def PrepareGFFFilesFromBGIForSeattleSeqAnnotation(GFFFilename=None, outputGFFFilename=None):

	#Open input
	lines = open(GFFFilename).readlines()

	#Open output
	output = open(outputGFFFilename, "w")
	#Write "# autoFile testAuto.txt" at the top of the file
	output.write("# autoFile testAuto.txt\n")

	#replace all alleles accurences with allele
	for line in lines: output.write(line.replace("alleles", "allele"))

	#Close output
	output.close()