Mercurial > repos > dfornika > snippy

comparison snippy_core_wrapper.py @ 16:a69f73853101 draft

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planemo upload for repository https://github.com/tseemann/snippy commit 93b22331ca83a82fdfbe8f2b274577e21f9bf025-dirty
author dfornika
date Tue, 22 Jan 2019 13:52:10 -0500
parents bf6dbc4d4957
children 412683e7a8fe
comparison
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15:bf6dbc4d4957 16:a69f73853101
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 input_datasets in args.input_datasets.split(','): 30 for input_dataset in args.indirs.split(','):
31 base_name = os.path.basename(indir) 31 base_name = os.path.basename(input_dataset)
32 copyfile(indir, '.') 32 print("base_name: " + base_name)
33 copyfile(input_dataset, base_name)
33 subprocess.Popen(['tar', '-xf', base_name]) 34 subprocess.Popen(['tar', '-xf', base_name])
34 35
35 extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ] 36 extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ]
36 37 print("extracted_dirs: " + str(extracted_dirs))
37 for extracted_dir in extracted_dirs: 38 for extracted_dir in extracted_dirs:
38 snippy_core_command_line.append(extracted_dir) 39 snippy_core_command_line.append(extracted_dir)
39 40 print(str(snippy_core_command_line))
40 subprocess.Popen(snippy_core_command_line) 41 subprocess.Popen(snippy_core_command_line).wait()
41 42
42 if __name__ == '__main__': 43 if __name__ == '__main__':
43 main() 44 main()