humann/tools/merge_abundance.py
def parse_arguments(args):
    """ 
    Parse the arguments from the user
    """
    
    parser = argparse.ArgumentParser(
        description= "Unpack pathway abundances to show genes included\n",
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument(
        "--input-genes",
        help="the gene family or EC abundance file\n",
        required=True)
    parser.add_argument(
        "--input-pathways",
        help="the pathway abundance file\n",
        required=True)
    parser.add_argument(
        "--gene-mapping",
        help="gene family to reaction mapping file\n")
    parser.add_argument(
        "--pathway-mapping",
        help="reaction to pathway mapping file\n")
    parser.add_argument(
        "-r","--remove-taxonomy",
        action="store_true",
        help="remove the taxonomy from the output file\n")
    parser.add_argument(
        "-o","--output",
        help="the table to write\n",
        required=True)

    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= "Unpack pathway abundances to show genes included\n",
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument(
        "--input-genes",
        help="the gene family or EC abundance file\n",
        required=True)
    parser.add_argument(
        "--input-pathways",
        help="the pathway abundance file\n",
        required=True)
    parser.add_argument(
        "--gene-mapping",
        help="gene family to reaction mapping file\n")
    parser.add_argument(
        "--pathway-mapping",
        help="reaction to pathway mapping file\n")
    parser.add_argument(
        "-r","--remove-taxonomy",
        action="store_true",
        help="remove the taxonomy from the output file\n")
    parser.add_argument(
        "-o","--output",
        help="the table to write\n",
        required=True)
    return parser.parse_args()
def parse_arguments ( args ) : parser = argparse . ArgumentParser ( description = "Unpack pathway abundances to show genes included\n" , formatter_class = argparse . RawTextHelpFormatter ) parser . add_argument ( "--input-genes" , help = "the gene family or EC abundance file\n" , required = True ) parser . add_argument ( "--input-pathways" , help = "the pathway abundance file\n" , required = True ) parser . add_argument ( "--gene-mapping" , help = "gene family to reaction mapping file\n" ) parser . add_argument ( "--pathway-mapping" , help = "reaction to pathway mapping file\n" ) parser . add_argument ( "-r" , "--remove-taxonomy" , action = "store_true" , help = "remove the taxonomy from the output file\n" ) parser . add_argument ( "-o" , "--output" , help = "the table to write\n" , required = True ) return parser . parse_args ( )
Parse the arguments from the user
Parse the arguments from the user
""" 
    Parse the arguments from the user
    """
args