compute_contigs_compatibility.py 文件源码

def parse_arguments():
    """
    Parse the command line, and check if arguments are correct
    """
    # Initiate argument parser
    parser = DefaultHelpParser(description='Program description',
                               # to precisely format help display
                               formatter_class=lambda prog: argparse.HelpFormatter(prog, width=120, max_help_position=80))

    # Main parameters
    group_main = parser.add_argument_group('Main parameters')
    # -i / --input_sam
    group_main.add_argument('-i', '--input_sam',
                            action = 'store',
                            metavar = 'INSAM',
                            type = argparse.FileType('r'),
                            default = '-',
                            help = 'Input sam file, sorted by subject and position')
    # -o / --output_sam
    group_main.add_argument('-o', '--output_sam',
                            action = 'store',
                            metavar = 'OUTSAM',
                            type = argparse.FileType('w'),
                            default = '-',
                            help = 'Output sam file')
    # -v / --verbose
    group_main.add_argument('-v', '--verbose',
                            action = 'store_true',
                            help = 'Increase verbosity')

    # Debug
    group_debug = parser.add_argument_group('Debug parameters')
    # --debug
    group_debug.add_argument('--debug',
                             action = 'store_true',
                             help = 'Output debug infos')

    args = parser.parse_args()

    #
    return args