aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
authorBonfaceKilz2021-04-30 12:16:51 +0300
committerBonfaceKilz2021-04-30 13:45:15 +0300
commitc7e661b8ff9f70955418fbc4527378904beb0cf4 (patch)
tree7a164b42d46e15b6f2775a50137b412c8713e2f3 /wqflask
parent385da724b63f57d0fb1bbe3476cea31ef837c081 (diff)
downloadgenenetwork2-c7e661b8ff9f70955418fbc4527378904beb0cf4.tar.gz
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
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/data_set.py18
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py16
-rw-r--r--wqflask/base/species.py2
-rw-r--r--wqflask/base/webqtlConfig.py40
-rw-r--r--wqflask/db/call.py6
-rw-r--r--wqflask/db/gn_server.py2
-rw-r--r--wqflask/db/webqtlDatabaseFunction.py10
-rw-r--r--wqflask/maintenance/convert_dryad_to_bimbam.py6
-rw-r--r--wqflask/maintenance/convert_geno_to_bimbam.py10
-rw-r--r--wqflask/maintenance/gen_select_dataset.py16
-rw-r--r--wqflask/maintenance/generate_kinship_from_bimbam.py4
-rw-r--r--wqflask/maintenance/geno_to_json.py26
-rw-r--r--wqflask/maintenance/quantile_normalize.py30
-rw-r--r--wqflask/maintenance/set_resource_defaults.py26
-rw-r--r--wqflask/tests/unit/wqflask/api/test_correlation.py4
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py14
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py24
-rw-r--r--wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py28
-rw-r--r--wqflask/tests/wqflask/show_trait/testSampleList.py6
-rw-r--r--wqflask/utility/Plot.py180
-rw-r--r--wqflask/utility/TDCell.py6
-rw-r--r--wqflask/utility/THCell.py8
-rw-r--r--wqflask/utility/__init__.py2
-rw-r--r--wqflask/utility/benchmark.py4
-rw-r--r--wqflask/utility/chunks.py2
-rw-r--r--wqflask/utility/corestats.py6
-rw-r--r--wqflask/utility/elasticsearch_tools.py8
-rw-r--r--wqflask/utility/external.py2
-rw-r--r--wqflask/utility/gen_geno_ob.py18
-rw-r--r--wqflask/utility/helper_functions.py2
-rw-r--r--wqflask/utility/logger.py34
-rw-r--r--wqflask/utility/pillow_utils.py2
-rw-r--r--wqflask/utility/startup_config.py10
-rw-r--r--wqflask/utility/svg.py624
-rw-r--r--wqflask/utility/temp_data.py2
-rw-r--r--wqflask/utility/tools.py112
-rw-r--r--wqflask/utility/type_checking.py6
-rw-r--r--wqflask/utility/webqtlUtil.py60
-rw-r--r--wqflask/wqflask/__init__.py8
-rw-r--r--wqflask/wqflask/api/correlation.py44
-rw-r--r--wqflask/wqflask/api/gen_menu.py4
-rw-r--r--wqflask/wqflask/api/mapping.py12
-rw-r--r--wqflask/wqflask/api/router.py196
-rw-r--r--wqflask/wqflask/collect.py20
-rw-r--r--wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py12
-rw-r--r--wqflask/wqflask/correlation/corr_scatter_plot.py76
-rw-r--r--wqflask/wqflask/correlation/correlation_functions.py34
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py38
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py52
-rw-r--r--wqflask/wqflask/ctl/ctl_analysis.py88
-rw-r--r--wqflask/wqflask/database.py2
-rw-r--r--wqflask/wqflask/do_search.py80
-rw-r--r--wqflask/wqflask/export_traits.py2
-rw-r--r--wqflask/wqflask/external_tools/send_to_bnw.py6
-rw-r--r--wqflask/wqflask/external_tools/send_to_geneweaver.py6
-rw-r--r--wqflask/wqflask/external_tools/send_to_webgestalt.py26
-rw-r--r--wqflask/wqflask/group_manager.py22
-rw-r--r--wqflask/wqflask/gsearch.py2
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py6
-rw-r--r--wqflask/wqflask/interval_analyst/GeneUtil.py24
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py1114
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py2
-rw-r--r--wqflask/wqflask/marker_regression/plink_mapping.py34
-rw-r--r--wqflask/wqflask/marker_regression/qtlreaper_mapping.py70
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py82
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py134
-rw-r--r--wqflask/wqflask/model.py8
-rw-r--r--wqflask/wqflask/parser.py4
-rw-r--r--wqflask/wqflask/resource_manager.py10
-rw-r--r--wqflask/wqflask/search_results.py16
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py14
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py18
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py42
-rw-r--r--wqflask/wqflask/submit_bnw.py2
-rw-r--r--wqflask/wqflask/update_search_results.py6
-rw-r--r--wqflask/wqflask/user_login.py88
-rw-r--r--wqflask/wqflask/user_manager.py143
