Mercurial > repos > dfornika > snippy

comparison snippy_core_wrapper.py @ 9:caed59c13f82 draft

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planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty
author dfornika
date Mon, 21 Jan 2019 18:35:52 -0500
parents c441153cb4c2
children 9d46ea31b273
comparison
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8:c441153cb4c2 9:caed59c13f82
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('-i', '--indirs') 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 indir in args.indirs.split(','):
31 base_name = os.path.basename(indir) 31 base_name = os.path.basename(indir)
32 sys.stderr.write(indir + '\n') 32 sys.stderr.write(indir + '\n')
33 copyfile(indir, base_name) 33 copyfile(indir, base_name)
34 sys.stderr.write('\n'.join([indir, base_name]) + '\n') 34 sys.stderr.write('\n'.join([indir, base_name]) + '\n')
35 subprocess.run(['tar', '-xf', base_name]) 35 subprocess.run(['tar', '-xf', base_name])