Mercurial > repos > dfornika > snippy

comparison snippy_core_wrapper.py @ 5:b9eacd069df6 draft

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planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
author dfornika
date Mon, 21 Jan 2019 15:46:37 -0500
parents 3f5ced130c5c
children ab3026667cdc
comparison
equal deleted inserted replaced
4:3f5ced130c5c 5:b9eacd069df6
20 from shutil import copyfile 20 from shutil import copyfile
21 21
22 def main(): 22 def main():
23 parser = argparse.ArgumentParser() 23 parser = argparse.ArgumentParser()
24 parser.add_argument('-r', '--ref', help='Reference fasta', required=True) 24 parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
25 parser.add_argument('inputs', nargs='+') 25 parser.add_argument('-i', '--indirs', nargs='+')
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 in args.inputs: 30 for indir in args.indirs:
31 bn = os.path.basename(input) 31 base_name = os.path.basename(indir)
32 sys.stderr.write(input + '\n') 32 sys.stderr.write(indir + '\n')
33 copyfile(input, bn) 33 copyfile(indir, base_name)
34 sys.stderr.write('\n'.join([input, bn]) + '\n') 34 sys.stderr.write('\n'.join([indir, base_name]) + '\n')
35 subprocess.run(['tar', '-xf', bn]) 35 subprocess.run(['tar', '-xf', base_name])
36 36
37 test_list = [f.path for f in os.scandir() if f.is_dir() ] 37 extracted_dirs = [f.path for f in os.scandir() if f.is_dir() ]
38 38
39 for dir in test_list: 39 for extracted_dir in extracted_dirs:
40 snippy_core_command_line.append(dir) 40 snippy_core_command_line.append(extracted_dir)
41 41
42 print(snippy_core_command_line) 42 print(snippy_core_command_line)
43 subprocess.run(snippy_core_command_line) 43 subprocess.run(snippy_core_command_line)
44
44 if __name__ == '__main__': 45 if __name__ == '__main__':
45 main() 46 main()