1 files changed, 0 insertions, 132 deletions
diff --git a/web/webqtl/correlationMatrix/tissueCorrelationMatrix.py b/web/webqtl/correlationMatrix/tissueCorrelationMatrix.py
deleted file mode 100755
index 23dc14eb..00000000
--- a/web/webqtl/correlationMatrix/tissueCorrelationMatrix.py
+++ /dev/null
@@ -1,132 +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 2010/11/10
-#
-# Last updated by Ning Liu, 2011/01/26
-
-
-#tissueCorrelationMatrix: funciton part for TissueCorrelationPage.py
-from htmlgen import HTMLgen2 as HT
-from correlation import correlationFunction
-from dbFunction import webqtlDatabaseFunction
-import sys
-
-#########################################
-#      Tissue Correlation Page
-#########################################
-
-class  tissueCorrelationMatrix:
-	def __init__(self,tissueProbeSetFreezeId=None):
-		
-		#initialize parameters
-		self.tProbeSetFreezeId = tissueProbeSetFreezeId
-		self.cursor = webqtlDatabaseFunction.getCursor()
-
-
-
-	#retreive dataSet info from database table TissueProbeSetFreeze to get all TissueProbeSetFreezeId(List), Name(List) and FullName(List)
-	def getTissueDataSet(self):	
-		tissProbeSetFreezeIds,Names,fullNames = webqtlDatabaseFunction.getTissueDataSet(cursor=self.cursor)
-		return tissProbeSetFreezeIds,Names,fullNames
-
-
-	#retrieve DatasetName, DatasetFullName based on TissueProbeSetFreezeId, return DatasetName(string), DatasetFullName(string)
-	def getFullnameofCurrentDataset(self):
-	
-		DatasetName, DatasetFullName =webqtlDatabaseFunction.getDatasetNamesByTissueProbeSetFreezeId(cursor=self.cursor, TissueProbeSetFreezeId=self.tProbeSetFreezeId)		
-		return DatasetName, DatasetFullName
-
-				
-	#retrieve how many tissue used in the specific dataset based on TissueProbeSetFreezeId, return TissueCount(int)
-	def getTissueCountofCurrentDataset(self):
-	
-		TissueCount =webqtlDatabaseFunction.getTissueCountByTissueProbeSetFreezeId(cursor=self.cursor,TissueProbeSetFreezeId=self.tProbeSetFreezeId)
-		return TissueCount
-
-
-		
-	#retrieve corrArray(array), pvArray(array) for display by calling  calculation function:calZeroOrderCorrForTiss
-	def getTissueCorrPvArray(self,geneNameLst=None,dataIdDict=None):	
-		#retrieve SymbolValuePairDict(Dict), dictionary of Symbol and Value Pair.key is symbol, value is one list of expression values of one probeSet
-		symbolValuepairDict =correlationFunction.getGeneSymbolTissueValueDict(cursor=self.cursor,symbolList=geneNameLst,dataIdDict=dataIdDict)
-		corrArray,pvArray = correlationFunction.getCorrPvArray(cursor=self.cursor,priGeneSymbolList=geneNameLst,symbolValuepairDict=symbolValuepairDict)
-		return corrArray,pvArray
-
-
-		
-	#retrieve symbolList,geneIdList,dataIdList,ChrList,MbList,descList,pTargetDescList (all are list type) to 
-	#get multi lists for short and long label functions, and for getSymbolValuePairDict and 
-	#getGeneSymbolTissueValueDict to build dict to get CorrPvArray
-	def getTissueProbeSetXRefInfo(self,GeneNameLst=[]):
-		symbolList,geneIdDict,dataIdDict,ChrDict,MbDict,descDict,pTargetDescDict =correlationFunction.getTissueProbeSetXRefInfo(cursor=self.cursor,GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=self.tProbeSetFreezeId)
-		return symbolList,geneIdDict,dataIdDict,ChrDict,MbDict,descDict,pTargetDescDict		
-
-
-
-	#retrieve corrArray(array), pvArray(array) for gene symbol pair
-	def getCorrPvArrayForGeneSymbolPair(self,geneNameLst=None):
-		corrArray = None
-		pvArray = None
-
-		if len(geneNameLst) == 2:
-			#retrieve SymbolValuePairDict(Dict), dictionary of Symbol and Value Pair.key is symbol, value is one list of expression values of one probeSet
-			symbolList,geneIdDict,dataIdDict,ChrDict,MbDict,descDict,pTargetDescDict =correlationFunction.getTissueProbeSetXRefInfo(cursor=self.cursor,GeneNameLst=geneNameLst,TissueProbeSetFreezeId=self.tProbeSetFreezeId)	
-			symbolValuepairDict =correlationFunction.getGeneSymbolTissueValueDict(cursor=self.cursor,symbolList=geneNameLst,dataIdDict=dataIdDict)
-			corrArray,pvArray = correlationFunction.getCorrPvArray(cursor=self.cursor,priGeneSymbolList=geneNameLst,symbolValuepairDict=symbolValuepairDict)
-
-		return corrArray,pvArray
-
-
-	#retrieve symbolCorrDict(dict), symbolPvalueDict(dict) to get all tissues' correlation value and P value; key is symbol	
-	def calculateCorrOfAllTissueTrait(self, primaryTraitSymbol=None, method='0'):
-		symbolCorrDict, symbolPvalueDict = correlationFunction.calculateCorrOfAllTissueTrait(cursor=self.cursor, primaryTraitSymbol=primaryTraitSymbol, TissueProbeSetFreezeId=self.tProbeSetFreezeId,method=method)
-		
-		return symbolCorrDict, symbolPvalueDict
-
-	#Translate GeneId to gene symbol and keep the original order.
-	def getGeneSymbolLst(self, geneSymbols=None):
-		geneSymbolLst=[]
-		geneIdLst=[]
-		#split the input string at every occurrence of the delimiter '\r', and return the substrings in an array. 
-		tokens=geneSymbols.strip().split('\r')
-
-		#Ning: To keep the original order of input symbols and GeneIds
-		for i in tokens:
-			i=i.strip()
-			if (len(i) >0) and (i not in geneSymbolLst):
-				geneSymbolLst.append(i)
-				# if input includes geneId(s), then put it/them into geneIdLst
-				if i.isdigit():
-					geneIdLst.append(i)
-
-		#Ning: Replace GeneId with symbol if applicable
-		if len(geneIdLst)>0:
-			# if input includes geneId(s), replace geneId by geneSymbol; 
-			geneIdSymbolPair =webqtlDatabaseFunction.getGeneIdSymbolPairByGeneId(cursor=self.cursor, geneIdLst =geneIdLst)
-			for geneId in geneIdLst:
-				if geneIdSymbolPair[geneId]:
-					index = geneSymbolLst.index(geneId)
-					geneSymbolLst[index] =geneIdSymbolPair[geneId]
-
-		return geneSymbolLst
-			
-		
-