-rw-r--r--wqflask/wqflask/user_session.py38
-rw-r--r--wqflask/wqflask/views.py6
-rw-r--r--wqflask/wsgi.py2
80 files changed, 1975 insertions, 1994 deletions
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)+'<![CDATA[')
+ f.write('\n' + '\t' * (level + 1) + '<![CDATA[')
for line in self.cdata.splitlines():
- f.write('\n'+'\t'*(level+2)+line)
- 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+'</'+self.type+'>\n')
+ f.write('\t' * level + '</' + self.type + '>\n')
elif self.text:
- f.write('</'+self.type+'>\n')
+ f.write('</' + self.type + '>\n')
elif self.cdata:
- f.write('\t'*level+'</'+self.type+'>\n')
+ f.write('\t' * level + '</' + self.type + '>\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("<?xml version='1.0' encoding='UTF-8'?>\n")
xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"")
if self.entity:
@@ -971,8 +971,8 @@ class drawing:
if not filename:
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)
@@ -980,18 +980,18 @@ class drawing:
else:
return xml.getvalue()
else:
- if filename[-4:]=='svgz':
+ 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:
- f=file(filename, 'w')
+ f = file(filename, 'w')
f.write(xml.getvalue())
f.close()
else:
- def toXml(self,filename='',compress=False):
+ def toXml(self, filename='', compress=False):
"""drawing.toXml() ---->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/<path:species_name>".format(version))
@app.route("/api/v_{}/species/<path:species_name>.<path:file_format>".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/<path:group_name>.<path:file_format>".format(version))
@app.route("/api/v_{}/group/<path:species_name>/<path:group_name>".format(version))
@app.route("/api/v_{}/group/<path:species_name>/<path:group_name>.<path:file_format>".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/<path:dataset_name>.<path:file_format>".format(version))
@app.route("/api/v_{}/dataset/<path:group_name>/<path:dataset_name>".format(version))
@app.route("/api/v_{}/dataset/<path:group_name>/<path:dataset_name>.<path:file_format>".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/<path:dataset_name>".format(version), methods=("GET",))
@app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".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/<path:dataset_name>".format(version))
@app.route("/api/v_{}/sample_data/<path:dataset_name>.<path:file_format>".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/<path:dataset_name>/<path:trait_name>".format(version))
@app.route("/api/v_{}/sample_data/<path:dataset_name>/<path:trait_name>.<path:file_format>".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/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
@app.route("/api/v_{}/trait_info/<path:dataset_name>/<path:trait_name>".format(version))
@app.route("/api/v_{}/trait_info/<path:dataset_name>/<path:trait_name>.<path:file_format>".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<endMb:
+ while startMb < endMb:
snp_count = g.db.execute("""
select
count(*) from BXDSnpPosition
where
Chr = '%s' AND Mb >= %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": "<INPUT TYPE=\"checkbox\" NAME=\"searchResult\" class=\"checkbox trait_checkbox\" style=\"transform: scale(1.5);\" VALUE=\"{}:{}\">".format(trait.name, trait.dataset.name),
- "index": i+1,
+ trait_row = {"checkbox": "<INPUT TYPE=\"checkbox\" NAME=\"searchResult\" class=\"checkbox trait_checkbox\" style=\"transform: scale(1.5);\" VALUE=\"{}:{}\">".format(trait.name, trait.dataset.name),
+ "index": i + 1,
"species": trait.dataset.group.species,
"group": trait.dataset.group.name,
"tissue": trait.dataset.tissue,
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index b6e7973f..3f5b43ee 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -33,9 +33,9 @@ def timestamp():
return datetime.datetime.utcnow().isoformat()
def basic_info():
- return dict(timestamp = timestamp(),
- ip_address = request.remote_addr,
- user_agent = request.headers.get('User-Agent'))
+ return dict(timestamp=timestamp(),
+ ip_address=request.remote_addr,
+ user_agent=request.headers.get('User-Agent'))
def encode_password(pass_gen_fields, unencrypted_password):
@@ -77,31 +77,31 @@ def get_signed_session_id(user):
session_id_signature = hmac.hmac_creation(session_id)
