humann/tools/join_tables.py
def parse_arguments(args):
    """ 
    Parse the arguments from the user
    """
    
    parser = argparse.ArgumentParser(
        description= "Join gene, pathway, or taxonomy tables\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 directory of tables\n",
        required=True)
    parser.add_argument(
        "-o","--output",
        help="the table to write\n",
        required=True)
    parser.add_argument(
        "--file_name",
        help="only join tables with this string included in the file name")
    parser.add_argument(
        "-s","--search-subdirectories", 
        help="search sub-directories of input folder for files\n", 
        action="store_true",
        default=False)

    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= "Join gene, pathway, or taxonomy tables\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 directory of tables\n",
        required=True)
    parser.add_argument(
        "-o","--output",
        help="the table to write\n",
        required=True)
    parser.add_argument(
        "--file_name",
        help="only join tables with this string included in the file name")
    parser.add_argument(
        "-s","--search-subdirectories", 
        help="search sub-directories of input folder for files\n", 
        action="store_true",
        default=False)
    return parser.parse_args()
def parse_arguments ( args ) : parser = argparse . ArgumentParser ( description = "Join gene, pathway, or taxonomy tables\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 directory of tables\n" , required = True ) parser . add_argument ( "-o" , "--output" , help = "the table to write\n" , required = True ) parser . add_argument ( "--file_name" , help = "only join tables with this string included in the file name" ) parser . add_argument ( "-s" , "--search-subdirectories" , help = "search sub-directories of input folder for files\n" , action = "store_true" , default = False ) return parser . parse_args ( )
Parse the arguments from the user
Parse the arguments from the user
""" 
    Parse the arguments from the user
    """
args