullname = None
self.type = None
self.data_scale = None # ZS: For example log2
+ self.accession_id = None
self.setup()
@@ -575,6 +576,17 @@ class DataSet:
self.group.get_samplelist()
self.species = species.TheSpecies(self)
+ def as_dict(self):
+ return {
+ 'name': self.name,
+ 'shortname': self.shortname,
+ 'fullname': self.fullname,
+ 'type': self.type,
+ 'data_scale': self.data_scale,
+ 'group': self.group.name,
+ 'accession_id': self.accession_id
+ }
+
def get_accession_id(self):
if self.type == "Publish":
results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
--
cgit v1.2.3
From 73195c1af57cbcf0fa38f1e73e8878c02938ef4b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 21:58:43 +0000
Subject: Changed the function jsonable in trait.py to return a couple extra
fields + take dataset as an optional argument (to avoid having to pointlessly
create it)
---
wqflask/base/trait.py | 17 +++++++++++++----
1 file changed, 13 insertions(+), 4 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index d09cfd40..10851e00 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -284,17 +284,19 @@ def get_sample_data():
return None
-def jsonable(trait):
+def jsonable(trait, dataset=None):
"""Return a dict suitable for using as json
Actual turning into json doesn't happen here though"""
- dataset = create_dataset(dataset_name=trait.dataset.name,
- dataset_type=trait.dataset.type,
- group_name=trait.dataset.group.name)
+ if not dataset:
+ dataset = create_dataset(dataset_name=trait.dataset.name,
+ dataset_type=trait.dataset.type,
+ group_name=trait.dataset.group.name)
if dataset.type == "ProbeSet":
return dict(name=trait.name,
+ view=trait.view,
symbol=trait.symbol,
dataset=dataset.name,
dataset_name=dataset.shortname,
@@ -308,37 +310,44 @@ def jsonable(trait):
elif dataset.type == "Publish":
if trait.pubmed_id:
return dict(name=trait.name,
+ view=trait.view,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
+ pubmed_id=trait.pubmed_id,
pubmed_text=trait.pubmed_text,
pubmed_link=trait.pubmed_link,
+ mean=trait.mean,
lrs_score=trait.LRS_score_repr,
lrs_location=trait.LRS_location_repr,
additive=trait.additive
)
else:
return dict(name=trait.name,
+ view=trait.view,
dataset=dataset.name,
dataset_name=dataset.shortname,
description=trait.description_display,
abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
+ mean=trait.mean,
lrs_score=trait.LRS_score_repr,
lrs_location=trait.LRS_location_repr,
additive=trait.additive
)
elif dataset.type == "Geno":
return dict(name=trait.name,
+ view=trait.view,
dataset=dataset.name,
dataset_name=dataset.shortname,
location=trait.location_repr
)
elif dataset.name == "Temp":
return dict(name=trait.name,
+ view=trait.view,
dataset="Temp",
dataset_name="Temp")
else:
--
cgit v1.2.3
From db9b0a9df8879921217bac353eaa2c3440e8337a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 24 May 2021 16:35:11 +0300
Subject: add query for fetching probeset data
---
wqflask/base/data_set.py | 258 +++++++++++++--------
wqflask/wqflask/correlation/correlation_gn3_api.py | 144 +++++++++++-
2 files changed, 303 insertions(+), 99 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index dc338971..7531ac81 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -166,7 +166,6 @@ class DatasetType:
if t in ['pheno', 'other_pheno']:
group_name = name.replace("Publish", "")
-
results = g.db.execute(sql_query_mapping[t] % group_name).fetchone()
if results:
self.datasets[name] = dataset_name_mapping[t]
@@ -278,7 +277,7 @@ class Markers:
filtered_markers = []
for marker in self.markers:
if marker['name'] in p_values:
- #logger.debug("marker {} IS in p_values".format(i))
+ # logger.debug("marker {} IS in p_values".format(i))
marker['p_value'] = p_values[marker['name']]
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
@@ -299,7 +298,7 @@ class HumanMarkers(Markers):
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
- #logger.debug("splat:", splat)
+ # logger.debug("splat:", splat)
if len(specified_markers) > 0:
if splat[1] in specified_markers:
marker = {}
@@ -441,7 +440,7 @@ class DatasetGroup:
# genotype_1 is Dataset Object without parents and f1
# genotype_2 is Dataset Object with parents and f1 (not for intercross)
- #genotype_1 = reaper.Dataset()
+ # genotype_1 = reaper.Dataset()
# reaper barfs on unicode filenames, so here we ensure it's a string
if self.genofile:
@@ -662,9 +661,39 @@ class DataSet:
- def get_trait_data(self, sample_list=None):
+
+ def chunk_dataset(self, dataset, n):
+
+
+ results = {}
+
+ query = """
+ SELECT ProbeSetXRef.DataId,ProbeSet.Name
+ FROM ProbeSet, ProbeSetXRef, ProbeSetFreeze
+ WHERE ProbeSetFreeze.Name = '{}' AND
+ ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND
+ ProbeSetXRef.ProbeSetId = ProbeSet.Id
+ """.format(self.name)
+
+ # should cache this
+
+ traits_name_dict= dict(g.db.execute(query).fetchall())
+
+
+
+
+ for i in range(0, len(dataset), n):
+ matrix = list(dataset[i:i + n])
+ trait_name = traits_name_dict[matrix[0][0]]
+
+ my_values = [value for (trait_name, strain, value) in matrix]
+ results[trait_name] = my_values
+ return results
+
+ def get_probeset_data(self, sample_list=None, trait_ids=None):
if sample_list:
self.samplelist = sample_list
+
else:
self.samplelist = self.group.samplelist
@@ -678,27 +707,59 @@ class DataSet:
and Strain.SpeciesId=Species.Id
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
- logger.sql(query)
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
+ query = """SELECT * from ProbeSetData
+ where StrainID in {}
+ and id in (SELECT ProbeSetXRef.DataId
+ FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
+ WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+ and ProbeSetFreeze.Name = '{}'
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids),self.name)
+
+ query_results=list(g.db.execute(query).fetchall())
+
+ data_results=self.chunk_dataset(query_results, len(sample_ids))
+ self.trait_data=data_results
+
+ def get_trait_data(self, sample_list=None):
+ if sample_list:
+ self.samplelist=sample_list
+ else:
+ self.samplelist=self.group.samplelist
+
+ if self.group.parlist != None and self.group.f1list != None:
+ if (self.group.parlist + self.group.f1list) in self.samplelist:
+ self.samplelist += self.group.parlist + self.group.f1list
+
+ query="""
+ SELECT Strain.Name, Strain.Id FROM Strain, Species
+ WHERE Strain.Name IN {}
+ and Strain.SpeciesId=Species.Id
+ and Species.name = '{}'
+ """.format(create_in_clause(self.samplelist), *mescape(self.group.species))
+ logger.sql(query)
+ results=dict(g.db.execute(query).fetchall())
+ sample_ids=[results[item] for item in self.samplelist]
+
# MySQL limits the number of tables that can be used in a join to 61,
# so we break the sample ids into smaller chunks
# Postgres doesn't have that limit, so we can get rid of this after we transition
- chunk_size = 50
- number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
