--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/LIMMA_options.py	Fri Jun 26 09:36:46 2020 -0400
@@ -0,0 +1,330 @@
+import re
+
+def get_column_names( file_path, toNotConsider=None, toNotConsiderBis=None):
+	options=[]
+	inputfile = open(file_path)
+	firstLine = next(inputfile).strip().split("\t")
+	for i, field_component in enumerate( firstLine ):
+		if i!=0 and field_component!=toNotConsider and field_component!=toNotConsiderBis:#to squeeze the first column
+			options.append( ( field_component, field_component, False ) )
+	inputfile.close()
+	return options
+
+def get_row_names( file_path, factorName ):
+	inputfile = open(file_path)
+	firstLine = next(inputfile).strip().split("\t")
+	iColumn=-1
+	for i, field_component in enumerate( firstLine ):
+		if field_component==factorName:#to test
+			iColumn=i
+	options=[]
+	if iColumn!=-1:
+		for nextLine in inputfile:
+			nextLine=nextLine.strip().split("\t")
+			if len(nextLine)>1:
+				if (nextLine[iColumn], nextLine[iColumn], False) not in options:
+					options.append( (nextLine[iColumn], nextLine[iColumn], False) )
+	inputfile.close()
+	return options
+
+def get_row_names_interaction( file_path, factorNameA, factorNameB ):
+	inputfile = open(file_path)
+	firstLine = next(inputfile).strip().split("\t")
+	iColumnA=-1
+	iColumnB=-1
+	for i, field_component in enumerate( firstLine ):
+		if field_component==factorNameA:#to test
+			iColumnA=i
+		if field_component==factorNameB:#to test
+			iColumnB=i
+	possibleValuesA=[]
+	possibleValuesB=[]
+	if iColumnA!=-1 and iColumnB!=-1:
+		for nextLine in inputfile:
+			nextLine=nextLine.strip().split("\t")
+			if len(nextLine)>1:
+				if nextLine[iColumnA] not in possibleValuesA:
+					possibleValuesA.append(nextLine[iColumnA])
+				if nextLine[iColumnB] not in possibleValuesB:
+					possibleValuesB.append(nextLine[iColumnB])
+	inputfile.close()	
+	options=[]
+	if len(possibleValuesA)>=1 and len(possibleValuesB)>=1 and possibleValuesA[0]!="None" and possibleValuesB[0]!="None":
+		for counterA in range(len(possibleValuesA)):
+			for counterB in range(len(possibleValuesB)):
+				options.append( (possibleValuesA[counterA]+"*"+possibleValuesB[counterB], possibleValuesA[counterA]+"*"+possibleValuesB[counterB], False) )	
+	return options
+
+def get_comparisonsA( factorA, valuesA ):
+	options=[]
+	formatValuesA=re.sub("(^\[u')|('\]$)","", str(valuesA))
+	possibleValues=formatValuesA.split("', u'")
+	if len(possibleValues)>=2:
+		for counter in range(len(possibleValues)-1):
+			for innerCounter in range(counter+1,len(possibleValues)):
+				options.append( (possibleValues[counter]+" - "+possibleValues[innerCounter], possibleValues[counter]+" - "+possibleValues[innerCounter], False) )
+				options.append( (possibleValues[innerCounter]+" - "+possibleValues[counter], possibleValues[innerCounter]+" - "+possibleValues[counter], False) )
+	return options
+
+def get_comparisonsAB(factorA, valuesA, factorB, valuesB, interaction):
+	options=[]
+	formatValuesA=re.sub("(^\[u')|('\]$)","", str(valuesA))
+	possibleValuesA=formatValuesA.split("', u'")
+	formatValuesB=re.sub("(^\[u')|('\]$)","", str(valuesB))
+	possibleValuesB=formatValuesB.split("', u'")
+	if str(interaction)=="False":
+		if len(possibleValuesA)>=2:
+			for counter in range(len(possibleValuesA)-1):
+				for innerCounter in range(counter+1,len(possibleValuesA)):
+					options.append( (possibleValuesA[counter]+" - "+possibleValuesA[innerCounter], possibleValuesA[counter]+" - "+possibleValuesA[innerCounter], False) )
+					options.append( (possibleValuesA[innerCounter]+" - "+possibleValuesA[counter], possibleValuesA[innerCounter]+" - "+possibleValuesA[counter], False) )
+		if len(possibleValuesB)>=2:
+			for counter in range(len(possibleValuesB)-1):
+				for innerCounter in range(counter+1,len(possibleValuesB)):
+					options.append( (possibleValuesB[counter]+" - "+possibleValuesB[innerCounter], possibleValuesB[counter]+" - "+possibleValuesB[innerCounter], False) )
+					options.append( (possibleValuesB[innerCounter]+" - "+possibleValuesB[counter], possibleValuesB[innerCounter]+" - "+possibleValuesB[counter], False) )
