scripts/release/rethreshold_family.py
def parse_arguments():
    """
    Uses python's argparse to parse the command line arguments

    return: Argparse parser object
    """

    # create a new argument parser object
    parser = argparse.ArgumentParser(description='Update scores for new release')

    # group required arguments together
    req_args = parser.add_argument_group("required arguments")
    req_args.add_argument('--dest-dir', help='destination directory where to checkout families',
                          type=str, required=True)

    mutually_exclusive_args = parser.add_mutually_exclusive_group()
    mutually_exclusive_args.add_argument('-f', help='a file containing a list of Rfam family accessions', type=str)
    mutually_exclusive_args.add_argument('--all', help='runs rfsearch on all families', action="store_true")
    mutually_exclusive_args.add_argument('--acc', help="a valid rfam family accession RFXXXXX",
                                         type=str, default=None)
    parser.add_argument('--rfmake', help='run rfmake after rfsearch completion', action="store_true")
    parser.add_argument('-v', help='runs validation checks', action="store_true")

    parser.add_argument('--report', help='generates search reports', action="store_true")

    # this is mutually exclusive with --acc option
    parser.add_argument('--exclude-type', help='type(s) of ncRNAs to exclude', type=str, default=None)

    return parser

    Uses python's argparse to parse the command line arguments

    return: Argparse parser object
    
Uses python's argparse to parse the command line arguments
return: Argparse parser object
Uses python ' s argparse to parse the command line arguments return : Argparse parser object
def parse_arguments():
    parser = argparse.ArgumentParser(description='Update scores for new release')
    req_args = parser.add_argument_group("required arguments")
    req_args.add_argument('--dest-dir', help='destination directory where to checkout families',
                          type=str, required=True)
    mutually_exclusive_args = parser.add_mutually_exclusive_group()
    mutually_exclusive_args.add_argument('-f', help='a file containing a list of Rfam family accessions', type=str)
    mutually_exclusive_args.add_argument('--all', help='runs rfsearch on all families', action="store_true")
    mutually_exclusive_args.add_argument('--acc', help="a valid rfam family accession RFXXXXX",
                                         type=str, default=None)
    parser.add_argument('--rfmake', help='run rfmake after rfsearch completion', action="store_true")
    parser.add_argument('-v', help='runs validation checks', action="store_true")
    parser.add_argument('--report', help='generates search reports', action="store_true")
    parser.add_argument('--exclude-type', help='type(s) of ncRNAs to exclude', type=str, default=None)
    return parser
def parse_arguments ( ) : parser = argparse . ArgumentParser ( description = 'Update scores for new release' ) req_args = parser . add_argument_group ( "required arguments" ) req_args . add_argument ( '--dest-dir' , help = 'destination directory where to checkout families' , type = str , required = True ) mutually_exclusive_args = parser . add_mutually_exclusive_group ( ) mutually_exclusive_args . add_argument ( '-f' , help = 'a file containing a list of Rfam family accessions' , type = str ) mutually_exclusive_args . add_argument ( '--all' , help = 'runs rfsearch on all families' , action = "store_true" ) mutually_exclusive_args . add_argument ( '--acc' , help = "a valid rfam family accession RFXXXXX" , type = str , default = None ) parser . add_argument ( '--rfmake' , help = 'run rfmake after rfsearch completion' , action = "store_true" ) parser . add_argument ( '-v' , help = 'runs validation checks' , action = "store_true" ) parser . add_argument ( '--report' , help = 'generates search reports' , action = "store_true" ) parser . add_argument ( '--exclude-type' , help = 'type(s) of ncRNAs to exclude' , type = str , default = None ) return parser
Uses python's argparse to parse the command line arguments
return: Argparse parser object
Uses python ' s argparse to parse the command line arguments return : Argparse parser object
"""
    Uses python's argparse to parse the command line arguments

    return: Argparse parser object
    """ # create a new argument parser object # group required arguments together # this is mutually exclusive with --acc option