zibra.py 文件源码

def main():
    parser = argparse.ArgumentParser(prog='zibra', formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument("-v", "--version", help="Installed zibra version",
                        action="version",
                        version="%(prog)s " + str(version.__version__))
    subparsers = parser.add_subparsers(title='[sub-commands]', dest='command', parser_class=ArgumentParserWithDefaults)

    # extract
    parser_extract = subparsers.add_parser('extract',
                                          help='Create an empty poredb database')
    parser_extract.add_argument('directory', metavar='directory',
                             help='The name of the database.')
    parser_extract.add_argument('--basecaller', metavar='basecaller',
                             default='ONT Albacore Sequencing Software',
                             help='The name of the basecaller')
    parser_extract.set_defaults(func=run_subtool)

    # callers
    parser_extract = subparsers.add_parser('basecaller', help='Display basecallers in files')
    parser_extract.add_argument('directory', metavar='directory', help='Directory of FAST5 files.')
    parser_extract.set_defaults(func=run_subtool)

    # demultiplex
    parser_demultiplex = subparsers.add_parser('demultiplex', help='Run demultiplex')
    parser_demultiplex.add_argument('fasta', metavar='fasta', help='Undemultiplexed FASTA file.')
    parser_demultiplex.add_argument('--threads', type=int, default=8, help='Number of threads')
    parser_demultiplex.add_argument('--prefix', help='Prefix for demultiplexed files')
    parser_demultiplex.add_argument('--no-remove-directory', dest='no_remove_directory', action='store_true')
    parser_demultiplex.set_defaults(func=run_subtool)

    # minion
    parser_minion = subparsers.add_parser('minion', help='Run demultiplex')
    parser_minion.add_argument('scheme', metavar='scheme', help='The name of the scheme.')
    parser_minion.add_argument('sample', metavar='sample', help='The name of the sample.')
        parser_minion.add_argument('--normalise', dest='normalise', type=int, default=100, help='Normalise down to moderate coverage to save runtime.')
    parser_minion.add_argument('--threads', type=int, default=8, help='Number of threads')
    parser_minion.add_argument('--scheme-directory', metavar='scheme_directory', default='/zibra/zika-pipeline/schemes', help='Default scheme directory')
    parser_minion.add_argument('--max-haplotypes', type=int, default=1000000, metavar='max_haplotypes', help='max-haplotypes value for nanopolish')
    parser_minion.add_argument('--read-file', metavar='read_file', help='Use alternative FASTA/FASTQ file to <sample>.fasta')
    parser_minion.add_argument('--skip-nanopolish', action='store_true')
    parser_minion.set_defaults(func=run_subtool)

    # import
    """parser_import = subparsers.add_parser('import',
                                          help='Import files into a poredb database')
    parser_import.add_argument('db', metavar='DB',
                               help='The poredb database.')
    parser_import.add_argument('fofn', metavar='FOFN',
                               help='A file containing a list of file names.')
    parser_import.add_argument('--alternate-path', metavar='alternate_path')
    parser_import.set_defaults(func=run_subtool)
    """

    args = parser.parse_args()

    if args.quiet:
        logger.setLevel(logging.ERROR)

    args.func(parser, args)