Mercurial > repos > dfornika > snippy

comparison snippy_core_wrapper.py @ 15:bf6dbc4d4957 draft

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planemo upload for repository https://github.com/tseemann/snippy commit 93b22331ca83a82fdfbe8f2b274577e21f9bf025-dirty
author dfornika
date Tue, 22 Jan 2019 13:26:27 -0500
parents c92d935dc8ab
children a69f73853101
comparison
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14:b102aece6b65 15:bf6dbc4d4957
25 parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets') 25 parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets')
26 args = parser.parse_args() 26 args = parser.parse_args()
27 27
28 snippy_core_command_line = ['snippy-core', '--ref', args.ref] 28 snippy_core_command_line = ['snippy-core', '--ref', args.ref]
29 29
30 for indir in args.indirs.split(','): 30 for input_datasets in args.input_datasets.split(','):
31 base_name = os.path.basename(indir) 31 base_name = os.path.basename(indir)
32 copyfile(indir, base_name) 32 copyfile(indir, '.')
33 subprocess.Popen(['tar', '-xf', base_name]) 33 subprocess.Popen(['tar', '-xf', base_name])
34 34
35 extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ] 35 extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ]
36 36
37 for extracted_dir in extracted_dirs: 37 for extracted_dir in extracted_dirs: