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authoracenteno2020-04-21 17:35:34 -0500
committerGitHub2020-04-21 17:35:34 -0500
commit660589b9c2a507529e8e51ca6ce66ca97ad982c5 (patch)
tree27f63957278581bc2fce2b88744bfe20c8a81558 /wqflask/base/trait.py
parentd97fdc18359233f07c1a1c7b83fe7e88eb225043 (diff)
parentf2a3ae13231a7d270a5bb6911c248aa713f1ef91 (diff)
downloadgenenetwork2-660589b9c2a507529e8e51ca6ce66ca97ad982c5.tar.gz
Merge pull request #1 from genenetwork/testing
Updating my testing branch
Diffstat (limited to 'wqflask/base/trait.py')
-rw-r--r--wqflask/base/trait.py356
1 files changed, 113 insertions, 243 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index bf87e879..5525472e 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -3,14 +3,17 @@ from __future__ import absolute_import, division, print_function
import string
import resource
import codecs
+import requests
-from htmlgen import HTMLgen2 as HT
+import redis
+Redis = redis.StrictRedis()
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
from base.data_set import create_dataset
from db import webqtlDatabaseFunction
from utility import webqtlUtil
+from utility import hmac
from wqflask import app
@@ -18,17 +21,11 @@ import simplejson as json
from MySQLdb import escape_string as escape
from pprint import pformat as pf
-from flask import Flask, g, request
+from flask import Flask, g, request, url_for
from utility.logger import getLogger
logger = getLogger(__name__ )
-from wqflask import user_manager
-
-def print_mem(stage=""):
- mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
- print("{}: {}".format(stage, mem/1024))
-
class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
@@ -39,13 +36,15 @@ class GeneralTrait(object):
def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
# xor assertion
assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
+ self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
if kw.get('dataset_name'):
- self.dataset = create_dataset(kw.get('dataset_name'))
- #print(" in GeneralTrait created dataset:", self.dataset)
+ if kw.get('dataset_name') == "Temp":
+ temp_group = self.name.split("_")[2]
+ self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+ else:
+ self.dataset = create_dataset(kw.get('dataset_name'))
else:
self.dataset = kw.get('dataset')
- self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
- #print("THE NAME IS:", self.name)
self.cellid = kw.get('cellid')
self.identification = kw.get('identification', 'un-named trait')
self.haveinfo = kw.get('haveinfo', False)
@@ -61,6 +60,10 @@ class GeneralTrait(object):
self.num_overlap = None
self.strand_probe = None
self.symbol = None
+ self.display_name = self.name
+
+ self.LRS_score_repr = "N/A"
+ self.LRS_location_repr = "N/A"
if kw.get('fullname'):
name2 = value.split("::")
@@ -72,94 +75,11 @@ class GeneralTrait(object):
# Todo: These two lines are necessary most of the time, but perhaps not all of the time
# So we could add a simple if statement to short-circuit this if necessary
- self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
+ if self.dataset.type != "Temp":
+ self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
if get_sample_info != False:
self = retrieve_sample_data(self, self.dataset)
-
- def get_name(self):
- stringy = ""
- if self.dataset and self.name:
- stringy = "%s::%s" % (self.dataset, self.name)
- if self.cellid:
- stringy += "::" + self.cellid
- else:
- stringy = self.description
- return stringy
-
-
- def get_given_name(self):
- """
- when user enter a trait or GN generate a trait, user want show the name
- not the name that generated by GN randomly, the two follow function are
- used to give the real name and the database. displayName() will show the
- database also, getGivenName() just show the name.
- For other trait, displayName() as same as getName(), getGivenName() as
- same as self.name
-
- Hongqiang 11/29/07
-
- """
- stringy = self.name
- if self.dataset and self.name:
- desc = self.dataset.get_desc()
- if desc:
- #desc = self.handle_pca(desc)
- stringy = desc
- return stringy
-
-
- def display_name(self):
- stringy = ""
- if self.dataset and self.name:
- desc = self.dataset.get_desc()
- #desc = self.handle_pca(desc)
- if desc:
- #desc = self.handle_pca(desc)
- #stringy = desc
- #if desc.__contains__('PCA'):
- # desc = desc[desc.rindex(':')+1:].strip()
- #else:
- # desc = desc[:desc.index('entered')].strip()
- #desc = self.handle_pca(desc)
- stringy = "%s::%s" % (self.dataset, desc)
- else:
- stringy = "%s::%s" % (self.dataset, self.name)
- if self.cellid:
- stringy += "::" + self.cellid
- else:
- stringy = self.description
-
- return stringy
-
-
- #def __str__(self):
- # #return "%s %s" % (self.getName(), self.group)
- # return self.getName()
- #__str__ = getName
- #__repr__ = __str__
-
- def export_data(self, samplelist, the_type="val"):
- """
- export data according to samplelist
- mostly used in calculating correlation
-
- """
- result = []
- for sample in samplelist:
- if self.data.has_key(sample):
- if the_type=='val':
- result.append(self.data[sample].val)
- elif the_type=='var':
- result.append(self.data[sample].var)
- elif the_type=='N':
- result.append(self.data[sample].N)
- else:
- raise KeyError, `the_type`+' the_type is incorrect.'