session_id_signed = session_id + ":" + session_id_signature
- #ZS: Need to check if this is ever actually used or exists
+ # ZS: Need to check if this is ever actually used or exists
if 'user_id' not in user:
user['user_id'] = str(uuid.uuid4())
save_user(user, user['user_id'])
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'])
+ 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'])
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'])
+ 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'])
else:
- session = dict(login_time = time.time(),
- user_type = "gn2",
- user_id = user['user_id'],
- user_name = user['full_name'],
- user_email_address = user['email_address'])
+ session = dict(login_time=time.time(),
+ user_type="gn2",
+ user_id=user['user_id'],
+ user_name=user['full_name'],
+ user_email_address=user['email_address'])
key = UserSession.user_cookie_name + ":" + session_id
Redis.hmset(key, session)
@@ -123,23 +123,23 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
server.login(SMTP_USERNAME, SMTP_PASSWORD)
server.sendmail(fromaddr, toaddr, msg)
server.quit()
- logger.info("Successfully sent email to "+toaddr)
+ 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
- data = json.dumps(dict(id=user_details['user_id'], timestamp = timestamp()))
+ data = json.dumps(dict(id=user_details['user_id'], timestamp=timestamp()))
Redis.set(key, data)
Redis.expire(key, THREE_DAYS)
recipient = user_details['email_address']
- body = render_template(template_name, verification_code = verification_code)
+ body = render_template(template_name, verification_code=verification_code)
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"):
+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)
@@ -154,7 +154,7 @@ def verify_email():
# 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 = 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:
@@ -165,15 +165,15 @@ def login():
params = request.form if request.form else request.args
logger.debug("in login params are:", params)
- if not params: #ZS: If coming to page for first time
+ if not params: # ZS: If coming to page for first time
from utility.tools import GITHUB_AUTH_URL, GITHUB_CLIENT_ID, ORCID_AUTH_URL, ORCID_CLIENT_ID
external_login = {}
if GITHUB_AUTH_URL and GITHUB_CLIENT_ID != 'UNKNOWN':
external_login["github"] = GITHUB_AUTH_URL
if ORCID_AUTH_URL and ORCID_CLIENT_ID != 'UNKNOWN':
external_login["orcid"] = ORCID_AUTH_URL
- return render_template("new_security/login_user.html", external_login = external_login, redis_is_available=is_redis_available())
- else: #ZS: After clicking sign-in
+ return render_template("new_security/login_user.html", external_login=external_login, redis_is_available=is_redis_available())
+ else: # ZS: After clicking sign-in
if 'type' in params and 'uid' in params:
user_details = get_user_by_unique_column("user_id", params['uid'])
if user_details:
@@ -204,13 +204,13 @@ def login():
encrypted_pass_fields = encode_password(pwfields, submitted_password)
password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password'])
- else: # Invalid e-mail
+ else: # Invalid e-mail
flash("Invalid e-mail address. Please try again.", "alert-danger")
response = make_response(redirect(url_for('login')))
return response
- if password_match: # If password correct
- if user_details['confirmed']: # If account confirmed
+ if password_match: # If password correct
+ if user_details['confirmed']: # If account confirmed
import_col = "false"
anon_id = ""
if 'import_collections' in params:
@@ -219,14 +219,14 @@ def login():
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 = 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
+ 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
flash("Invalid password. Please try again.", "alert-danger")
response = make_response(redirect(url_for('login')))
@@ -243,7 +243,7 @@ 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("&")]}
+ 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"])
@@ -261,12 +261,12 @@ def github_oauth2():
}
save_user(user_details, user_details["user_id"])
- url = "/n/login?type=github&uid="+user_details["user_id"]
+ 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
