Mercurial > repos > drosofff > cherry_pick_fasta

comparison cherry_pick_fasta.py @ 0:726b1e233a08 draft

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planemo upload for repository https://bitbucket.org/drosofff/gedtools/
author drosofff
date Mon, 08 Jun 2015 18:55:07 -0400
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-1:000000000000 0:726b1e233a08
1 #!/usr/bin/env python
2 # -*- coding: utf-8 -*-
3 """
4 Chery pick of fasta sequences satisfying a query string in their header/name
5 """
6
7 import argparse
8
9 def Parser():
10 the_parser = argparse.ArgumentParser(
11 description="Cherry pick fasta sequences")
12 the_parser.add_argument(
13 '--input', action="store", type=str, help="input fasta file")
14 the_parser.add_argument(
15 '--query-string', dest="query_string", action="store", type=str,
16 help="header containing the string will be extracted as well as the corresponding sequence")
17 the_parser.add_argument(
18 '--output', action="store", type=str, help="output fasta file")
19 args = the_parser.parse_args()
20 return args
21
22 def __main__():
23 """ main function """
24 args = Parser()
25 search_term = args.query_string
26 CrudeFasta = open (args.input, "r").read()
27 Output = open (args.output, "w")
28 FastaListe = CrudeFasta.split(">")
29 for sequence in FastaListe:
30 if search_term in sequence:
31 print >> Output, ">%s" % sequence.rstrip()
32 Output.close()
33
34
35 if __name__ == "__main__":
36 __main__()