- trait_sample_data = []
+ chunk_size=50
+ number_chunks=int(math.ceil(len(sample_ids) / chunk_size))
+ trait_sample_data=[]
for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
if self.type == "Publish":
- dataset_type = "Phenotype"
+ dataset_type="Phenotype"
else:
- dataset_type = self.type
- temp = ['T%s.value' % item for item in sample_ids_step]
+ dataset_type=self.type
+ temp=['T%s.value' % item for item in sample_ids_step]
if self.type == "Publish":
- query = "SELECT {}XRef.Id,".format(escape(self.type))
+ query="SELECT {}XRef.Id,".format(escape(self.type))
else:
- query = "SELECT {}.Name,".format(escape(dataset_type))
- data_start_pos = 1
+ query="SELECT {}.Name,".format(escape(dataset_type))
+ data_start_pos=1
query += ', '.join(temp)
query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
self.type,
@@ -727,27 +788,27 @@ class DataSet:
""".format(*mescape(self.type, self.type, self.type, self.type,
self.name, dataset_type, self.type, self.type, dataset_type))
- results = g.db.execute(query).fetchall()
+ results=g.db.execute(query).fetchall()
trait_sample_data.append(results)
- trait_count = len(trait_sample_data[0])
- self.trait_data = collections.defaultdict(list)
+ trait_count=len(trait_sample_data[0])
+ self.trait_data=collections.defaultdict(list)
# put all of the separate data together into a dictionary where the keys are
# trait names and values are lists of sample values
for trait_counter in range(trait_count):
- trait_name = trait_sample_data[0][trait_counter][0]
+ trait_name=trait_sample_data[0][trait_counter][0]
for chunk_counter in range(int(number_chunks)):
self.trait_data[trait_name] += (
trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
class PhenotypeDataSet(DataSet):
- DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
+ DS_NAME_MAP['Publish']='PhenotypeDataSet'
def setup(self):
# Fields in the database table
- self.search_fields = ['Phenotype.Post_publication_description',
+ self.search_fields=['Phenotype.Post_publication_description',
'Phenotype.Pre_publication_description',
'Phenotype.Pre_publication_abbreviation',
'Phenotype.Post_publication_abbreviation',
@@ -760,7 +821,7 @@ class PhenotypeDataSet(DataSet):
'PublishXRef.Id']
# Figure out what display_fields is
- self.display_fields = ['name', 'group_code',
+ self.display_fields=['name', 'group_code',
'pubmed_id',
'pre_publication_description',
'post_publication_description',
@@ -778,7 +839,7 @@ class PhenotypeDataSet(DataSet):
'sequence', 'units', 'comments']
# Fields displayed in the search results table header
- self.header_fields = ['Index',
+ self.header_fields=['Index',
'Record',
'Description',
'Authors',
@@ -787,9 +848,9 @@ class PhenotypeDataSet(DataSet):
'Max LRS Location',
'Additive Effect']
- self.type = 'Publish'
+ self.type='Publish'
- self.query_for_group = '''
+ self.query_for_group='''
SELECT
InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
@@ -809,13 +870,13 @@ class PhenotypeDataSet(DataSet):
if not this_trait.haveinfo:
this_trait.retrieve_info(get_qtl_info=True)
- description = this_trait.post_publication_description
+ description=this_trait.post_publication_description
# If the dataset is confidential and the user has access to confidential
# phenotype traits, then display the pre-publication description instead
# of the post-publication description
if this_trait.confidential:
- this_trait.description_display = ""
+ this_trait.description_display=""
continue # for now, because no authorization features
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
@@ -823,46 +884,46 @@ class PhenotypeDataSet(DataSet):
userName=self.userName,
authorized_users=this_trait.authorized_users):
- description = this_trait.pre_publication_description
+ description=this_trait.pre_publication_description
if len(description) > 0:
- this_trait.description_display = description.strip()
+ this_trait.description_display=description.strip()
else:
- this_trait.description_display = ""
+ this_trait.description_display=""
if not this_trait.year.isdigit():
- this_trait.pubmed_text = "N/A"
+ this_trait.pubmed_text="N/A"
else:
- this_trait.pubmed_text = this_trait.year
+ this_trait.pubmed_text=this_trait.year
if this_trait.pubmed_id:
- this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
+ this_trait.pubmed_link=webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
# LRS and its location
- this_trait.LRS_score_repr = "N/A"
- this_trait.LRS_location_repr = "N/A"
+ this_trait.LRS_score_repr="N/A"
+ this_trait.LRS_location_repr="N/A"
if this_trait.lrs:
- query = """
+ query="""
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '%s' and
Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, this_trait.locus)
logger.sql(query)
- result = g.db.execute(query).fetchone()
+ result=g.db.execute(query).fetchone()
if result:
if result[0] and result[1]:
- LRS_Chr = result[0]
- LRS_Mb = result[1]
+ LRS_Chr=result[0]
+ LRS_Mb=result[1]
- this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
+ this_trait.LRS_score_repr=LRS_score_repr='%3.1f' % this_trait.lrs
+ this_trait.LRS_location_repr=LRS_location_repr='Chr%s: %.6f' % (
LRS_Chr, float(LRS_Mb))
def retrieve_sample_data(self, trait):
- query = """
+ query="""
SELECT
Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2
FROM
@@ -880,34 +941,34 @@ class PhenotypeDataSet(DataSet):
Strain.Name
"""
logger.sql(query)
- results = g.db.execute(query, (trait, self.id)).fetchall()
+ results=g.db.execute(query, (trait, self.id)).fetchall()
return results
class GenotypeDataSet(DataSet):
- DS_NAME_MAP['Geno'] = 'GenotypeDataSet'
+ DS_NAME_MAP['Geno']='GenotypeDataSet'
def setup(self):
# Fields in the database table
- self.search_fields = ['Name',
+ self.search_fields=['Name',
'Chr']
# Find out what display_fields is
- self.display_fields = ['name',
+ self.display_fields=['name',
'chr',
'mb',
'source2',
'sequence']
# Fields displayed in the search results table header
- self.header_fields = ['Index',
+ self.header_fields=['Index',
'ID',
'Location']
# Todo: Obsolete or rename this field
- self.type = 'Geno'
+ self.type='Geno'
- self.query_for_group = '''
+ self.query_for_group='''
SELECT
InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
@@ -926,11 +987,11 @@ class GenotypeDataSet(DataSet):
this_trait.retrieveInfo()
if this_trait.chr and this_trait.mb:
- this_trait.location_repr = 'Chr%s: %.6f' % (
+ this_trait.location_repr='Chr%s: %.6f' % (
this_trait.chr, float(this_trait.mb))
def retrieve_sample_data(self, trait):
- query = """
+ query="""
SELECT
Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2
FROM
@@ -947,7 +1008,7 @@ class GenotypeDataSet(DataSet):
Strain.Name
"""
logger.sql(query)
- results = g.db.execute(query,
+ results=g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
return results
@@ -961,11 +1022,11 @@ class MrnaAssayDataSet(DataSet):
platform and is far too specific.
