def GetNumberOfColumnsOfTabularFile(filename=None, separator="\t"):
	file = open(filename)
	toReturn = len(file.readline().split(separator))
	file.close()
	return toReturn


def MergeHorizontallyFilesAccordingToCommonColumns(
	listOfFilenamesToBeAnnotated=None,
	listOfColumnsFromFileToBeAnnotated=None,
	listOfListsOfInputFilenames=None,
	listOfAnnotationFileColumns=None,
	listOfFirstLinesToIgnore=None,
	listOfOutputFilenames=None
	):

	#If None list of columns is provided then we take all columns
	if listOfColumnsFromFileToBeAnnotated == None:
		listOfColumnsFromFileToBeAnnotated=range(GetNumberOfColumnsOfTabularFile(listOfFilenamesToBeAnnotated[0]))

	for index, filenameToBeAnnotated in enumerate(listOfFilenamesToBeAnnotated):
		
		print "Annotating file: ", filenameToBeAnnotated
		
		outputFile = open(listOfOutputFilenames[index], "w")
		
		fileToBeAnnotated = open(filenameToBeAnnotated)
		
		listOfAnnotationFiles = []
		for indexOfInputFilenames, listOfInputFilenames in enumerate(listOfListsOfInputFilenames):
			print "Annotating from: ", listOfInputFilenames[index]
			currentOpenedFile = open(listOfInputFilenames[index])

			#Skip first lines
			if listOfFirstLinesToIgnore != None:
				for x in xrange(listOfFirstLinesToIgnore[indexOfInputFilenames]):
					currentOpenedFile.readline()

			listOfAnnotationFiles += [currentOpenedFile]
		
		lineCounter = 0
		while True:
			lineOfFileToBeAnnotated = fileToBeAnnotated.readline()
			if lineOfFileToBeAnnotated == "": break
			
			lineCounter += 1
			
			lineOfFileToBeAnnotatedSplitted = lineOfFileToBeAnnotated.replace("\n", "").split("\t")
		
			toPrint = []
		
			for columnFromFileToBeAnnotated in listOfColumnsFromFileToBeAnnotated:
				if columnFromFileToBeAnnotated >= len(lineOfFileToBeAnnotatedSplitted):
					cell = ""
				else:
					cell = lineOfFileToBeAnnotatedSplitted[columnFromFileToBeAnnotated]
				
				toPrint += [cell]

			
			for annotationIndex, annotationFile in enumerate(listOfAnnotationFiles):
				lineOfAnnotationFileSplitted = annotationFile.readline().replace("\n", "").split("\t")
				
				for columnOfAnnotationFile in listOfAnnotationFileColumns[annotationIndex]:
					if columnOfAnnotationFile >= len(lineOfAnnotationFileSplitted):
						cell = ""
					else:
						cell = lineOfAnnotationFileSplitted[columnOfAnnotationFile]
						
					toPrint += [cell]
			
			outputFile.write(str.join("\t", toPrint) + "\n")
			
		outputFile.close()