smartSam2Fastq.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)

    # General options
    parser.add_argument("--input_sam", type=argparse.FileType("r"),
        default=sys.stdin,
        help="input SAM in name-sorted order.")
    parser.add_argument("--fq1", type=argparse.FileType("w"),
        default=sys.stdout,
        help="FASTQ file to save the READ1 reads in (+READ2 if interleaved)")
    parser.add_argument("--fq2", type=argparse.FileType("w"),
        default=sys.stdout,
        help="FASTQ file to save the READ2 reads in")
    parser.add_argument("--interleaved", action="store_true",
        help="write interleaved FASTQ to fq1")
    parser.add_argument("--drop_secondary", action="store_true",
        help="drop pairs where a primary alignment is not seen at both ends")
    parser.add_argument("--expect_paired", action="store_true",
        help="expect all reads to have a pair partner and abort otherwise")

    # 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)