+ result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
return json.loads(result)
@@ -303,14 +303,14 @@ def orcid_oauth2():
}
save_user(user_details, user_details["user_id"])
- url = "/n/login?type=orcid&uid="+user_details["user_id"]
+ url = "/n/login?type=orcid&uid=" + user_details["user_id"]
else:
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
+ result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
return json.loads(result)
@@ -337,7 +337,7 @@ def send_forgot_password_email(verification_email):
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
- template_name = "email/forgot_password.txt"
+ template_name = "email/forgot_password.txt"
key_prefix = "forgot_password_code"
subject = "GeneNetwork password reset"
fromaddr = "no-reply@genenetwork.org"
@@ -353,7 +353,7 @@ def send_forgot_password_email(verification_email):
save_verification_code(verification_email, verification_code)
- body = render_template(template_name, verification_code = verification_code)
+ body = render_template(template_name, verification_code=verification_code)
msg = MIMEMultipart()
msg["To"] = verification_email
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index fcec3b67..013920f9 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -74,11 +74,11 @@ class AnonUser:
self.key = "anon_collection:v1:{}".format(self.anon_id)
def add_collection(self, new_collection):
- collection_dict = dict(name = new_collection.name,
- created_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
- changed_timestamp = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
- num_members = new_collection.num_members,
- members = new_collection.get_members())
+ collection_dict = dict(name=new_collection.name,
+ created_timestamp=datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
+ changed_timestamp=datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
+ num_members=new_collection.num_members,
+ members=new_collection.get_members())
Redis.set(self.key, json.dumps(collection_dict))
Redis.expire(self.key, 60 * 60 * 24 * 365)
@@ -111,7 +111,7 @@ class AnonUser:
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):
@@ -182,13 +182,13 @@ class UserSession:
# weekend and the site hasn't been visited by the user
self.logged_in = False
- ########### Grrr...this won't work because of the way flask handles cookies
+ # Grrr...this won't work because of the way flask handles cookies
# Delete the cookie
#response = make_response(redirect(url_for('login')))
#response.set_cookie(self.cookie_name, '', expires=0)
- #flash(
+ # flash(
# "Due to inactivity your session has expired. If you'd like please login again.")
- #return response
+ # return response
return
if Redis.ttl(self.redis_key) < THREE_DAYS:
@@ -213,7 +213,7 @@ class UserSession:
user_email = self.record['user_email_address']
- #ZS: Get user's collections if they exist
+ # ZS: Get user's collections if they exist
user_id = None
user_id = get_user_id("email_address", user_email)
return user_id
@@ -230,7 +230,7 @@ class UserSession:
def user_collections(self):
"""List of user's collections"""
- #ZS: Get user's collections if they exist
+ # ZS: Get user's collections if they exist
collections = get_user_collections(self.redis_user_id)
return collections
@@ -248,7 +248,7 @@ class UserSession:
'created_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
'changed_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
'num_members': len(traits),
- 'members': list(traits) }
+ 'members': list(traits)}
current_collections = self.user_collections
current_collections.append(collection_dict)
@@ -347,7 +347,7 @@ def get_cookie():
g.user_session = UserSession()
g.cookie_session = AnonUser()
-#@app.after_request
+# @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)
@@ -455,7 +455,7 @@ def set_password(password, user):
class VerificationEmail:
- template_name = "email/verification.txt"
+ template_name = "email/verification.txt"
key_prefix = "verification_code"
subject = "GeneNetwork email verification"
@@ -473,7 +473,7 @@ class VerificationEmail:
to = user.email_address
subject = self.subject
body = render_template(self.template_name,
- verification_code = verification_code)
+ verification_code=verification_code)
send_email(to, subject, body)