+	else:
+		if len(possibleValuesA)>=1 and len(possibleValuesB)>=1 and possibleValuesA[0]!="None" and possibleValuesB[0]!="None":
+			for counterA in range(len(possibleValuesA)):
+				for innerCounterA in range(len(possibleValuesA)):
+					for counterB in range(len(possibleValuesB)):
+						for innerCounterB in range(len(possibleValuesB)):
+							if not(counterA==innerCounterA and counterB==innerCounterB):
+								options.append( ("("+possibleValuesA[counterA]+" * "+possibleValuesB[counterB]+") - ("+possibleValuesA[innerCounterA]+" * "+possibleValuesB[innerCounterB]+")","("+possibleValuesA[counterA]+" * "+possibleValuesB[counterB]+") - ("+possibleValuesA[innerCounterA]+" * "+possibleValuesB[innerCounterB]+")", False) )
+	return options
+
+def get_row_names_allInteractions( file_path, factorSelected):
+	formatFactors=re.sub("(^\[u')|('\]$)","", str(factorSelected))
+	factorsList=formatFactors.split("', u'")
+	iColumn=[None] * len(factorsList)
+	valuesList=[None] * len(factorsList)
+
+	inputfile = open(file_path)
+	firstLine = next(inputfile).strip().split("\t")
+	for iField, fieldComponent in enumerate( firstLine ):
+		for iFactor, factorComponent in enumerate(factorsList):
+			if fieldComponent==factorComponent:
+				iColumn[iFactor]=iField
+				valuesList[iFactor]=[]
+
+	for nextLine in inputfile:
+		nextLine=nextLine.strip().split("\t")
+		if len(nextLine)>1:
+			for iFactor, factorComponent in enumerate(factorsList):
+				if nextLine[iColumn[iFactor]] not in valuesList[iFactor]:
+					valuesList[iFactor].append(nextLine[iColumn[iFactor]])
+	inputfile.close()
+
+	allCombinations=[]
+	for iFactor, factorComponent in enumerate(factorsList):
+		if iFactor==0:
+			allCombinations=valuesList[iFactor]
+		else:
+			currentCombinations=allCombinations
+			allCombinations=[]	
+			for iValue, valueComponent in enumerate(valuesList[iFactor]):
+				for iCombination, combination in enumerate(currentCombinations):
+					allCombinations.append(combination+"*"+valueComponent)	
+
+	options=[]
+	for iCombination, combination in enumerate(allCombinations):
+		options.append((combination,combination,False))
+
+	return options
+
+def get_allrow_names( file_path, factorSelected ):
+	formatFactors=re.sub("(^\[u')|('\]$)","", str(factorSelected))
+	factorsList=formatFactors.split("', u'")
+	iColumn=[None] * len(factorsList)
+	valuesList=[None] * len(factorsList)
+
+	inputfile = open(file_path)
+	firstLine = next(inputfile).strip().split("\t")
+	for iField, fieldComponent in enumerate( firstLine ):
+		for iFactor, factorComponent in enumerate(factorsList):
+			if fieldComponent==factorComponent:
+				iColumn[iFactor]=iField
+				valuesList[iFactor]=[]
+
+	for nextLine in inputfile:
+		nextLine=nextLine.strip().split("\t")
+		if len(nextLine)>1:
+			for iFactor, factorComponent in enumerate(factorsList):
+				if nextLine[iColumn[iFactor]] not in valuesList[iFactor]:
+					valuesList[iFactor].append(nextLine[iColumn[iFactor]])
+	inputfile.close()
+
+	allValues=[]
+	for iFactor, factorComponent in enumerate(factorsList):
+		for iValue, valueComponent in enumerate(valuesList[iFactor]):
+			allValues.append(factorComponent+":"+valueComponent)	
+
+	options=[]
+	for iValue, valueComponent in enumerate(allValues):
+		options.append((valueComponent,valueComponent,False))
+
+	return options
+
+def replaceNamesInFiles(expressionFile_name,conditionFile_name,outputExpressionFile,outputConditionFile,ouputDictionnary):
+	dico={}
+	forbidenCharacters={"*",":",",","|"}
+	##start with expression file, read only the first line
+	inputfile = open(expressionFile_name)
+	outputfile = open(outputExpressionFile, 'w')
+	firstLine = next(inputfile).rstrip().split("\t")
+	iCondition=1
+	newFirstLine=""
+	for i, field_component in enumerate( firstLine ):
+		if (i>0):
+			#conditions names should not be redundant with other conditions
+			if(field_component not in dico):
+				dico[field_component]="Condition"+str(iCondition)
+				newFirstLine+="\t"+"Condition"+str(iCondition)
+				iCondition+=1
+			else:
+				raise NameError('condition name allready exists!')
