view trim.py @ 0:cb08a27e5fc2 draft

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import argparse

#docs.python.org/dev/library/argparse.html
parser = argparse.ArgumentParser()
parser.add_argument("--input", help="Input fasta")
parser.add_argument("--output", help="Output fasta")
parser.add_argument("--start", help="How many nucleotides to trim from the start", type=int)
parser.add_argument("--end", help="How many nucleotides to trim from the end", type=int)

args = parser.parse_args()
start = int(args.start)
end = int(args.end)

print args.input
print args.output
print start
print end

if end <= 0 and start <= 0:
	import shutil
	shutil.copy(args.input, args.output)
	import sys
	sys.exit()
	


currentSeq = ""
currentId = ""

if end is 0:
	with open(args.input, 'r') as i:
		with open(args.output, 'w') as o:
			for line in i.readlines():
				if line[0] is ">":
					currentSeq = currentSeq[start:]
					if currentSeq is not "" and currentId is not "":
						o.write(currentId)
						o.write(currentSeq + "\n")
					currentId = line
					currentSeq = ""
				else:
					currentSeq += line.rstrip()
			o.write(currentId)
			o.write(currentSeq[start:] + "\n")
else:
	with open(args.input, 'r') as i:
		with open(args.output, 'w') as o:
			for line in i.readlines():
				if line[0] is ">":
					currentSeq = currentSeq[start:-end]
					if currentSeq is not "" and currentId is not "":
						o.write(currentId)
						o.write(currentSeq + "\n")
					currentId = line
					currentSeq = ""
				else:
					currentSeq += line.rstrip()
			o.write(currentId)
			o.write(currentSeq[start:-end] + "\n")