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# 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
# as published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
# See the GNU Affero General Public License for more details.
#
# This program is available from Source Forge: at GeneNetwork Project
# (sourceforge.net/projects/genenetwork/).
#
# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
#
#
#
# This module is used by GeneNetwork project (www.genenetwork.org)
#
# Created by GeneNetwork Core Team 2010/08/10
#
# Last updated by GeneNetwork Core Team 2010/10/20
import os
import string
from math import *
import time
import reaper
from base import webqtlConfig
from utility import webqtlUtil
from cmdClass import cmdClass
#########################################
# Correlation Class
#########################################
class cmdCorrelation(cmdClass):
calFunction = 'webqtlUtil.calCorrelation'
def __init__(self,fd=None):
cmdClass.__init__(self,fd)
if not webqtlConfig.TEXTUI:
self.contents.append("Please send your request to http://robot.genenetwork.org")
return
self.example = '###Example : <a href="%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue">%s%s?cmd=%s&probeset=100001_at&probe=136415&db=bra03-03Mas5&searchdb=BXDPublish&return=500&sort=pvalue</a>' % (webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID, webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE, self.cmdID)
if self.accessError:
return
self.searchDB = self.data.getvalue('searchdb')
if not self.searchDB or self.error:
self.contents.append("###Error: source trait doesn't exist or no target database was given")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
try:
self.returnNumber = int(self.data.getvalue('return'))
except:
self.returnNumber = None
self.sort = self.data.getvalue('sort')
prefix, dbId = self.getDBId(self.database)
if not prefix or not dbId or (self.probe and string.lower(self.probe) in ("all","mm","pm")):
self.contents.append("###Error: source trait doesn't exist or SELECT more than one trait.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
RISet = self.getRISet(prefix, dbId)
prefix2, dbId2 = self.getDBId(self.searchDB)
if not prefix2 or not dbId2:
self.contents.append("###Error: target database doesn't exist.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
RISet2 = self.getRISet(prefix2, dbId2)
if RISet2 != RISet:
self.contents.append("###Error: target database has different Mouse InbredSet.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
traitdata, heads = self.getTraitData(prefix, dbId, self.probeset, self.probe)
if not traitdata:
self.contents.append("###Error: source trait doesn't exist.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
StrainNames = []
sourceTrait = []
StrainIds = []
#XZ, Jan 27, 2011: Only the strains that are of the same inbredset are used to calculate correlation.
for item in traitdata:
one_strain_name = item[0]
one_strain_value = item[1]
self.cursor.execute('SELECT Strain.Id from Strain,StrainXRef, InbredSet WHERE Strain.Name="%s" and Strain.Id = StrainXRef.StrainId and StrainXRef.InbredSetId = InbredSet.Id and InbredSet.Name = "%s"' % (one_strain_name, RISet2))
Results = self.cursor.fetchall()
if Results:
StrainIds.append('%d' % Results[0][0])
StrainNames.append( one_strain_name )
sourceTrait.append( one_strain_value )
correlationArray = []
useFastMethod = False
if prefix2 == "ProbeSet":
DatabaseFileName = self.getFileName( target_db_id=dbId2 )
DirectoryList = os.listdir(webqtlConfig.TEXTDIR) ### List of existing text files. Used to check if a text file already exists
if DatabaseFileName in DirectoryList:
useFastMethod = True
if useFastMethod:
datasetFile = open(webqtlConfig.TEXTDIR+DatabaseFileName,'r')
#XZ, 01/08/2009: read the first line
line = datasetFile.readline()
dataset_strains = webqtlUtil.readLineCSV(line)[1:]
#XZ, 01/08/2009: This step is critical. It is necessary for this new method.
