run_basespace.py 文件源码

def parse_args():
    class FullPaths(argparse.Action):
        """Expand user- and relative-paths"""
        def __call__(self, parser, namespace, values, option_string=None):
            setattr(namespace, self.dest, os.path.abspath(os.path.expanduser(values)))

    usage = " "
    parser = argparse.ArgumentParser(description="STAR-SEQR Parameters:", epilog=usage)
    parser.add_argument('-j', '--json', type=str, required=False, action=FullPaths,
                        default='/data/input/AppSession.json',
                        help='json input file from basespace app')
    parser.add_argument('-s', '--sample_path', type=str, required=False, action=FullPaths,
                        default='/data/input/samples/',
                        help='default path for samples')
    parser.add_argument('-r', '--results_path', type=str, required=False, action=FullPaths,
                        default='/data/output/appresults/',
                        help='default path for results')
    parser.add_argument('-t', '--scratch_path', type=str, required=False, action=FullPaths,
                        default='/data/scratch/',
                        help='default path for scratch')
    args = parser.parse_args()
    return args