Mercurial > repos > artbio > cherry_pick_fasta

comparison cherry_pick_fasta.py @ 0:e3aee4ba49c6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
author artbio
date Sun, 15 Oct 2017 13:26:45 -0400
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children ea8fde9c6f82
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-1:000000000000 0:e3aee4ba49c6
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
10 def Parser():
11 the_parser = argparse.ArgumentParser(
12 description="Cherry pick fasta sequences")
13 the_parser.add_argument('--input', action="store", type=str,
14 help="input fasta file")
15 the_parser.add_argument('--query-string', dest="query_string",
16 action="store", type=str,
17 help="header containing the string will be\
18 extracted as well as the corresponding\
19 sequence")
20 the_parser.add_argument(
21 '--output', action="store", type=str, help="output fasta file")
22 args = the_parser.parse_args()
23 return args
24
25
26 def __main__():
27 """ main function """
28 args = Parser()
29 search_term = args.query_string
30 CrudeFasta = open(args.input, "r").read()
31 Output = open(args.output, "w")
32 FastaListe = CrudeFasta.split(">")
33 for sequence in FastaListe:
34 if search_term in sequence:
35 Output.write(">%s\n" % sequence.rstrip())
36 Output.close()
37
38
39 if __name__ == "__main__":
40 __main__()