'''
- DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet'
+ DS_NAME_MAP['ProbeSet']='MrnaAssayDataSet'
def setup(self):
# Fields in the database table
- self.search_fields = ['Name',
+ self.search_fields=['Name',
'Description',
'Probe_Target_Description',
'Symbol',
@@ -975,7 +1036,7 @@ class MrnaAssayDataSet(DataSet):
'RefSeq_TranscriptId']
# Find out what display_fields is
- self.display_fields = ['name', 'symbol',
+ self.display_fields=['name', 'symbol',
'description', 'probe_target_description',
'chr', 'mb',
'alias', 'geneid',
@@ -995,7 +1056,7 @@ class MrnaAssayDataSet(DataSet):
'flag']
# Fields displayed in the search results table header
- self.header_fields = ['Index',
+ self.header_fields=['Index',
'Record',
'Symbol',
'Description',
@@ -1006,9 +1067,9 @@ class MrnaAssayDataSet(DataSet):
'Additive Effect']
# Todo: Obsolete or rename this field
- self.type = 'ProbeSet'
+ self.type='ProbeSet'
- self.query_for_group = '''
+ self.query_for_group='''
SELECT
InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
@@ -1026,7 +1087,7 @@ class MrnaAssayDataSet(DataSet):
# Note: setting trait_list to [] is probably not a great idea.
if not trait_list:
- trait_list = []
+ trait_list=[]
for this_trait in trait_list:
@@ -1034,33 +1095,33 @@ class MrnaAssayDataSet(DataSet):
this_trait.retrieveInfo(QTL=1)
if not this_trait.symbol:
- this_trait.symbol = "N/A"
+ this_trait.symbol="N/A"
# XZ, 12/08/2008: description
# XZ, 06/05/2009: Rob asked to add probe target description
- description_string = str(
+ description_string=str(
str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
- target_string = str(
+ target_string=str(
str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
if len(description_string) > 1 and description_string != 'None':
- description_display = description_string
+ description_display=description_string
else:
- description_display = this_trait.symbol
+ description_display=this_trait.symbol
if (len(description_display) > 1 and description_display != 'N/A'
and len(target_string) > 1 and target_string != 'None'):
- description_display = description_display + '; ' + target_string.strip()
+ description_display=description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
- this_trait.description_display = description_display
+ this_trait.description_display=description_display
if this_trait.chr and this_trait.mb:
- this_trait.location_repr = 'Chr%s: %.6f' % (
+ this_trait.location_repr='Chr%s: %.6f' % (
this_trait.chr, float(this_trait.mb))
# Get mean expression value
- query = (
+ query=(
"""select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSet.Id = ProbeSetXRef.ProbeSetId and
@@ -1068,44 +1129,45 @@ class MrnaAssayDataSet(DataSet):
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
- #logger.debug("query is:", pf(query))
+ # logger.debug("query is:", pf(query))
logger.sql(query)
- result = g.db.execute(query).fetchone()
+ result=g.db.execute(query).fetchone()
- mean = result[0] if result else 0
+ mean=result[0] if result else 0
if mean:
- this_trait.mean = "%2.3f" % mean
+ this_trait.mean="%2.3f" % mean
# LRS and its location
- this_trait.LRS_score_repr = 'N/A'
- this_trait.LRS_location_repr = 'N/A'
+ this_trait.LRS_score_repr='N/A'
+ this_trait.LRS_location_repr='N/A'
# Max LRS and its Locus location
if this_trait.lrs and this_trait.locus:
- query = """
+ query="""
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '{}' and
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(species, this_trait.locus)
logger.sql(query)
- result = g.db.execute(query).fetchone()
+ result=g.db.execute(query).fetchone()
if result:
- lrs_chr, lrs_mb = result
- this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
+ lrs_chr, lrs_mb=result
+ this_trait.LRS_score_repr='%3.1f' % this_trait.lrs
+ this_trait.LRS_location_repr='Chr%s: %.6f' % (
lrs_chr, float(lrs_mb))
return trait_list
def retrieve_sample_data(self, trait):
- query = """
+ query="""
SELECT
Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
FROM
- (ProbeSetData, ProbeSetFreeze, Strain, ProbeSet, ProbeSetXRef)
+ (ProbeSetData, ProbeSetFreeze,
+ Strain, ProbeSet, ProbeSetXRef)
left join ProbeSetSE on
(ProbeSetSE.DataId = ProbeSetData.Id AND ProbeSetSE.StrainId = ProbeSetData.StrainId)
left join NStrain on
@@ -1121,19 +1183,19 @@ class MrnaAssayDataSet(DataSet):
Strain.Name
""" % (escape(trait), escape(self.name))
logger.sql(query)
- results = g.db.execute(query).fetchall()
- #logger.debug("RETRIEVED RESULTS HERE:", results)
+ results=g.db.execute(query).fetchall()
+ # logger.debug("RETRIEVED RESULTS HERE:", results)
return results
def retrieve_genes(self, column_name):
- query = """
+ query="""
select ProbeSet.Name, ProbeSet.%s
from ProbeSet,ProbeSetXRef
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
""" % (column_name, escape(str(self.id)))
logger.sql(query)
- results = g.db.execute(query).fetchall()
+ results=g.db.execute(query).fetchall()
return dict(results)
@@ -1141,40 +1203,40 @@ class MrnaAssayDataSet(DataSet):
class TempDataSet(DataSet):
'''Temporary user-generated data set'''
- DS_NAME_MAP['Temp'] = 'TempDataSet'
+ DS_NAME_MAP['Temp']='TempDataSet'
def setup(self):
- self.search_fields = ['name',
+ self.search_fields=['name',
'description']
- self.display_fields = ['name',
+ self.display_fields=['name',
'description']
- self.header_fields = ['Name',
+ self.header_fields=['Name',
'Description']
- self.type = 'Temp'
+ self.type='Temp'
# Need to double check later how these are used
- self.id = 1
- self.fullname = 'Temporary Storage'
- self.shortname = 'Temp'
+ self.id=1
+ self.fullname='Temporary Storage'
+ self.shortname='Temp'
def geno_mrna_confidentiality(ob):
- dataset_table = ob.type + "Freeze"
- #logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
+ dataset_table=ob.type + "Freeze"
+ # logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
- query = '''SELECT Id, Name, FullName, confidentiality,
+ query='''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
logger.sql(query)
- result = g.db.execute(query)
+ result=g.db.execute(query)
(dataset_id,
name,
full_name,
confidential,
- authorized_users) = result.fetchall()[0]
+ authorized_users)=result.fetchall()[0]
if confidential:
return True
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index df0afba6..9fbfee48 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -27,6 +27,34 @@ def create_target_this_trait(start_vars):
return (this_dataset, this_trait, target_dataset, sample_data)
+
+def test_process_data(this_trait,dataset,start_vars):
+ """test function for bxd,all and other sample data"""
+
+ corr_samples_group = start_vars["corr_samples_group"]
+
+
+ primary_samples = dataset.group.samplelist
+ if dataset.group.parlist != None:
+ primary_samples += dataset.group.parlist
+ if dataset.group.f1list != None:
+ primary_samples += dataset.group.f1list
+
+ # If either BXD/whatever Only or All Samples, append all of that group's samplelist
+ if corr_samples_group != 'samples_other':
+ sample_data = process_samples(start_vars, primary_samples)
+
+ # If either Non-BXD/whatever or All Samples, get all samples from this_trait.data and
+ # exclude the primary samples (because they would have been added in the previous
+ # if statement if the user selected All Samples)
+ if corr_samples_group != 'samples_primary':
+ if corr_samples_group == 'samples_other':