+		else:
+			newFirstLine+=field_component
+	outputfile.write(newFirstLine+"\n")
+	for line in inputfile:
+		outputfile.write(line)
+	outputfile.close()
+	inputfile.close()
+	#then parse condition file, read all lines in this case
+	inputfile = open(conditionFile_name)
+	outputfile = open(outputConditionFile, 'w')
+	firstLine=1
+	iFactor=1
+	iValue=1
+	for line in inputfile:
+		currentLine = line.rstrip().split("\t")
+		newCurrentLine=""
+		for i, field_component in enumerate( currentLine ):
+			#special treatment for the first line
+			if (firstLine==1):
+				if (i==0):
+					newCurrentLine=field_component
+				else:
+					#factor names should not be redundant with other factors or conditions
+					if(field_component not in dico):
+						dico[field_component]="Factor"+str(iFactor)
+						newCurrentLine+="\t"+"Factor"+str(iFactor)
+						iFactor+=1
+					else:
+						raise NameError('factor name allready exists!')
+			else:	
+				if (i==0):
+					#check if condition name allready exist and used it if it is, or create a new one if not
+					if(field_component not in dico):
+						dico[field_component]="Condition"+str(iCondition)
+						newCurrentLine="Condition"+str(iCondition)
+						iCondition+=1
+					else:
+						newCurrentLine=dico[field_component]
+				else:
+					if(field_component not in dico):
+						dico[field_component]="Value"+str(iValue)
+						newCurrentLine+="\tValue"+str(iValue)
+						iValue+=1
+					else:
+						newCurrentLine+="\t"+dico[field_component]
+		outputfile.write(newCurrentLine+"\n")
+		firstLine=0
+	outputfile.close()
+	inputfile.close()
+	##check if any entries in dictionnary contains forbiden character
+	for key, value in dico.items():
+		for specialCharacter in forbidenCharacters:
+			if value.startswith("Condition")==False and key.find(specialCharacter)!=-1:
+				return 1
+	##then write dictionnary in a additional file
+	outputfile = open(ouputDictionnary, 'w')
+	for key, value in dico.items():
+		outputfile.write(key+"\t"+value+"\n")
+	outputfile.close()
+	return 0
+
+
+def replaceNamesBlockInFiles(expressionFile_name,conditionFile_name,blockingFile_name,outputExpressionFile,outputConditionFile,outputBlockingFile,ouputDictionnary):
+	dico={}
+	forbidenCharacters={"*",":",",","|"}
+	##start with expression file, read only the first line
+	inputfile = open(expressionFile_name)
+	outputfile = open(outputExpressionFile, 'w')
+	firstLine = next(inputfile).rstrip().split("\t")
+	iCondition=1
+	newFirstLine=""
+	for i, field_component in enumerate( firstLine ):
+		if (i>0):
+			#conditions names should not be redundant with other conditions
+			if(field_component not in dico):
+				dico[field_component]="Condition"+str(iCondition)
+				newFirstLine+="\t"+"Condition"+str(iCondition)
+				iCondition+=1
+			else:
+				raise NameError('condition name allready exists!')
+		else:
+			newFirstLine+=field_component
+	outputfile.write(newFirstLine+"\n")
+	for line in inputfile:
+		outputfile.write(line)
+	outputfile.close()
+	inputfile.close()
+	#then parse condition file, read all lines in this case
+	iFactor=1
+	iValue=1
+	for fileNum in range(2):
+		if fileNum==0:
+			inputfile = open(conditionFile_name)
+			outputfile = open(outputConditionFile, 'w')
+		else:
+			inputfile = open(blockingFile_name)
+			outputfile = open(outputBlockingFile, 'w')
+		firstLine=1
+		for line in inputfile:
+			currentLine = line.rstrip().split("\t")
+			newCurrentLine=""
+			for i, field_component in enumerate( currentLine ):
+				#special treatment for the first line
+				if (firstLine==1):
+					if (i==0):
+						newCurrentLine=field_component
+					else:
+						#factor names should not be redundant with other factors or conditions
+						if(field_component not in dico):
+							dico[field_component]="Factor"+str(iFactor)
+							newCurrentLine+="\t"+"Factor"+str(iFactor)
+							iFactor+=1
+						else:
+							raise NameError('factor name allready exists!')
+				else:	
+					if (i==0):
+						#check if condition name allready exist and used it if it is, or create a new one if not
+						if(field_component not in dico):
+							dico[field_component]="Condition"+str(iCondition)
+							newCurrentLine="Condition"+str(iCondition)
+							iCondition+=1
+						else:
+							newCurrentLine=dico[field_component]
+					else:
+						if(field_component not in dico):
+							dico[field_component]="Value"+str(iValue)
+							newCurrentLine+="\tValue"+str(iValue)
+							iValue+=1
+						else:
+							newCurrentLine+="\t"+dico[field_component]
+			outputfile.write(newCurrentLine+"\n")
+			firstLine=0
+		outputfile.close()
+		inputfile.close()
+	##check if any entries in dictionnary contains forbiden character
+	for key, value in dico.items():
+		for specialCharacter in forbidenCharacters:
+			if value.startswith("Condition")==False and key.find(specialCharacter)!=-1:
+				return 1
+	##then write dictionnary in a additional file
+	outputfile = open(ouputDictionnary, 'w')
+	for key, value in dico.items():
+		outputfile.write(key+"\t"+value+"\n")
+	outputfile.close()
+	return 0