Extract records from multi-fasta

extract-fasta.py

#!/usr/bin/env python2.7

"""
Extract records from multi-fasta
"""

__author__ = 'Yasunobu OKAMURA'
__copyright__ = 'Copyright (C) 2012 Yasunobu OKAMURA All Rights Reserved.'

import argparse
import sys

import Bio.SeqIO
import Bio.Seq
import Bio.SeqRecord

def _main():
    parser = argparse.ArgumentParser(description='Extract records')
    parser.add_argument('input')
    parser.add_argument('query')
    parser.add_argument('output', default=sys.stdout, nargs='?', type=argparse.FileType('w'))
    options = parser.parse_args()

    for record in Bio.SeqIO.parse(options.input, "fasta"):
        if options.query in record.id:
            Bio.SeqIO.write(record, options.output, 'fasta')

    print >>sys.stderr, "{} record/s found".format(found_count)

if __name__ == '__main__':
    _main()