+ primary_samples = [x for x in primary_samples if x not in (
+ dataset.group.parlist + dataset.group.f1list)]
+ sample_data = process_samples(start_vars, list(this_trait.data.keys()), primary_samples)
+
+ return sample_data
+
def process_samples(start_vars, sample_names, excluded_samples=None):
"""process samples"""
sample_data = {}
@@ -118,13 +146,22 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
sample_data = process_samples(
start_vars, this_dataset.group.samplelist)
- target_dataset.get_trait_data(list(sample_data.keys()))
+
+ # sample_data = test_process_data(this_trait,this_dataset,start_vars)
+
+ if target_dataset.type =="ProbeSet":
+ # pass
+ target_dataset.get_probeset_data(list(sample_data.keys()))
+ else:
+ target_dataset.get_trait_data(list(sample_data.keys()))
this_trait = retrieve_sample_data(this_trait, this_dataset)
this_trait_data = {
"trait_sample_data": sample_data,
"trait_id": start_vars["trait_id"]
}
+ # should remove this len(samplelist) == len(strain_values)
+
results = map_shared_keys_to_values(
target_dataset.samplelist, target_dataset.trait_data)
@@ -205,6 +242,7 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
"target_dataset": start_vars['corr_dataset'],
"return_results": corr_return_results}
+
return correlation_data
@@ -265,3 +303,107 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict):
}
return (primary_tissue_data, target_tissue_data)
return None
+
+
+def generate_corr_data(corr_results, target_dataset):
+ counter = 0
+ results_list = []
+ for (index, trait_corr) in enumerate(corr_results):
+ trait_name = list(trait_corr.keys())[0]
+ trait = create_trait(dataset=target_dataset,
+ name=trait_name)
+
+ trait_corr_data = trait_corr[trait_name]
+
+ if trait.view == False:
+ continue
+ results_dict = {}
+ results_dict['index'] = index + 1
+ results_dict['trait_id'] = trait.name
+ results_dict['dataset'] = trait.dataset.name
+ # results_dict['hmac'] = hmac.data_hmac(
+ # '{}:{}'.format(trait.name, trait.dataset.name))
+ if target_dataset.type == "ProbeSet":
+ results_dict['symbol'] = trait.symbol
+ results_dict['description'] = "N/A"
+ results_dict['location'] = trait.location_repr
+ results_dict['mean'] = "N/A"
+ results_dict['additive'] = "N/A"
+ if bool(trait.description_display):
+ results_dict['description'] = trait.description_display
+ if bool(trait.mean):
+ results_dict['mean'] = f"{float(trait.mean):.3f}"
+ try:
+ results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
+ except:
+ results_dict['lod_score'] = "N/A"
+ results_dict['lrs_location'] = trait.LRS_location_repr
+ if bool(trait.additive):
+ results_dict['additive'] = f"{float(trait.additive):.3f}"
+ results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
+ results_dict['num_overlap'] = trait.num_overlap
+ results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
+ results_dict['lit_corr'] = "--"
+ results_dict['tissue_corr'] = "--"
+ results_dict['tissue_pvalue'] = "--"
+ tissue_corr = trait_corr_data.get('tissue_corr',0)
+ lit_corr = trait_corr_data.get('lit_corr',0)
+ if bool(lit_corr):
+ results_dict['lit_corr'] = f"{float(trait_corr_data.get('lit_corr',0)):.3f}"
+ if bool(tissue_corr):
+ results_dict['tissue_corr'] = f"{float(trait_corr_data.get('tissue_corr',0)):.3f}"
+ results_dict['tissue_pvalue'] = f"{float(trait_corr_data.get('tissue_pvalue',0)):.3e}"
+ elif target_dataset.type == "Publish":
+ results_dict['abbreviation_display'] = "N/A"
+ results_dict['description'] = "N/A"
+ results_dict['mean'] = "N/A"
+ results_dict['authors_display'] = "N/A"
+ results_dict['additive'] = "N/A"
+ if for_api:
+ results_dict['pubmed_id'] = "N/A"
+ results_dict['year'] = "N/A"
+ else:
+ results_dict['pubmed_link'] = "N/A"
+ results_dict['pubmed_text'] = "N/A"
+
+ if bool(trait.abbreviation):
+ results_dict['abbreviation_display'] = trait.abbreviation
+ if bool(trait.description_display):
+ results_dict['description'] = trait.description_display
+ if bool(trait.mean):
+ results_dict['mean'] = f"{float(trait.mean):.3f}"
+ if bool(trait.authors):
+ authors_list = trait.authors.split(',')
+ if len(authors_list) > 6:
+ results_dict['authors_display'] = ", ".join(
+ authors_list[:6]) + ", et al."
+ else:
+ results_dict['authors_display'] = trait.authors
+ if bool(trait.pubmed_id):
+ if for_api:
+ results_dict['pubmed_id'] = trait.pubmed_id
+ results_dict['year'] = trait.pubmed_text
+ else:
+ results_dict['pubmed_link'] = trait.pubmed_link
+ results_dict['pubmed_text'] = trait.pubmed_text
+ try:
+ results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
+ except:
+ results_dict['lod_score'] = "N/A"
+ results_dict['lrs_location'] = trait.LRS_location_repr
+ if bool(trait.additive):
+ results_dict['additive'] = f"{float(trait.additive):.3f}"
+ results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
+ results_dict['num_overlap'] = trait.num_overlap
+ results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
+ else:
+ results_dict['location'] = trait.location_repr
+ results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
+ results_dict['num_overlap'] = trait.num_overlap
+ results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
+
+ results_list.append(results_dict)
+
+ return results_list
+
+
--
cgit v1.2.3
From c9a133e75d32e0bb9c8e63443b0f43f084363996 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 24 May 2021 16:37:36 +0300
Subject: pep8 formatting
---
wqflask/base/data_set.py | 214 ++++++++++++++++++++++++-----------------------
1 file changed, 109 insertions(+), 105 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 7531ac81..39296f6a 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -659,12 +659,8 @@ class DataSet:
"Dataset {} is not yet available in GeneNetwork.".format(self.name))
pass
-
-
-
def chunk_dataset(self, dataset, n):
-
results = {}
query = """
@@ -677,10 +673,7 @@ class DataSet:
# should cache this
- traits_name_dict= dict(g.db.execute(query).fetchall())
-
-
-
+ traits_name_dict = dict(g.db.execute(query).fetchall())
for i in range(0, len(dataset), n):
matrix = list(dataset[i:i + n])
@@ -716,50 +709,50 @@ class DataSet:
FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
and ProbeSetFreeze.Name = '{}'
- and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids),self.name)
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids), self.name)
- query_results=list(g.db.execute(query).fetchall())
+ query_results = list(g.db.execute(query).fetchall())
- data_results=self.chunk_dataset(query_results, len(sample_ids))
- self.trait_data=data_results
+ data_results = self.chunk_dataset(query_results, len(sample_ids))
+ self.trait_data = data_results
def get_trait_data(self, sample_list=None):
if sample_list:
- self.samplelist=sample_list
+ self.samplelist = sample_list
else:
- self.samplelist=self.group.samplelist
+ self.samplelist = self.group.samplelist
if self.group.parlist != None and self.group.f1list != None:
if (self.group.parlist + self.group.f1list) in self.samplelist:
self.samplelist += self.group.parlist + self.group.f1list
- query="""
+ query = """
SELECT Strain.Name, Strain.Id FROM Strain, Species
WHERE Strain.Name IN {}
and Strain.SpeciesId=Species.Id
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
logger.sql(query)
- results=dict(g.db.execute(query).fetchall())
- sample_ids=[results[item] for item in self.samplelist]
+ results = dict(g.db.execute(query).fetchall())
