humann/tools/reduce_table.py
def parse_arguments(args):
    """ 
    Parse the arguments from the user
    """
    
    parser = argparse.ArgumentParser(
        description= "Reduce table\n",
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument(
        "-v","--verbose", 
        help="additional output is printed\n", 
        action="store_true",
        default=False)
    parser.add_argument(
        "-i","--input",
        help="the input table\n",
        required=True)
    parser.add_argument(
        "-o","--output",
        help="the output table\n",
        required=True)
    parser.add_argument(
        "--function",
        choices=list(FUNCTION_OPTIONS),
        default=DEFAULT_FUNCTION,
        help="the function to apply")
    parser.add_argument(
        "--sort-by",
        choices=list(SORT_OPTIONS),
        help="sort the output by the selection")

    return parser.parse_args()
 
    Parse the arguments from the user
    
Parse the arguments from the user
Parse the arguments from the user
def parse_arguments(args):
    parser = argparse.ArgumentParser(
        description= "Reduce table\n",
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument(
        "-v","--verbose", 
        help="additional output is printed\n", 
        action="store_true",
        default=False)
    parser.add_argument(
        "-i","--input",
        help="the input table\n",
        required=True)
    parser.add_argument(
        "-o","--output",
        help="the output table\n",
        required=True)
    parser.add_argument(
        "--function",
        choices=list(FUNCTION_OPTIONS),
        default=DEFAULT_FUNCTION,
        help="the function to apply")
    parser.add_argument(
        "--sort-by",
        choices=list(SORT_OPTIONS),
        help="sort the output by the selection")
    return parser.parse_args()
def parse_arguments ( args ) : parser = argparse . ArgumentParser ( description = "Reduce table\n" , formatter_class = argparse . RawTextHelpFormatter ) parser . add_argument ( "-v" , "--verbose" , help = "additional output is printed\n" , action = "store_true" , default = False ) parser . add_argument ( "-i" , "--input" , help = "the input table\n" , required = True ) parser . add_argument ( "-o" , "--output" , help = "the output table\n" , required = True ) parser . add_argument ( "--function" , choices = list ( FUNCTION_OPTIONS ) , default = DEFAULT_FUNCTION , help = "the function to apply" ) parser . add_argument ( "--sort-by" , choices = list ( SORT_OPTIONS ) , help = "sort the output by the selection" ) return parser . parse_args ( )
Parse the arguments from the user
Parse the arguments from the user
""" 
    Parse the arguments from the user
    """
args