- else:
- result.append(None)
- return result
-
def export_informative(self, include_variance=0):
"""
export informative sample
@@ -179,19 +99,6 @@ class GeneralTrait(object):
sample_aliases.append(sample_data.name2)
return samples, vals, the_vars, sample_aliases
-
- @property
- def name_header_fmt(self):
- '''Return a human-readable name for use in page header'''
- if self.dataset.type == 'ProbeSet':
- return self.symbol
- elif self.dataset.type == 'Geno':
- return self.name
- elif self.dataset.type == 'Publish':
- return self.post_publication_abbreviation
- else:
- return "unnamed"
-
@property
def description_fmt(self):
'''Return a text formated description'''
@@ -200,6 +107,8 @@ class GeneralTrait(object):
formatted = self.description
if self.probe_target_description:
formatted += "; " + self.probe_target_description
+ else:
+ formatted = "Not available"
elif self.dataset.type == 'Publish':
if self.confidential:
formatted = self.pre_publication_description
@@ -212,11 +121,36 @@ class GeneralTrait(object):
@property
def alias_fmt(self):
'''Return a text formatted alias'''
+
+ alias = 'Not available'
if self.alias:
alias = string.replace(self.alias, ";", " ")
alias = string.join(string.split(alias), ", ")
- else:
- alias = 'Not available'
+
+ return alias
+
+ @property
+ def wikidata_alias_fmt(self):
+ '''Return a text formatted alias'''
+
+ alias = 'Not available'
+ if self.symbol:
+ human_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.upper())
+ mouse_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.capitalize())
+ other_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.lower())
+
+ if human_response and mouse_response and other_response:
+ alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content)
+
+ filtered_aliases = []
+ seen = set()
+ for item in alias_list:
+ if item in seen:
+ continue
+ else:
+ filtered_aliases.append(item)
+ seen.add(item)
+ alias = "; ".join(filtered_aliases)
return alias
@@ -244,60 +178,33 @@ class GeneralTrait(object):
fmt += (' on the minus strand ')
return fmt
-
-# In ProbeSet, there are maybe several annotations match one sequence
-# so we need use sequence(BlatSeq) as the identification, when we update
-# one annotation, we update the others who match the sequence also.
-#
-# Hongqiang Li, 3/3/2008
-def getSequence(trait, dataset_name):
- dataset = create_dataset(dataset_name)
-
- if dataset.type == 'ProbeSet':
- results = g.db.execute('''
- SELECT
- ProbeSet.BlatSeq
- FROM
- ProbeSet, ProbeSetFreeze, ProbeSetXRef
- WHERE
- ProbeSet.Id=ProbeSetXRef.ProbeSetId and
- ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
- ProbeSet.Name = %s
- ProbeSetFreeze.Name = %s
- ''', trait.name, dataset.name).fetchone()
-
- return results[0]
def retrieve_sample_data(trait, dataset, samplelist=None):
if samplelist == None:
samplelist = []
- results = dataset.retrieve_sample_data(trait.name)
+ if dataset.type == "Temp":
+ results = Redis.get(trait.name).split()
+ else:
+ results = dataset.retrieve_sample_data(trait.name)
# Todo: is this necessary? If not remove
trait.data.clear()
- all_samples_ordered = dataset.group.all_samples_ordered()
-
if results:
- for item in results:
- name, value, variance, num_cases, name2 = item
- if not samplelist or (samplelist and name in samplelist):
- trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
-
- return trait
-
-def convert_location_to_value(chromosome, mb):
- try:
- location_value = int(chromosome)*1000 + float(mb)
- except ValueError:
- if chromosome.upper() == 'X':
- location_value = 20*1000 + float(mb)
+ if dataset.type == "Temp":
+ all_samples_ordered = dataset.group.all_samples_ordered()
+ for i, item in enumerate(results):
+ try:
+ trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
+ except:
+ pass
else:
- location_value = (ord(str(chromosome).upper()[0])*1000 +
- float(mb))
-
- return location_value
+ for item in results:
+ name, value, variance, num_cases, name2 = item
+ if not samplelist or (samplelist and name in samplelist):
+ trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
+ return trait
@app.route("/trait/get_sample_data")
def get_sample_data():
@@ -307,25 +214,37 @@ def get_sample_data():
trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
- return json.dumps([trait, {key: value.value for key, value in trait_ob.data.iteritems() }])
-
- #jsonable_sample_data = {}
- #for sample in trait_ob.data.iteritems():
