Mercurial > repos > artbio > cherry_pick_fasta

annotate cherry_pick_fasta.py @ 0:e3aee4ba49c6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children ea8fde9c6f82
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
1 #!/usr/bin/env python
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
2 # -*- coding: utf-8 -*-
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
3 """
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
4 Chery pick of fasta sequences satisfying a query string in their header/name
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
5 """
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
6
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
7 import argparse
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
8
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
9
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
10 def Parser():
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
11 the_parser = argparse.ArgumentParser(
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
12 description="Cherry pick fasta sequences")
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
13 the_parser.add_argument('--input', action="store", type=str,
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
14 help="input fasta file")
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
15 the_parser.add_argument('--query-string', dest="query_string",
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
16 action="store", type=str,
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
17 help="header containing the string will be\
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
18 extracted as well as the corresponding\
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
19 sequence")
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
20 the_parser.add_argument(
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
21 '--output', action="store", type=str, help="output fasta file")
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
22 args = the_parser.parse_args()
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
23 return args
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
24
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
25
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
26 def __main__():
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
27 """ main function """
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
28 args = Parser()
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
29 search_term = args.query_string
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
30 CrudeFasta = open(args.input, "r").read()
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
31 Output = open(args.output, "w")
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
32 FastaListe = CrudeFasta.split(">")
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
33 for sequence in FastaListe:
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
34 if search_term in sequence:
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
35 Output.write(">%s\n" % sequence.rstrip())
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
36 Output.close()
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
37
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
38
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
39 if __name__ == "__main__":
e3aee4ba49c6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit a5e865d017e0434dae013565929ad5e6e5129fd3
artbio
parents:
diff changeset
40 __main__()