|
14
|
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
|
