Merge branch 'master' into lmm

1 files changed, 0 insertions, 325 deletions

diff --git a/web/webqtl/textUI/cmdCorrelation.py b/web/webqtl/textUI/cmdCorrelation.py
deleted file mode 100755
index 04595fc5..00000000
--- a/web/webqtl/textUI/cmdCorrelation.py
+++ /dev/null
@@ -1,325 +0,0 @@
-# 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
-