Mercurial > repos > artbio > pindel
comparison create_config_file.py @ 0:decc6b5631dc draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
author | artbio |
---|---|
date | Wed, 29 Sep 2021 21:30:31 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:decc6b5631dc |
---|---|
1 import argparse | |
2 | |
3 | |
4 description = ("This script will create a configuration file for samples \ | |
5 to be run in Pindel") | |
6 | |
7 | |
8 parser = argparse.ArgumentParser() | |
9 parser.add_argument("--input_file", nargs="*", | |
10 help="One or more alignment files") | |
11 parser.add_argument("--insert_size", nargs="+", | |
12 help="Expected Insert size") | |
13 parser.add_argument("--sample_label", nargs="+", | |
14 help="Sample label") | |
15 parser.add_argument("--output_config_file", | |
16 help="Output config file") | |
17 args = parser.parse_args() | |
18 | |
19 template = "{input_file}\t{insert_size}\t{sample_label}\n" | |
20 with open(args.output_config_file, "w") as output: | |
21 for input_file, insert_size, sample_label in zip(args.input_file, | |
22 args.insert_size, | |
23 args.sample_label): | |
24 config_line = template.format(input_file=input_file, | |
25 insert_size=insert_size, | |
26 sample_label=sample_label) | |
27 output.write(config_line) |