+ sample_ids = [results[item] for item in self.samplelist]
# MySQL limits the number of tables that can be used in a join to 61,
# so we break the sample ids into smaller chunks
# Postgres doesn't have that limit, so we can get rid of this after we transition
- chunk_size=50
- number_chunks=int(math.ceil(len(sample_ids) / chunk_size))
- trait_sample_data=[]
+ chunk_size = 50
+ number_chunks = int(math.ceil(len(sample_ids) / chunk_size))
+ trait_sample_data = []
for sample_ids_step in chunks.divide_into_chunks(sample_ids, number_chunks):
if self.type == "Publish":
- dataset_type="Phenotype"
+ dataset_type = "Phenotype"
else:
- dataset_type=self.type
- temp=['T%s.value' % item for item in sample_ids_step]
+ dataset_type = self.type
+ temp = ['T%s.value' % item for item in sample_ids_step]
if self.type == "Publish":
- query="SELECT {}XRef.Id,".format(escape(self.type))
+ query = "SELECT {}XRef.Id,".format(escape(self.type))
else:
- query="SELECT {}.Name,".format(escape(dataset_type))
- data_start_pos=1
+ query = "SELECT {}.Name,".format(escape(dataset_type))
+ data_start_pos = 1
query += ', '.join(temp)
query += ' FROM ({}, {}XRef, {}Freeze) '.format(*mescape(dataset_type,
self.type,
@@ -788,27 +781,27 @@ class DataSet:
""".format(*mescape(self.type, self.type, self.type, self.type,
self.name, dataset_type, self.type, self.type, dataset_type))
- results=g.db.execute(query).fetchall()
+ results = g.db.execute(query).fetchall()
trait_sample_data.append(results)
- trait_count=len(trait_sample_data[0])
- self.trait_data=collections.defaultdict(list)
+ trait_count = len(trait_sample_data[0])
+ self.trait_data = collections.defaultdict(list)
# put all of the separate data together into a dictionary where the keys are
# trait names and values are lists of sample values
for trait_counter in range(trait_count):
- trait_name=trait_sample_data[0][trait_counter][0]
+ trait_name = trait_sample_data[0][trait_counter][0]
for chunk_counter in range(int(number_chunks)):
self.trait_data[trait_name] += (
trait_sample_data[chunk_counter][trait_counter][data_start_pos:])
class PhenotypeDataSet(DataSet):
- DS_NAME_MAP['Publish']='PhenotypeDataSet'
+ DS_NAME_MAP['Publish'] = 'PhenotypeDataSet'
def setup(self):
# Fields in the database table
- self.search_fields=['Phenotype.Post_publication_description',
+ self.search_fields = ['Phenotype.Post_publication_description',
'Phenotype.Pre_publication_description',
'Phenotype.Pre_publication_abbreviation',
'Phenotype.Post_publication_abbreviation',
@@ -821,7 +814,7 @@ class PhenotypeDataSet(DataSet):
'PublishXRef.Id']
# Figure out what display_fields is
- self.display_fields=['name', 'group_code',
+ self.display_fields = ['name', 'group_code',
'pubmed_id',
'pre_publication_description',
'post_publication_description',
@@ -839,7 +832,7 @@ class PhenotypeDataSet(DataSet):
'sequence', 'units', 'comments']
# Fields displayed in the search results table header
- self.header_fields=['Index',
+ self.header_fields = ['Index',
'Record',
'Description',
'Authors',
@@ -848,9 +841,9 @@ class PhenotypeDataSet(DataSet):
'Max LRS Location',
'Additive Effect']
- self.type='Publish'
+ self.type = 'Publish'
- self.query_for_group='''
+ self.query_for_group = '''
SELECT
InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
@@ -870,13 +863,13 @@ class PhenotypeDataSet(DataSet):
if not this_trait.haveinfo:
this_trait.retrieve_info(get_qtl_info=True)
- description=this_trait.post_publication_description
+ description = this_trait.post_publication_description
# If the dataset is confidential and the user has access to confidential
# phenotype traits, then display the pre-publication description instead
# of the post-publication description
if this_trait.confidential:
- this_trait.description_display=""
+ this_trait.description_display = ""
continue # for now, because no authorization features
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
@@ -884,46 +877,46 @@ class PhenotypeDataSet(DataSet):
userName=self.userName,
authorized_users=this_trait.authorized_users):
- description=this_trait.pre_publication_description
+ description = this_trait.pre_publication_description
if len(description) > 0:
- this_trait.description_display=description.strip()
+ this_trait.description_display = description.strip()
else:
- this_trait.description_display=""
+ this_trait.description_display = ""
if not this_trait.year.isdigit():
- this_trait.pubmed_text="N/A"
+ this_trait.pubmed_text = "N/A"
else:
- this_trait.pubmed_text=this_trait.year
+ this_trait.pubmed_text = this_trait.year
if this_trait.pubmed_id:
- this_trait.pubmed_link=webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
+ this_trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % this_trait.pubmed_id
# LRS and its location
- this_trait.LRS_score_repr="N/A"
- this_trait.LRS_location_repr="N/A"
+ this_trait.LRS_score_repr = "N/A"
+ this_trait.LRS_location_repr = "N/A"
if this_trait.lrs:
- query="""
+ query = """
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '%s' and
Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, this_trait.locus)
logger.sql(query)
- result=g.db.execute(query).fetchone()
+ result = g.db.execute(query).fetchone()
if result:
if result[0] and result[1]:
- LRS_Chr=result[0]
- LRS_Mb=result[1]
+ LRS_Chr = result[0]
+ LRS_Mb = result[1]
- this_trait.LRS_score_repr=LRS_score_repr='%3.1f' % this_trait.lrs
- this_trait.LRS_location_repr=LRS_location_repr='Chr%s: %.6f' % (
+ this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
+ this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
LRS_Chr, float(LRS_Mb))
def retrieve_sample_data(self, trait):
- query="""
+ query = """
SELECT
Strain.Name, PublishData.value, PublishSE.error, NStrain.count, Strain.Name2
FROM
@@ -941,34 +934,34 @@ class PhenotypeDataSet(DataSet):
Strain.Name
"""
logger.sql(query)
- results=g.db.execute(query, (trait, self.id)).fetchall()
+ results = g.db.execute(query, (trait, self.id)).fetchall()
return results
class GenotypeDataSet(DataSet):
- DS_NAME_MAP['Geno']='GenotypeDataSet'
+ DS_NAME_MAP['Geno'] = 'GenotypeDataSet'
def setup(self):
# Fields in the database table
- self.search_fields=['Name',
+ self.search_fields = ['Name',
'Chr']
# Find out what display_fields is
- self.display_fields=['name',
+ self.display_fields = ['name',
'chr',
'mb',
'source2',
'sequence']
# Fields displayed in the search results table header
- self.header_fields=['Index',
+ self.header_fields = ['Index',
'ID',
'Location']
# Todo: Obsolete or rename this field
- self.type='Geno'
+ self.type = 'Geno'
- self.query_for_group='''
+ self.query_for_group = '''
SELECT
InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
@@ -987,11 +980,11 @@ class GenotypeDataSet(DataSet):
this_trait.retrieveInfo()
if this_trait.chr and this_trait.mb:
- this_trait.location_repr='Chr%s: %.6f' % (
+ this_trait.location_repr = 'Chr%s: %.6f' % (
this_trait.chr, float(this_trait.mb))
def retrieve_sample_data(self, trait):
- query="""
+ query = """
SELECT
Strain.Name, GenoData.value, GenoSE.error, "N/A", Strain.Name2
FROM
@@ -1008,7 +1001,7 @@ class GenotypeDataSet(DataSet):
Strain.Name
"""
logger.sql(query)
- results=g.db.execute(query,
+ results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
return results
@@ -1022,11 +1015,11 @@ class MrnaAssayDataSet(DataSet):
platform and is far too specific.
