chromMatcher.py 文件源码

def parse_args(args):
    """
    Takes in the command-line arguments list (args), and returns a nice argparse
    result with fields for all the options.

    Borrows heavily from the argparse documentation examples:
    <http://docs.python.org/library/argparse.html>
    """

    # Construct the parser (which is stored in parser)
    # Module docstring lives in __doc__
    # See http://python-forum.com/pythonforum/viewtopic.php?f=3&t=36847
    # And a formatter class so our examples in the docstring look good. Isn't it
    # convenient how we already wrapped it to 80 characters?
    # See http://docs.python.org/library/argparse.html#formatter-class
    parser = argparse.ArgumentParser(description=__doc__, 
        formatter_class=argparse.RawDescriptionHelpFormatter)

    parser.add_argument("ref_name",
        help="name of BWA-indexed reference FASTA")
    parser.add_argument("query_name",
        help="name of query FASTA")

    parser.add_argument("--chunk_size", type=int, default=10000,
        help="size of chunks to align")
    parser.add_argument("--chunk_stride", type=int, default=100000,
        help="distabnce between chunks to align")
    parser.add_argument("--max_children", type=int, default=10,
        help="number of bwa children to run")
    parser.add_argument("--batch_size", type=int, default=1000,
        help="number of chunks to align at once")
    parser.add_argument("--match_threshold", type=float, default=0.95,
        help="min score for a hit as a fraction of possible score")
    parser.add_argument("--out_file", type=argparse.FileType("w"),
        default=sys.stdout,
        help="TSV file of contig pairings to write")
    parser.add_argument("--debug", action="store_true",
        help="add extra debugging comments to output TSV")

    # The command line arguments start with the program name, which we don't
    # want to treat as an argument for argparse. So we remove it.
    args = args[1:]

    return parser.parse_args(args)