comparison interproscan5/fake_ips.py @ 0:0da2847fc108 draft default tip

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author si-datascience
date Thu, 24 May 2018 14:57:30 -0400
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-1:000000000000 0:0da2847fc108
1 """
2 """
3
4 __author__ = 'mkh'
5
6 if __name__ == '__main__':
7 import argparse
8 import os
9 from shutil import copyfile
10 import sys
11
12 parser = argparse.ArgumentParser(description='Fake IPS.')
13
14 parser.add_argument('-dp', action='store_true')
15 parser.add_argument('--input')
16 parser.add_argument('--seqtype', default='p')
17 parser.add_argument('-f', dest='formats', default='tsv')
18 parser.add_argument('--applications')
19 parser.add_argument('--tempdir')
20 parser.add_argument('--pathways', action='store_true')
21 parser.add_argument('--goterms', action='store_true')
22 parser.add_argument('--iprlookup', action='store_true')
23 parser.add_argument('--mode')
24 parser.add_argument('--clusterrunid')
25 parser.add_argument('--output-file-base', dest='output_file_base')
26 parser.add_argument('-o', dest='output_file', default="/tmp/junk")
27
28 args = parser.parse_args()
29 formats = args.formats.split(',')
30 src_data_dir = os.path.dirname(__file__) + '/data-' + args.seqtype
31
32 for ext in formats:
33 if ext in ['html', 'svg']:
34 ext += '.tar.gz'
35 copyfile(src_data_dir + '/' + '__base__' + '.' + ext, args.output_file_base + '.' + ext)