'''
- DS_NAME_MAP['ProbeSet']='MrnaAssayDataSet'
+ DS_NAME_MAP['ProbeSet'] = 'MrnaAssayDataSet'
def setup(self):
# Fields in the database table
- self.search_fields=['Name',
+ self.search_fields = ['Name',
'Description',
'Probe_Target_Description',
'Symbol',
@@ -1036,7 +1029,7 @@ class MrnaAssayDataSet(DataSet):
'RefSeq_TranscriptId']
# Find out what display_fields is
- self.display_fields=['name', 'symbol',
+ self.display_fields = ['name', 'symbol',
'description', 'probe_target_description',
'chr', 'mb',
'alias', 'geneid',
@@ -1056,7 +1049,7 @@ class MrnaAssayDataSet(DataSet):
'flag']
# Fields displayed in the search results table header
- self.header_fields=['Index',
+ self.header_fields = ['Index',
'Record',
'Symbol',
'Description',
@@ -1067,9 +1060,9 @@ class MrnaAssayDataSet(DataSet):
'Additive Effect']
# Todo: Obsolete or rename this field
- self.type='ProbeSet'
+ self.type = 'ProbeSet'
- self.query_for_group='''
+ self.query_for_group = '''
SELECT
InbredSet.Name, InbredSet.Id, InbredSet.GeneticType
FROM
@@ -1087,7 +1080,7 @@ class MrnaAssayDataSet(DataSet):
# Note: setting trait_list to [] is probably not a great idea.
if not trait_list:
- trait_list=[]
+ trait_list = []
for this_trait in trait_list:
@@ -1095,33 +1088,33 @@ class MrnaAssayDataSet(DataSet):
this_trait.retrieveInfo(QTL=1)
if not this_trait.symbol:
- this_trait.symbol="N/A"
+ this_trait.symbol = "N/A"
# XZ, 12/08/2008: description
# XZ, 06/05/2009: Rob asked to add probe target description
- description_string=str(
+ description_string = str(
str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8')
- target_string=str(
+ target_string = str(
str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
if len(description_string) > 1 and description_string != 'None':
- description_display=description_string
+ description_display = description_string
else:
- description_display=this_trait.symbol
+ description_display = this_trait.symbol
if (len(description_display) > 1 and description_display != 'N/A'
and len(target_string) > 1 and target_string != 'None'):
- description_display=description_display + '; ' + target_string.strip()
+ description_display = description_display + '; ' + target_string.strip()
# Save it for the jinja2 template
- this_trait.description_display=description_display
+ this_trait.description_display = description_display
if this_trait.chr and this_trait.mb:
- this_trait.location_repr='Chr%s: %.6f' % (
+ this_trait.location_repr = 'Chr%s: %.6f' % (
this_trait.chr, float(this_trait.mb))
# Get mean expression value
- query=(
+ query = (
"""select ProbeSetXRef.mean from ProbeSetXRef, ProbeSet
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSet.Id = ProbeSetXRef.ProbeSetId and
@@ -1131,38 +1124,38 @@ class MrnaAssayDataSet(DataSet):
# logger.debug("query is:", pf(query))
logger.sql(query)
- result=g.db.execute(query).fetchone()
+ result = g.db.execute(query).fetchone()
- mean=result[0] if result else 0
+ mean = result[0] if result else 0
if mean:
- this_trait.mean="%2.3f" % mean
+ this_trait.mean = "%2.3f" % mean
# LRS and its location
- this_trait.LRS_score_repr='N/A'
- this_trait.LRS_location_repr='N/A'
+ this_trait.LRS_score_repr = 'N/A'
+ this_trait.LRS_location_repr = 'N/A'
# Max LRS and its Locus location
if this_trait.lrs and this_trait.locus:
- query="""
+ query = """
select Geno.Chr, Geno.Mb from Geno, Species
where Species.Name = '{}' and
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(species, this_trait.locus)
logger.sql(query)
- result=g.db.execute(query).fetchone()
+ result = g.db.execute(query).fetchone()
if result:
- lrs_chr, lrs_mb=result
- this_trait.LRS_score_repr='%3.1f' % this_trait.lrs
- this_trait.LRS_location_repr='Chr%s: %.6f' % (
+ lrs_chr, lrs_mb = result
+ this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
+ this_trait.LRS_location_repr = 'Chr%s: %.6f' % (
lrs_chr, float(lrs_mb))
return trait_list
def retrieve_sample_data(self, trait):
- query="""
+ query = """
SELECT
Strain.Name, ProbeSetData.value, ProbeSetSE.error, NStrain.count, Strain.Name2
FROM
@@ -1183,19 +1176,19 @@ class MrnaAssayDataSet(DataSet):
Strain.Name
""" % (escape(trait), escape(self.name))
logger.sql(query)
- results=g.db.execute(query).fetchall()
+ results = g.db.execute(query).fetchall()
# logger.debug("RETRIEVED RESULTS HERE:", results)
return results
def retrieve_genes(self, column_name):
- query="""
+ query = """
select ProbeSet.Name, ProbeSet.%s
from ProbeSet,ProbeSetXRef
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
""" % (column_name, escape(str(self.id)))
logger.sql(query)
- results=g.db.execute(query).fetchall()
+ results = g.db.execute(query).fetchall()
return dict(results)
@@ -1203,40 +1196,51 @@ class MrnaAssayDataSet(DataSet):
class TempDataSet(DataSet):
'''Temporary user-generated data set'''
- DS_NAME_MAP['Temp']='TempDataSet'
+ DS_NAME_MAP['Temp'] = 'TempDataSet'
def setup(self):
- self.search_fields=['name',
+ self.search_fields = ['name',
'description']
- self.display_fields=['name',
+ self.display_fields = ['name',
'description']
- self.header_fields=['Name',
+ self.header_fields = ['Name',
'Description']
- self.type='Temp'
+ self.type = 'Temp'
# Need to double check later how these are used
- self.id=1
- self.fullname='Temporary Storage'
- self.shortname='Temp'
+ self.id = 1
+ self.fullname = 'Temporary Storage'
+ self.shortname = 'Temp'
def geno_mrna_confidentiality(ob):
- dataset_table=ob.type + "Freeze"
+ dataset_table = ob.type + "Freeze"
# logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
- query='''SELECT Id, Name, FullName, confidentiality,
+ query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
logger.sql(query)
- result=g.db.execute(query)
+ result = g.db.execute(query)
+
+ (dataset_id,
+ name,
+ full_name,
+ confidential,
+ authorized_users) = result.fetchall()[0]
+
+ if confidential:
+ return True
+uery)
+ result = g.db.execute(query)
(dataset_id,
name,
full_name,
confidential,
- authorized_users)=result.fetchall()[0]
+ authorized_users) = result.fetchall()[0]
if confidential:
return True
--
cgit v1.2.3
From d8d3a8311106ea97c1fba4ef4606929eb9b0fdcb Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 24 May 2021 16:43:45 +0300
Subject: minor fix
---
wqflask/base/data_set.py | 1 -
1 file changed, 1 deletion(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 39296f6a..4a150e86 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1233,7 +1233,6 @@ def geno_mrna_confidentiality(ob):
if confidential:
return True
-uery)
result = g.db.execute(query)
(dataset_id,
--
cgit v1.2.3
From aaacfe3a0abc7ca4fe5bdb486651e018cdc7aba0 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 9 Jun 2021 07:25:03 +0300
Subject: remove unused functions + minor fixes
---
wqflask/base/data_set.py | 2 +
wqflask/wqflask/correlation/correlation_gn3_api.py | 115 +--------------------
2 files changed, 7 insertions(+), 110 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4a150e86..4d54cfae 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -684,6 +684,8 @@ class DataSet:
return results
def get_probeset_data(self, sample_list=None, trait_ids=None):
+
+ # improvement of get trait data--->>>
if sample_list:
self.samplelist = sample_list
diff --git a/wqflask/wqflask/correlation/correlation_gn3_api.py b/wqflask/wqflask/correlation/correlation_gn3_api.py