- # jsonable_sample_data[sample] = trait_ob.data[sample].value
- #
- #return jsonable_sample_data
+ trait_dict = {}
+ trait_dict['name'] = trait
+ trait_dict['db'] = dataset
+ trait_dict['type'] = trait_ob.dataset.type
+ trait_dict['group'] = trait_ob.dataset.group.name
+ trait_dict['tissue'] = trait_ob.dataset.tissue
+ trait_dict['species'] = trait_ob.dataset.group.species
+ trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
+ trait_dict['description'] = trait_ob.description_display
+ if trait_ob.dataset.type == "ProbeSet":
+ trait_dict['symbol'] = trait_ob.symbol
+ trait_dict['location'] = trait_ob.location_repr
+ elif trait_ob.dataset.type == "Publish":
+ if trait_ob.pubmed_id:
+ trait_dict['pubmed_link'] = trait_ob.pubmed_link
+ trait_dict['pubmed_text'] = trait_ob.pubmed_text
+
+ return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
-def jsonable(trait, dataset_name):
+def jsonable(trait):
"""Return a dict suitable for using as json
Actual turning into json doesn't happen here though"""
- dataset = create_dataset(dataset_name)
+ dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
if dataset.type == "ProbeSet":
return dict(name=trait.name,
symbol=trait.symbol,
dataset=dataset.name,
+ dataset_name = dataset.shortname,
description=trait.description_display,
mean=trait.mean,
location=trait.location_repr,
@@ -337,7 +256,9 @@ def jsonable(trait, dataset_name):
if trait.pubmed_id:
return dict(name=trait.name,
dataset=dataset.name,
+ dataset_name = dataset.shortname,
description=trait.description_display,
+ abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
pubmed_link=trait.pubmed_link,
@@ -348,7 +269,9 @@ def jsonable(trait, dataset_name):
else:
return dict(name=trait.name,
dataset=dataset.name,
+ dataset_name = dataset.shortname,
description=trait.description_display,
+ abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
lrs_score=trait.LRS_score_repr,
@@ -358,6 +281,7 @@ def jsonable(trait, dataset_name):
elif dataset.type == "Geno":
return dict(name=trait.name,
dataset=dataset.name,
+ dataset_name = dataset.shortname,
location=trait.location_repr
)
else:
@@ -379,7 +303,7 @@ def jsonable_table_row(trait, dataset_name, index):
additive = "N/A"
else:
additive = "%.3f" % round(float(trait.additive), 2)
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
'<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
trait.symbol,
@@ -395,7 +319,7 @@ def jsonable_table_row(trait, dataset_name, index):
else:
additive = "%.2f" % round(float(trait.additive), 2)
if trait.pubmed_id:
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
'<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
trait.description_display,
@@ -405,7 +329,7 @@ def jsonable_table_row(trait, dataset_name, index):
trait.LRS_location_repr,
additive]
else:
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
'<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
trait.description_display,
@@ -415,7 +339,7 @@ def jsonable_table_row(trait, dataset_name, index):
trait.LRS_location_repr,
additive]
elif dataset.type == "Geno":
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
'<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
trait.location_repr]
@@ -428,21 +352,22 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if dataset.type == 'Publish':
query = """
SELECT
- PublishXRef.Id, Publication.PubMed_ID,
+ PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
- Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+ Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
Publication.Authors, Publication.Title, Publication.Abstract,
Publication.Journal, Publication.Volume, Publication.Pages,
Publication.Month, Publication.Year, PublishXRef.Sequence,
Phenotype.Units, PublishXRef.comments
FROM
- PublishXRef, Publication, Phenotype, PublishFreeze
+ PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
WHERE
PublishXRef.Id = %s AND
Phenotype.Id = PublishXRef.PhenotypeId AND
Publication.Id = PublishXRef.PublicationId AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+ PublishXRef.InbredSetId = InbredSet.Id AND
PublishFreeze.Id = %s
""" % (trait.name, dataset.id)
@@ -492,17 +417,25 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait_info = g.db.execute(query,
(string.join(dataset.display_fields,','),
dataset.type, trait.name)).fetchone()
+
if trait_info:
trait.haveinfo = True
#XZ: assign SQL query result to trait attributes.
