Honey.py 文件源码

def parseArgs():
    parser = argparse.ArgumentParser(prog="Honey.py", description=USAGE, \
            formatter_class=argparse.RawDescriptionHelpFormatter)

    #parser.add_argument("-h", "--help", action="store_true")
    parser.add_argument("stage", metavar="STAGE", choices=STAGES.keys(), type=str, \
                        help="Stage to execute")
    parser.add_argument("options", metavar="OPTIONS", nargs=argparse.REMAINDER,\
                         help="Options to pass to the stage")

    args = parser.parse_args()

    sys.stderr.write("""
Please Cite: English, Adam C., William J. Salerno, Jeffery G.
             Reid. "PBHoney: identyfying genomic variants via
             long-read discordance and interrupted mapping."
             BMC Bioinformatics 2014, 15:180 (June 10, 2014).
             doi:10.1186/1471-2105-15-180\n\n""")

    STAGES[args.stage](args.options)