class ForgotPasswordEmail(VerificationEmail):
@@ -500,7 +500,7 @@ class ForgotPasswordEmail(VerificationEmail):
subject = self.subject
body = render_template(
self.template_name,
- verification_code = verification_code)
+ verification_code=verification_code)
msg = MIMEMultipart()
msg["To"] = toaddr
@@ -525,11 +525,11 @@ class Password:
def basic_info():
- return dict(timestamp = timestamp(),
- ip_address = request.remote_addr,
- user_agent = request.headers.get('User-Agent'))
+ return dict(timestamp=timestamp(),
+ ip_address=request.remote_addr,
+ user_agent=request.headers.get('User-Agent'))
-#@app.route("/manage/verify_email")
+# @app.route("/manage/verify_email")
def verify_email():
user = DecodeUser(VerificationEmail.key_prefix).user
user.confirmed = json.dumps(basic_info(), sort_keys=True)
@@ -543,7 +543,7 @@ def verify_email():
response.set_cookie(UserSession.cookie_name, session_id_signed)
return response
-#@app.route("/n/password_reset", methods=['GET'])
+# @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)
@@ -567,7 +567,7 @@ def password_reset():
else:
return redirect(url_for("login"))
-#@app.route("/n/password_reset_step2", methods=('POST',))
+# @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)
@@ -611,7 +611,7 @@ class DecodeUser:
logger.debug("data is:", data)
return model.User.query.get(data['id'])
-#@app.route("/n/login", methods=('GET', 'POST'))
+# @app.route("/n/login", methods=('GET', 'POST'))
def login():
lu = LoginUser()
login_type = request.args.get("type")
@@ -621,7 +621,7 @@ def login():
else:
return lu.standard_login()
-#@app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
+# @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")
@@ -631,28 +631,21 @@ 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 [token.encode("utf-8") for token in result.text.split("&")]]}
+ 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"])
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"])
- url = "/n/login?type=github&uid="+user_details["user_id"]
+ url = "/n/login?type=github&uid=" + user_details["user_id"]
return redirect(url)
-#@app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
+# @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
@@ -661,10 +654,7 @@ def orcid_oauth2():
url = "/n/login"
if code:
data = {
- "client_id": ORCID_CLIENT_ID
- , "client_secret": ORCID_CLIENT_SECRET
- , "grant_type": "authorization_code"
- , "code": code
+ "client_id": ORCID_CLIENT_ID, "client_secret": ORCID_CLIENT_SECRET, "grant_type": "authorization_code", "code": code
}
result = requests.post(ORCID_TOKEN_URL, data=data)
result_dict = json.loads(result.text.encode("utf-8"))
@@ -672,31 +662,24 @@ 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" % (
+ "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"])
- url = "/n/login?type=orcid&uid="+user_details["user_id"]
+ url = "/n/login?type=orcid&uid=" + user_details["user_id"]
else:
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})
+ 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
+ remember_time = 60 * 60 * 24 * 30 # One month in seconds
def __init__(self):
self.remember_me = False
@@ -730,9 +713,7 @@ class LoginUser:
external_login["orcid"] = ORCID_AUTH_URL
return render_template(
- "new_security/login_user.html"
- , external_login=external_login
- , redis_is_available = is_redis_available())
+ "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(es, "email_address", params["email_address"])
@@ -770,7 +751,7 @@ class LoginUser:
else:
import_col = "false"
- #g.cookie_session.import_traits_to_user()
+ # g.cookie_session.import_traits_to_user()
self.logged_in = True
@@ -810,10 +791,10 @@ class LoginUser:
if not user.id:
user.id = ''
- session = dict(login_time = time.time(),
- user_id = user.id,
- user_name = user.full_name,
- user_email_address = user.email_address)
+ session = dict(login_time=time.time(),
+ user_id=user.id,
+ user_name=user.full_name,
+ user_email_address=user.email_address)
key = UserSession.cookie_name + ":" + login_rec.session_id
logger.debug("Key when signing:", key)
@@ -832,7 +813,7 @@ class LoginUser:
db_session.add(login_rec)
db_session.commit()
-#@app.route("/n/logout")
+# @app.route("/n/logout")
def logout():
logger.debug("Logging out...")
