コード例 #1
0
	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
コード例 #2
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	def getTissueLabelsValues(self, X_geneSymbol=None, Y_geneSymbol=None, TissueProbeSetFreezeId=None ):

	    dataX = []
	    dataY = []
	    data_fullLabel = []
	    data_shortLabel = []
		# updated by NL, 2011-01-11 using new function getTissueProbeSetXRefInfo to get dataId value
	    X_symbolList,X_geneIdDict,X_dataIdDict,X_ChrDict,X_MbDict,X_descDict,X_pTargetDescDict = correlationFunction.getTissueProbeSetXRefInfo(cursor=self.cursor,GeneNameLst=[X_geneSymbol],TissueProbeSetFreezeId=TissueProbeSetFreezeId)
	    Y_symbolList,Y_geneIdDict,Y_dataIdDict,Y_ChrDict,Y_MbDict,Y_descDict,Y_pTargetDescDict = correlationFunction.getTissueProbeSetXRefInfo(cursor=self.cursor,GeneNameLst=[Y_geneSymbol],TissueProbeSetFreezeId=TissueProbeSetFreezeId)
		# in dataIdDict, key is the lower cased geneSymbol
	    X_DataId = X_dataIdDict[X_geneSymbol.lower()]
	    Y_DataId = Y_dataIdDict[Y_geneSymbol.lower()]

	    self.cursor.execute("SELECT TissueID,value FROM  TissueProbeSetData WHERE Id = %d ORDER BY TissueID" % int(X_DataId) )
	    results = self.cursor.fetchall()
	    for item in results:
	        TissueID, Value = item
	        dataX.append(Value)
	        self.cursor.execute("SELECT Tissue.Name, Tissue.Short_Name FROM Tissue WHERE Id = %d" % int(TissueID) )
	        temp = self.cursor.fetchone()
	        data_fullLabel.append( temp[0] )
	        data_shortLabel.append( temp[1] )

	    self.cursor.execute("SELECT TissueID,value FROM  TissueProbeSetData WHERE Id = %d ORDER BY TissueID" % int(Y_DataId) )
	    results = self.cursor.fetchall()
	    for item in results:
	        TissueID, Value = item
	        dataY.append(Value)

	    X_label = "%s" % X_geneSymbol
	    Y_label = "%s" % Y_geneSymbol
		
	    return dataX, dataY, X_label, Y_label, data_shortLabel, data_fullLabel
コード例 #3
0
	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