humann/tools/split_table.py
def parse_arguments(args):
    """ 
    Parse the arguments from the user
    """
    
    parser = argparse.ArgumentParser(
        description= "Split gene table to input to HUMAnN\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 gene table to read\n",
        required=True)
    parser.add_argument(
        "-o","--output",
        help="the directory for output files\n",
        required=True)
    parser.add_argument(
        "--taxonomy_index",
        help="the index of the gene in the taxonomy data\n",
        type=int)
    parser.add_argument(
        "--taxonomy_level",
        help="the level of taxonomy for the output (if input is from picrust metagenome_contributions.py)",
        choices=PICRUST_METAGENOME_HEADER.split("\t"),
        default="Genus")

    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= "Split gene table to input to HUMAnN\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 gene table to read\n",
        required=True)
    parser.add_argument(
        "-o","--output",
        help="the directory for output files\n",
        required=True)
    parser.add_argument(
        "--taxonomy_index",
        help="the index of the gene in the taxonomy data\n",
        type=int)
    parser.add_argument(
        "--taxonomy_level",
        help="the level of taxonomy for the output (if input is from picrust metagenome_contributions.py)",
        choices=PICRUST_METAGENOME_HEADER.split("\t"),
        default="Genus")
    return parser.parse_args()
def parse_arguments ( args ) : parser = argparse . ArgumentParser ( description = "Split gene table to input to HUMAnN\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 gene table to read\n" , required = True ) parser . add_argument ( "-o" , "--output" , help = "the directory for output files\n" , required = True ) parser . add_argument ( "--taxonomy_index" , help = "the index of the gene in the taxonomy data\n" , type = int ) parser . add_argument ( "--taxonomy_level" , help = "the level of taxonomy for the output (if input is from picrust metagenome_contributions.py)" , choices = PICRUST_METAGENOME_HEADER . split ( "\t" ) , default = "Genus" ) return parser . parse_args ( )
Parse the arguments from the user
Parse the arguments from the user
""" 
    Parse the arguments from the user
    """
args