tear.py 文件源码

def build_parser():
    """Build argument parser."""

    parser = argparse.ArgumentParser(
        description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    # Required args
    parser.add_argument("--in_gct_path", "-i", required=True,
                        help="filepath to input gct")

    # Optional args
    parser.add_argument("--out_name", "-o", default=None,
                        help="name of output file (default is <INPUT_GCT>.tear.processed.gct")
    parser.add_argument("--divide_by_mad", "-dm", action="store_true", default=False,
                    help=("whether to divide by median absolute deviation " +
                          "in addition to subtracting the probe median"))
    parser.add_argument("--ignore_subset_norm", "-ig", action="store_true", default=False,
                        help="whether to ignore subset-specific normalization")
    parser.add_argument("-psp_config_path", type=str,
                        default="~/psp_production.cfg",
                        help="filepath to PSP config file")
    parser.add_argument("-verbose", "-v", action="store_true", default=False,
                        help="increase the number of messages reported")

    return parser