index 9fbfee48..5fa33027 100644
--- a/wqflask/wqflask/correlation/correlation_gn3_api.py
+++ b/wqflask/wqflask/correlation/correlation_gn3_api.py
@@ -27,13 +27,11 @@ def create_target_this_trait(start_vars):
return (this_dataset, this_trait, target_dataset, sample_data)
-
-def test_process_data(this_trait,dataset,start_vars):
+def test_process_data(this_trait, dataset, start_vars):
"""test function for bxd,all and other sample data"""
corr_samples_group = start_vars["corr_samples_group"]
-
primary_samples = dataset.group.samplelist
if dataset.group.parlist != None:
primary_samples += dataset.group.parlist
@@ -51,10 +49,12 @@ def test_process_data(this_trait,dataset,start_vars):
if corr_samples_group == 'samples_other':
primary_samples = [x for x in primary_samples if x not in (
dataset.group.parlist + dataset.group.f1list)]
- sample_data = process_samples(start_vars, list(this_trait.data.keys()), primary_samples)
+ sample_data = process_samples(start_vars, list(
+ this_trait.data.keys()), primary_samples)
return sample_data
+
def process_samples(start_vars, sample_names, excluded_samples=None):
"""process samples"""
sample_data = {}
@@ -149,7 +149,7 @@ def fetch_sample_data(start_vars, this_trait, this_dataset, target_dataset):
# sample_data = test_process_data(this_trait,this_dataset,start_vars)
- if target_dataset.type =="ProbeSet":
+ if target_dataset.type == "ProbeSet":
# pass
target_dataset.get_probeset_data(list(sample_data.keys()))
else:
@@ -242,7 +242,6 @@ def compute_correlation(start_vars, method="pearson", compute_all=False):
"target_dataset": start_vars['corr_dataset'],
"return_results": corr_return_results}
-
return correlation_data
@@ -303,107 +302,3 @@ def get_tissue_correlation_input(this_trait, trait_symbol_dict):
}
return (primary_tissue_data, target_tissue_data)
return None
-
-
-def generate_corr_data(corr_results, target_dataset):
- counter = 0
- results_list = []
- for (index, trait_corr) in enumerate(corr_results):
- trait_name = list(trait_corr.keys())[0]
- trait = create_trait(dataset=target_dataset,
- name=trait_name)
-
- trait_corr_data = trait_corr[trait_name]
-
- if trait.view == False:
- continue
- results_dict = {}
- results_dict['index'] = index + 1
- results_dict['trait_id'] = trait.name
- results_dict['dataset'] = trait.dataset.name
- # results_dict['hmac'] = hmac.data_hmac(
- # '{}:{}'.format(trait.name, trait.dataset.name))
- if target_dataset.type == "ProbeSet":
- results_dict['symbol'] = trait.symbol
- results_dict['description'] = "N/A"
- results_dict['location'] = trait.location_repr
- results_dict['mean'] = "N/A"
- results_dict['additive'] = "N/A"
- if bool(trait.description_display):
- results_dict['description'] = trait.description_display
- if bool(trait.mean):
- results_dict['mean'] = f"{float(trait.mean):.3f}"
- try:
- results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
- except:
- results_dict['lod_score'] = "N/A"
- results_dict['lrs_location'] = trait.LRS_location_repr
- if bool(trait.additive):
- results_dict['additive'] = f"{float(trait.additive):.3f}"
- results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
- results_dict['num_overlap'] = trait.num_overlap
- results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
- results_dict['lit_corr'] = "--"
- results_dict['tissue_corr'] = "--"
- results_dict['tissue_pvalue'] = "--"
- tissue_corr = trait_corr_data.get('tissue_corr',0)
- lit_corr = trait_corr_data.get('lit_corr',0)
- if bool(lit_corr):
- results_dict['lit_corr'] = f"{float(trait_corr_data.get('lit_corr',0)):.3f}"
- if bool(tissue_corr):
- results_dict['tissue_corr'] = f"{float(trait_corr_data.get('tissue_corr',0)):.3f}"
- results_dict['tissue_pvalue'] = f"{float(trait_corr_data.get('tissue_pvalue',0)):.3e}"
- elif target_dataset.type == "Publish":
- results_dict['abbreviation_display'] = "N/A"
- results_dict['description'] = "N/A"
- results_dict['mean'] = "N/A"
- results_dict['authors_display'] = "N/A"
- results_dict['additive'] = "N/A"
- if for_api:
- results_dict['pubmed_id'] = "N/A"
- results_dict['year'] = "N/A"
- else:
- results_dict['pubmed_link'] = "N/A"
- results_dict['pubmed_text'] = "N/A"
-
- if bool(trait.abbreviation):
- results_dict['abbreviation_display'] = trait.abbreviation
- if bool(trait.description_display):
- results_dict['description'] = trait.description_display
- if bool(trait.mean):
- results_dict['mean'] = f"{float(trait.mean):.3f}"
- if bool(trait.authors):
- authors_list = trait.authors.split(',')
- if len(authors_list) > 6:
- results_dict['authors_display'] = ", ".join(
- authors_list[:6]) + ", et al."
- else:
- results_dict['authors_display'] = trait.authors
- if bool(trait.pubmed_id):
- if for_api:
- results_dict['pubmed_id'] = trait.pubmed_id
- results_dict['year'] = trait.pubmed_text
- else:
- results_dict['pubmed_link'] = trait.pubmed_link
- results_dict['pubmed_text'] = trait.pubmed_text
- try:
- results_dict['lod_score'] = f"{float(trait.LRS_score_repr) / 4.61:.1f}"
- except:
- results_dict['lod_score'] = "N/A"
- results_dict['lrs_location'] = trait.LRS_location_repr
- if bool(trait.additive):
- results_dict['additive'] = f"{float(trait.additive):.3f}"
- results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
- results_dict['num_overlap'] = trait.num_overlap
- results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
- else:
- results_dict['location'] = trait.location_repr
- results_dict['sample_r'] = f"{float(trait_corr_data.get('sample_r',0)):.3f}"
- results_dict['num_overlap'] = trait.num_overlap
- results_dict['sample_p'] = f"{float(trait_corr_data.get('sample_p',0)):.3e}"
-
- results_list.append(results_dict)
-
- return results_list
-
-
--
cgit v1.2.3
From 48e66dc230292a9c0b66da946106d8c9f611074f Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 14 Jun 2021 00:54:02 +0300
Subject: sort sample name by sample_ids
---
wqflask/base/data_set.py | 6 +++++-
1 file changed, 5 insertions(+), 1 deletion(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4d54cfae..991c9fee 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -705,6 +705,9 @@ class DataSet:
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
+ sorted_samplelist = [strain_name for strain_name, strain_id in sorted(
+ results.items(), key=lambda item: item[1])]
+
query = """SELECT * from ProbeSetData
where StrainID in {}
and id in (SELECT ProbeSetXRef.DataId
@@ -714,9 +717,10 @@ class DataSet:
and ProbeSet.Id = ProbeSetXRef.ProbeSetId)""".format(create_in_clause(sample_ids), self.name)
query_results = list(g.db.execute(query).fetchall())
-
data_results = self.chunk_dataset(query_results, len(sample_ids))
+ self.samplelist = sorted_samplelist
self.trait_data = data_results
+
def get_trait_data(self, sample_list=None):
if sample_list:
--
cgit v1.2.3
From 8521ba973ccf14b6918948a93cfde07d6cf1e27a Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Mon, 14 Jun 2021 09:28:46 +0300
Subject: delete loggers and comments
---
wqflask/base/data_set.py | 4 ----
1 file changed, 4 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 991c9fee..4cb82665 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -440,7 +440,6 @@ class DatasetGroup:
# genotype_1 is Dataset Object without parents and f1
# genotype_2 is Dataset Object with parents and f1 (not for intercross)
- # genotype_1 = reaper.Dataset()
