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#!/usr/bin/env python3
'''
Created on May 13, 2014
@author: namphuon
'''
import argparse
import os
from sepp.alignment import MutableAlignment
def parse_args():
parser = argparse.ArgumentParser(
description='Performs various tools for TIPP.')
parser.add_argument(
'-t', '--threshold', default=None, metavar='THRESHOLD',
help='Split based on this threshold of length',
type=int, dest='threshold')
parser.add_argument(
'-i', '--input', default=None, metavar='INPUT',
help='INPUT sequence file (default=None)', required=True,
type=str, dest='input')
parser.add_argument(
'-o', '--output', default='output', metavar='OUTPUT',
help=('OUTPUT prefix, will write fragmentary file to OUTPUT.frag.fas '
'and full-length file to OUTPUT.full.fas (default=output)'),
type=str, dest='output')
args = parser.parse_args()
return args
def main():
args = parse_args()
sequences = MutableAlignment()
assert os.path.isfile(args.input) and os.access(args.input, os.R_OK), \
"Input file %s does not exist\n" % args.input
sequences.read_file_object(args.input)
frag = MutableAlignment()
full = MutableAlignment()
for (key, seq) in sequences.items():
if (len(seq) <= args.threshold):
frag[key] = seq
else:
full[key] = seq
frag.write_to_path("%s.frag.fas" % args.output)
full.write_to_path("%s.full.fas" % args.output)
if __name__ == "__main__":
main()
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