for i, field in enumerate(dataset.display_fields):
holder = trait_info[i]
+ # if isinstance(trait_info[i], basestring):
+ # logger.debug("HOLDER:", holder)
+ # logger.debug("HOLDER2:", holder.decode(encoding='latin1'))
+ # holder = unicode(trait_info[i], "utf-8", "ignore")
if isinstance(trait_info[i], basestring):
- holder = unicode(trait_info[i], "utf-8", "ignore")
+ holder = holder.encode('latin1')
setattr(trait, field, holder)
if dataset.type == 'Publish':
+ if trait.group_code:
+ trait.display_name = trait.group_code + "_" + str(trait.name)
+
trait.confidential = 0
if trait.pre_publication_description and not trait.pubmed_id:
trait.confidential = 1
@@ -513,6 +446,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#phenotype traits, then display the pre-publication description instead
#of the post-publication description
if trait.confidential:
+ trait.abbreviation = trait.pre_publication_abbreviation
trait.description_display = trait.pre_publication_description
#if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
@@ -522,11 +456,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#
# description = self.pre_publication_description
else:
+ trait.abbreviation = trait.post_publication_abbreviation
if description:
trait.description_display = description.strip()
else:
trait.description_display = ""
+ trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
+ trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
+ trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
+
if not trait.year.isdigit():
trait.pubmed_text = "N/A"
else:
@@ -535,38 +474,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if trait.pubmed_id:
trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
-
- trait.homologeneid = None
if dataset.type == 'ProbeSet' and dataset.group:
- if trait.geneid:
- #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number.
- #XZ: So I have to test if geneid is number before execute the query.
- #XZ: The geneid values in database should be cleaned up.
- #try:
- # float(self.geneid)
- # geneidIsNumber = True
- #except ValueError:
- # geneidIsNumber = False
- #if geneidIsNumber:
- query = """
- SELECT
- HomologeneId
- FROM
- Homologene, Species, InbredSet
- WHERE
- Homologene.GeneId ='%s' AND
- InbredSet.Name = '%s' AND
- InbredSet.SpeciesId = Species.Id AND
- Species.TaxonomyId = Homologene.TaxonomyId
- """ % (escape(str(trait.geneid)), escape(dataset.group.name))
- logger.sql(query)
- result = g.db.execute(query).fetchone()
- #else:
- # result = None
-
- if result:
- trait.homologeneid = result[0]
-
description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
@@ -582,47 +490,22 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
# Save it for the jinja2 template
trait.description_display = description_display
- #XZ: trait_location_value is used for sorting
trait.location_repr = 'N/A'
- trait.location_value = 1000000
-
if trait.chr and trait.mb:
- #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
- #This is so we can convert the location to a number used for sorting
- trait_location_value = convert_location_to_value(trait.chr, trait.mb)
- #try:
- # trait_location_value = int(self.chr)*1000 + self.mb
- #except ValueError:
- # if self.chr.upper() == 'X':
- # trait_location_value = 20*1000 + self.mb
- # else:
- # trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
- # self.mb)
-
- #ZS: Put this in function currently called "convert_location_to_value"
trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
- trait.location_value = trait_location_value
elif dataset.type == "Geno":
trait.location_repr = 'N/A'
- trait.location_value = 1000000
-
if trait.chr and trait.mb:
- #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
- #This is so we can convert the location to a number used for sorting
- trait_location_value = convert_location_to_value(trait.chr, trait.mb)
-
- #ZS: Put this in function currently called "convert_location_to_value"
trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
- trait.location_value = trait_location_value
if get_qtl_info:
#LRS and its location
trait.LRS_score_repr = "N/A"
- trait.LRS_score_value = 0
trait.LRS_location_repr = "N/A"
- trait.LRS_location_value = 1000000
+ trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
if dataset.type == 'ProbeSet' and not trait.cellid:
+ trait.mean = ""
query = """
SELECT
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
@@ -653,9 +536,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
else:
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
- else:
- trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = ""
-
if dataset.type == 'Publish':
query = """
@@ -692,19 +572,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.locus = trait.lrs = trait.additive = ""
if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
- #XZ: LRS_location_value is used for sorting
- try:
- LRS_location_value = int(trait.locus_chr)*1000 + float(trait.locus_mb)
- except:
- if trait.locus_chr.upper() == 'X':
- LRS_location_value = 20*1000 + float(trait.locus_mb)
- else:
- LRS_location_value = ord(str(trait.locus_chr).upper()[0])*1000 + float(trait.locus_mb)
-
trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
if trait.lrs != "":
trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
- trait.LRS_score_value = LRS_score_value = trait.lrs
else:
raise KeyError, `trait.name`+' information is not found in the database.'