# reaper barfs on unicode filenames, so here we ensure it's a string
if self.genofile:
@@ -1128,7 +1127,6 @@ class MrnaAssayDataSet(DataSet):
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
- # logger.debug("query is:", pf(query))
logger.sql(query)
result = g.db.execute(query).fetchone()
@@ -1183,7 +1181,6 @@ class MrnaAssayDataSet(DataSet):
""" % (escape(trait), escape(self.name))
logger.sql(query)
results = g.db.execute(query).fetchall()
- # logger.debug("RETRIEVED RESULTS HERE:", results)
return results
def retrieve_genes(self, column_name):
@@ -1224,7 +1221,6 @@ class TempDataSet(DataSet):
def geno_mrna_confidentiality(ob):
dataset_table = ob.type + "Freeze"
- # logger.debug("dataset_table [%s]: %s" % (type(dataset_table), dataset_table))
query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
--
cgit v1.2.3
From f4fbb6d53419a19c6ee67977d18605cdcbb09c0e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 22:35:53 +0000
Subject: add function for reading in JSON file that lists sample lists unique
to each study within a group (in this case only BXD Longevity for now)
---
wqflask/base/data_set.py | 9 +++++++++
wqflask/wqflask/show_trait/show_trait.py | 1 +
2 files changed, 10 insertions(+)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4cb82665..b8f2f9fb 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -398,6 +398,15 @@ class DatasetGroup:
if maternal and paternal:
self.parlist = [maternal, paternal]
+ def get_study_samplelists(self):
+ study_sample_file = "%s/study_sample_lists/%s.json" % (webqtlConfig.GENODIR, self.name)
+ try:
+ f = open(study_sample_file)
+ except:
+ return None
+ study_samples = json.load(f)
+ return study_samples
+
def get_genofiles(self):
jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
try:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c07430dd..d3356bc3 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -192,6 +192,7 @@ class ShowTrait:
[self.dataset.species.chromosomes.chromosomes[this_chr].name, i])
self.genofiles = self.dataset.group.get_genofiles()
+ self.study_samplelists = self.dataset.group.get_study_samplelists()
# ZS: No need to grab scales from .geno file unless it's using
# a mapping method that reads .geno files
--
cgit v1.2.3
From 98683bd5cc809aa03e0bd58a67733498b4f56a9d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 23:17:04 +0000
Subject: Fix the way the study_sample_lists path is set and checked
---
wqflask/base/data_set.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index b8f2f9fb..1042e1bd 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -399,7 +399,7 @@ class DatasetGroup:
self.parlist = [maternal, paternal]
def get_study_samplelists(self):
- study_sample_file = "%s/study_sample_lists/%s.json" % (webqtlConfig.GENODIR, self.name)
+ study_sample_file = locate_ignore_error(self.name + ".json", 'study_sample_lists')
try:
f = open(study_sample_file)
except:
--
cgit v1.2.3
From 810b2ace0a9cb2511cf0ef6f0c01f70a0ce11915 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 12 Aug 2021 23:19:38 +0000
Subject: Return empty list instead of None in get_study_samplelists
---
wqflask/base/data_set.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1042e1bd..0ea61faa 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -403,7 +403,7 @@ class DatasetGroup:
try:
f = open(study_sample_file)
except:
- return None
+ return []
study_samples = json.load(f)
return study_samples
--
cgit v1.2.3
From 579ae94b08f0b1cef00350b54dadc12869ad70de Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 6 Aug 2021 16:15:17 +0300
Subject: base: data_set: Remove unnecessary comments and logging statements
---
wqflask/base/data_set.py | 12 ------------
1 file changed, 12 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4cb82665..edc22540 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -277,7 +277,6 @@ class Markers:
filtered_markers = []
for marker in self.markers:
if marker['name'] in p_values:
- # logger.debug("marker {} IS in p_values".format(i))
marker['p_value'] = p_values[marker['name']]
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
@@ -298,7 +297,6 @@ class HumanMarkers(Markers):
self.markers = []
for line in marker_data_fh:
splat = line.strip().split()
- # logger.debug("splat:", splat)
if len(specified_markers) > 0:
if splat[1] in specified_markers:
marker = {}
@@ -737,7 +735,6 @@ class DataSet:
and Strain.SpeciesId=Species.Id
and Species.name = '{}'
""".format(create_in_clause(self.samplelist), *mescape(self.group.species))
- logger.sql(query)
results = dict(g.db.execute(query).fetchall())
sample_ids = [results[item] for item in self.samplelist]
@@ -908,7 +905,6 @@ class PhenotypeDataSet(DataSet):
Geno.Name = '%s' and
Geno.SpeciesId = Species.Id
""" % (species, this_trait.locus)
- logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
@@ -938,7 +934,6 @@ class PhenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
- logger.sql(query)
results = g.db.execute(query, (trait, self.id)).fetchall()
return results
@@ -1005,7 +1000,6 @@ class GenotypeDataSet(DataSet):
Order BY
Strain.Name
"""
- logger.sql(query)
results = g.db.execute(query,
(webqtlDatabaseFunction.retrieve_species_id(self.group.name),
trait, self.name)).fetchall()
@@ -1126,8 +1120,6 @@ class MrnaAssayDataSet(DataSet):
ProbeSet.Name = '%s'
""" % (escape(str(this_trait.dataset.id)),
escape(this_trait.name)))
-
- logger.sql(query)
result = g.db.execute(query).fetchone()
mean = result[0] if result else 0
@@ -1147,7 +1139,6 @@ class MrnaAssayDataSet(DataSet):
Geno.Name = '{}' and
Geno.SpeciesId = Species.Id
""".format(species, this_trait.locus)
- logger.sql(query)
result = g.db.execute(query).fetchone()
if result:
@@ -1179,7 +1170,6 @@ class MrnaAssayDataSet(DataSet):
Order BY
Strain.Name
""" % (escape(trait), escape(self.name))
- logger.sql(query)
results = g.db.execute(query).fetchall()
return results
@@ -1190,7 +1180,6 @@ class MrnaAssayDataSet(DataSet):
where ProbeSetXRef.ProbeSetFreezeId = %s and
ProbeSetXRef.ProbeSetId=ProbeSet.Id;
""" % (column_name, escape(str(self.id)))
- logger.sql(query)
results = g.db.execute(query).fetchall()
return dict(results)
@@ -1224,7 +1213,6 @@ def geno_mrna_confidentiality(ob):
query = '''SELECT Id, Name, FullName, confidentiality,
AuthorisedUsers FROM %s WHERE Name = "%s"''' % (dataset_table, ob.name)
- logger.sql(query)
result = g.db.execute(query)
(dataset_id,
--
cgit v1.2.3
From 898b80d34442c16399366a5744cc26a157a727cb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 20 Aug 2021 17:46:20 +0000
Subject: Fixed some logic in trait.py that could cause a problem if a
dataset_name was passed that wasn't Temp
---
wqflask/base/trait.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
(limited to 'wqflask/base')
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 10851e00..96a09302 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -27,11 +27,13 @@ def create_trait(**kw):
assert bool(kw.get('name')), "Needs trait name"
- if kw.get('dataset_name'):
+ if bool(kw.get('dataset')):
+ dataset = kw.get('dataset')
+ else:
if kw.get('dataset_name') != "Temp":
dataset = create_dataset(kw.get('dataset_name'))
- else:
- dataset = kw.get('dataset')
+ else:
+ dataset = create_dataset("Temp", group_name=kw.get('group_name'))
if dataset.type == 'Publish':
permissions = check_resource_availability(
--
cgit v1.2.3