UserSession().delete_session()
@@ -843,7 +824,7 @@ def logout():
return response
-#@app.route("/n/forgot_password", methods=['GET'])
+# @app.route("/n/forgot_password", methods=['GET'])
def forgot_password():
"""Entry point for forgotten password"""
print("ARGS: ", request.args)
@@ -851,7 +832,7 @@ def forgot_password():
print("ERRORS: ", errors)
return render_template("new_security/forgot_password.html", errors=errors)
-#@app.route("/n/forgot_password_submit", methods=('POST',))
+# @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
@@ -886,7 +867,7 @@ def is_redis_available():
###
# ZS: The following 6 functions require the old MySQL User accounts; I'm leaving them commented out just in case we decide to reimplement them using ElasticSearch
###
-#def super_only():
+# def super_only():
# try:
# superuser = g.user_session.user_ob.superuser
# except AttributeError:
@@ -895,26 +876,26 @@ def is_redis_available():
# flash("You must be a superuser to access that page.", "alert-error")
# abort(401)
-#@app.route("/manage/users")
-#def manage_users():
+# @app.route("/manage/users")
+# def manage_users():
# super_only()
# template_vars = UsersManager()
# return render_template("admin/user_manager.html", **template_vars.__dict__)
-#@app.route("/manage/user")
-#def manage_user():
+# @app.route("/manage/user")
+# def manage_user():
# super_only()
# template_vars = UserManager(request.args)
# return render_template("admin/ind_user_manager.html", **template_vars.__dict__)
-#@app.route("/manage/groups")
-#def manage_groups():
+# @app.route("/manage/groups")
+# def manage_groups():
# super_only()
# template_vars = GroupsManager(request.args)
# return render_template("admin/group_manager.html", **template_vars.__dict__)
-#@app.route("/manage/make_superuser")
-#def make_superuser():
+# @app.route("/manage/make_superuser")
+# def make_superuser():
# super_only()
# params = request.args
# user_id = params['user_id']
@@ -926,8 +907,8 @@ def is_redis_available():
# flash("We've made {} a superuser!".format(user.name_and_org))
# return redirect(url_for("manage_users"))
-#@app.route("/manage/assume_identity")
-#def assume_identity():
+# @app.route("/manage/assume_identity")
+# def assume_identity():
# super_only()
# params = request.args
# user_id = params['user_id']
@@ -936,7 +917,7 @@ def is_redis_available():
# return LoginUser().actual_login(user, assumed_by=assumed_by)
-#@app.route("/n/register", methods=('GET', 'POST'))
+# @app.route("/n/register", methods=('GET', 'POST'))
def register():
params = None
errors = None
@@ -1023,21 +1004,21 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
"""
if SMTP_USERNAME == 'UNKNOWN':
- logger.debug("SMTP: connecting with host "+SMTP_CONNECT)
+ logger.debug("SMTP: connecting with host " + SMTP_CONNECT)
server = SMTP(SMTP_CONNECT)
server.sendmail(fromaddr, toaddr, msg)
else:
- logger.debug("SMTP: connecting TLS with host "+SMTP_CONNECT)
+ logger.debug("SMTP: connecting TLS with host " + SMTP_CONNECT)
server = SMTP(SMTP_CONNECT)
server.starttls()
- logger.debug("SMTP: login with user "+SMTP_USERNAME)
+ logger.debug("SMTP: login with user " + SMTP_USERNAME)
server.login(SMTP_USERNAME, SMTP_PASSWORD)
- logger.debug("SMTP: "+fromaddr)
- logger.debug("SMTP: "+toaddr)
- logger.debug("SMTP: "+msg)
+ logger.debug("SMTP: " + fromaddr)
+ logger.debug("SMTP: " + toaddr)
+ logger.debug("SMTP: " + msg)
server.sendmail(fromaddr, toaddr, msg)
server.quit()
- logger.info("Successfully sent email to "+toaddr)
+ logger.info("Successfully sent email to " + toaddr)
class GroupsManager:
def __init__(self, kw):
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index cc0ac744..78db7bd2 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -24,7 +24,7 @@ THIRTY_DAYS = 60 * 60 * 24 * 30
def get_user_session():
logger.info("@app.before_request get_session")
g.user_session = UserSession()
- #ZS: I think this should solve the issue of deleting the cookie and redirecting to the home page when a user's session has expired
+ # ZS: I think this should solve the issue of deleting the cookie and redirecting to the home page when a user's session has expired
if not g.user_session:
response = make_response(redirect(url_for('login')))
response.set_cookie('session_id_v2', '', expires=0)
@@ -51,7 +51,7 @@ def create_signed_cookie():
logger.debug("uuid_signed:", uuid_signed)
return the_uuid, uuid_signed
-@app.route("/user/manage", methods=('GET','POST'))
+@app.route("/user/manage", methods=('GET', 'POST'))
def manage_user():
params = request.form if request.form else request.args
if 'new_full_name' in params:
@@ -61,7 +61,7 @@ def manage_user():
user_details = get_user_by_unique_column("user_id", g.user_session.user_id)
- return render_template("admin/manage_user.html", user_details = user_details)
+ return render_template("admin/manage_user.html", user_details=user_details)
class UserSession:
"""Logged in user handling"""
@@ -89,25 +89,25 @@ class UserSession:
self.session_id = session_id
self.record = Redis.hgetall(self.redis_key)
- #ZS: If user correctled logged in but their session expired
- #ZS: Need to test this by setting the time-out to be really short or something
+ # ZS: If user correctled logged in but their session expired
+ # ZS: Need to test this by setting the time-out to be really short or something
if not self.record or self.record == []:
if user_cookie:
self.logged_in = False
- self.record = dict(login_time = time.time(),
- user_type = "anon",
- user_id = str(uuid.uuid4()))
+ self.record = dict(login_time=time.time(),
+ user_type="anon",
+ user_id=str(uuid.uuid4()))
Redis.hmset(self.redis_key, self.record)
Redis.expire(self.redis_key, THIRTY_DAYS)
- ########### Grrr...this won't work because of the way flask handles cookies
+ # 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.")
