parallelcopy.py 文件源码

python
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项目:hgvm-builder 作者: BD2KGenomics 项目源码 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)

    # Add the Toil options so the job store is the first argument
    Job.Runner.addToilOptions(parser)

    # General options
    parser.add_argument("in_store", type=IOStore.absolute,
        help="input IOStore to download from")
    parser.add_argument("out_store", type=IOStore.absolute,
        help="output IOStore to put things in")
    parser.add_argument("--pattern", default="*", 
        help="fnmatch-style pattern for file names to copy")
    parser.add_argument("--overwrite", default=False, action="store_true",
        help="overwrite existing files")
    parser.add_argument("--check_size", default=False, action="store_true",
        help="check sizes on existing files and replace if wrong")
    parser.add_argument("--batch_size", type=int, default=1000,
        help="number of files to copy in a batch")

    # 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)
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