comparison snippy_core_wrapper.py @ 5:b9eacd069df6 draft

planemo upload for repository https://github.com/tseemann/snippy commit 73ec6ea773b1b88f7c32a2e8bc57b644b82f7ff9-dirty

4:3f5ced130c5c

from shutil import copyfile

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
    parser.add_argument('inputs', nargs='+')
    args = parser.parse_args()

    snippy_core_command_line = ['snippy-core', '--ref', args.ref]

    for input in args.inputs:
        bn = os.path.basename(input)
        sys.stderr.write(input + '\n')
        copyfile(input, bn)
        sys.stderr.write('\n'.join([input, bn]) + '\n')
        subprocess.run(['tar', '-xf', bn])

    test_list = [f.path for f in os.scandir() if f.is_dir() ]

    for dir in test_list:
        snippy_core_command_line.append(dir)

    print(snippy_core_command_line)
    subprocess.run(snippy_core_command_line)
if __name__ == '__main__':
    main()

5:b9eacd069df6

from shutil import copyfile

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
    parser.add_argument('-i', '--indirs', nargs='+')
    args = parser.parse_args()

    snippy_core_command_line = ['snippy-core', '--ref', args.ref]

    for indir in args.indirs:
        base_name = os.path.basename(indir)
        sys.stderr.write(indir + '\n')
        copyfile(indir, base_name)
        sys.stderr.write('\n'.join([indir, base_name]) + '\n')
        subprocess.run(['tar', '-xf', base_name])

    extracted_dirs = [f.path for f in os.scandir() if f.is_dir() ]

    for extracted_dir in extracted_dirs:
        snippy_core_command_line.append(extracted_dir)

    print(snippy_core_command_line)
    subprocess.run(snippy_core_command_line)

if __name__ == '__main__':
    main()