_newvals = []
for item in dataset_strains:
if item in StrainNames:
_newvals.append(sourceTrait[StrainNames.index(item)])
else:
_newvals.append('None')
nnCorr = len(_newvals)
for line in datasetFile:
traitdata=webqtlUtil.readLineCSV(line)
traitdataName = traitdata[0]
traitvals = traitdata[1:]
corr,nOverlap = webqtlUtil.calCorrelationText(traitvals,_newvals,nnCorr)
traitinfo = [traitdataName,corr,nOverlap]
correlationArray.append( traitinfo )
#calculate correlation with slow method
else:
correlationArray = self.calCorrelation(sourceTrait, self.readDB(StrainIds, prefix2, dbId2) )
correlationArray.sort(self.cmpCorr) #XZ: Do not forget the sort step
if not self.returnNumber:
correlationArray = correlationArray[:100]
else:
if self.returnNumber < len(correlationArray):
correlationArray = correlationArray[:self.returnNumber]
NN = len(correlationArray)
for i in range(NN):
nOverlap = correlationArray[i][-1]
corr = correlationArray[i][-2]
if nOverlap < 3:
corrPValue = 1.0
else:
if abs(corr) >= 1.0:
corrPValue = 0.0
else:
ZValue = 0.5*log((1.0+corr)/(1.0-corr))
ZValue = ZValue*sqrt(nOverlap-3)
corrPValue = 2.0*(1.0 - reaper.normp(abs(ZValue)))
correlationArray[i].append(corrPValue)
if self.sort == 'pvalue':
correlationArray.sort(self.cmpPValue)
if prefix2 == 'Publish':
self.contents.append("RecordID\tCorrelation\t#Strains\tp-value")
elif prefix2 == 'Geno':
self.contents.append("Locus\tCorrelation\t#Strains\tp-value")
else:
pass
if prefix2 == 'Publish' or prefix2 == 'Geno':
for item in correlationArray:
self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))
else:
id = self.data.getvalue('id')
if id == 'yes':
self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value\tGeneID")
for item in correlationArray:
query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
self.cursor.execute(query)
results = self.cursor.fetchall()
if not results:
item = item + [None]
else:
item = item + list(results[0])
self.contents.append("%s\t%2.6f\t%d\t%2.6f\t%s" % tuple(item))
elif id == 'only':
self.contents.append("GenID")
for item in correlationArray:
query = """SELECT GeneID from %s WHERE Name = '%s'""" % (prefix2,item[0])
self.cursor.execute(query)
results = self.cursor.fetchall()
if not results:
self.contents.append('None')
else:
self.contents.append(results[0][0])
else:
self.contents.append("ProbesetID\tCorrelation\t#Strains\tp-value")
for item in correlationArray:
self.contents.append("%s\t%2.6f\t%d\t%2.6f" % tuple(item))
def getFileName(self, target_db_id):
query = 'SELECT Id, FullName FROM ProbeSetFreeze WHERE Id = %s' % target_db_id
self.cursor.execute(query)
result = self.cursor.fetchone()
Id = result[0]
FullName = result[1]
FullName = FullName.replace(' ','_')
FullName = FullName.replace('/','_')
FileName = 'ProbeSetFreezeId_' + str(Id) + '_FullName_' + FullName + '.txt'
return FileName
def calCorrelation(self,source,target):
allcorrelations = []
NN = len(source)
if len(source) != len(target[0]) - 1:
return allcorrelations
else:
for traitData in target:
corr,nOverlap = eval("%s(traitData[1:],source,NN)" % self.calFunction)
traitinfo = [traitData[0],corr,nOverlap]
allcorrelations.append(traitinfo)
return allcorrelations
def cmpCorr(self,A,B):
try:
if abs(A[1]) < abs(B[1]):
return 1
elif abs(A[1]) == abs(B[1]):
return 0
else:
return -1
except:
return 0
def cmpPValue(self,A,B):
try:
if A[-1] > B[-1]:
return 1
elif A[-1] == B[-1]:
return 0
else:
return -1
except:
return 0
def readDB(self, StrainIds=[], prefix2='', dbId2=''):
#retrieve data from target database
nnn = len(StrainIds) / 25
if len(StrainIds) % 25:
nnn += 1
oridata = []
for step in range(nnn):
temp = []
StrainIdstep = StrainIds[step*25:min(len(StrainIds), (step+1)*25)]
for item in StrainIdstep:
temp.append('T%s.value' % item)
#XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDPublish&return=500&sort=pvalue
if prefix2 == "Publish":
query = "SELECT PublishXRef.Id, "
dataStartPos = 1
query += string.join(temp,', ')
query += ' from (PublishXRef, PublishFreeze)\n'
#XZ, 03/05/2009: Xiaodong changed Data to PublishData
for item in StrainIdstep:
query += 'left join PublishData as T%s on T%s.Id = PublishXRef.DataId and T%s.StrainId=%s\n' %(item,item,item,item)
query += "WHERE PublishXRef.InbredSetId = PublishFreeze.InbredSetId and PublishFreeze.Id = %d" % (dbId2, )
#XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=HC_M2_1005_M&return=500&sort=pvalue
#XZ, 03/05/2009: test http://www.genenetwork.org/webqtl/WebQTL.py?cmd=cor&probeset=100001_at&probe=136415&db=bra08-03MAS5&searchdb=BXDGeno&return=500&sort=pvalue
else:
query = "SELECT %s.Name," % prefix2
query += string.join(temp,', ')
query += ' from (%s, %sXRef, %sFreeze) \n' % (prefix2,prefix2,prefix2)
#XZ, 03/05/2009: Xiaodong changed Data to %sData
for item in StrainIdstep:
query += 'left join %sData as T%s on T%s.Id = %sXRef.DataId and T%s.StrainId=%s\n' %(prefix2,item,item,prefix2,item,item)
query += "WHERE %sXRef.%sFreezeId = %sFreeze.Id and %sFreeze.Id = %d and %s.Id = %sXRef.%sId" % (prefix2, prefix2, prefix2, prefix2, dbId2, prefix2, prefix2, prefix2)
self.cursor.execute(query)
results = self.cursor.fetchall()
if not results:
self.contents.append("###Error: target database doesn't exist.")
self.contents.append(self.example)
self.contents.append(self.accessCode)
return
oridata.append(results)
datasize = len(oridata[0])
targetTrait = []
for j in range(datasize):
traitdata = list(oridata[0][j])
for i in range(1,nnn):
traitdata += list(oridata[i][j][1:])
targetTrait.append(traitdata)
return targetTrait
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