Mercurial > repos > petr-novak > dante

comparison parse_aln.py @ 14:a6c55d1bdb6c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author petr-novak
date Wed, 28 Aug 2019 08:08:47 -0400
parents
children 3151a72a6671
comparison
equal deleted inserted replaced
13:ab56b34d67d8 14:a6c55d1bdb6c
1 #!/usr/bin/env python3
2 '''
3 parse .aln file - output from cap3 program. Output is fasta file and
4 profile file
5 '''
6 import argparse
7
8
9 def parse_args():
10 '''Argument parsin'''
11 description = """
12 parsing cap3 assembly aln output
13 """
14 parser = argparse.ArgumentParser(description=description,
15 formatter_class=argparse.RawTextHelpFormatter)
16 parser.add_argument(
17 '-a', '--aln_file',
18 default=None, required=True,
19 help="Aln file input",
20 type=str,
21 action='store')
22 parser.add_argument(
23 '-f', '--fasta',
24 default=None, required=True,
25 help="fasta output file name",
26 type=str,
27 action='store')
28 parser.add_argument(
29 '-p', '--profile',
30 default=None, required=True,
31 help="output file for coverage profile",
32 type=str,
33 action="store"
34 )
35 return parser.parse_args()
36
37
38 if __name__ == "__main__":
39
40 args = parse_args()
41 print(args.profile)
42
43