return None
else:
- self.record = dict(login_time = time.time(),
- user_type = "anon",
- user_id = str(uuid.uuid4()))
+ self.record = dict(login_time=time.time(),
+ user_type="anon",
+ user_id=str(uuid.uuid4()))
Redis.hmset(self.redis_key, self.record)
Redis.expire(self.redis_key, THIRTY_DAYS)
else:
@@ -138,13 +138,13 @@ class UserSession:
def redis_user_id(self):
"""User id from Redis (need to check if this is the same as the id stored in self.records)"""
- #ZS: This part is a bit weird. Some accounts used to not have saved user ids, and in the process of testing I think I created some duplicate accounts for myself.
- #ZS: Accounts should automatically generate user_ids if they don't already have one now, so this might not be necessary for anything other than my account's collections
+ # ZS: This part is a bit weird. Some accounts used to not have saved user ids, and in the process of testing I think I created some duplicate accounts for myself.
+ # ZS: Accounts should automatically generate user_ids if they don't already have one now, so this might not be necessary for anything other than my account's collections
if 'user_email_address' in self.record:
user_email = self.record['user_email_address']
- #ZS: Get user's collections if they exist
+ # ZS: Get user's collections if they exist
user_id = None
user_id = get_user_id("email_address", user_email)
elif 'user_id' in self.record:
@@ -153,7 +153,7 @@ class UserSession:
user_github_id = self.record['github_id']
user_id = None
user_id = get_user_id("github_id", user_github_id)
- else: #ZS: Anonymous user
+ else: # ZS: Anonymous user
return None
return user_id
@@ -170,9 +170,9 @@ class UserSession:
def user_collections(self):
"""List of user's collections"""
- #ZS: Get user's collections if they exist
+ # 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
@@ -189,7 +189,7 @@ class UserSession:
'created_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
'changed_timestamp': datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
'num_members': len(traits),
- 'members': list(traits) }
+ 'members': list(traits)}
current_collections = self.user_collections
current_collections.append(collection_dict)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 37f2094f..2c53012a 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
@@ -240,7 +240,7 @@ def search_page():
if USE_REDIS and valid_search:
Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
- Redis.expire(key, 60*60)
+ Redis.expire(key, 60 * 60)
if valid_search:
return render_template("search_result_page.html", **result)
@@ -601,7 +601,7 @@ def heatmap_page():
pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
logger.info("pickled result length:", len(pickled_result))
Redis.set(key, pickled_result)
- Redis.expire(key, 60*60)
+ Redis.expire(key, 60 * 60)
with Bench("Rendering template"):
rendered_template = render_template("heatmap.html", **result)
diff --git a/wqflask/wsgi.py b/wqflask/wsgi.py
index be9c7b37..755da333 100644
--- a/wqflask/wsgi.py
+++ b/wqflask/wsgi.py
@@ -1,4 +1,4 @@
-from run_gunicorn import app as application # expect application as a name
+from run_gunicorn import app as application # expect application as a name
if __name__ == "__main__":
application.run()