humann/search/blastx_coverage.py
def parse_arguments(args):
    """ 
    Parse the arguments from the user
    """
    parser = argparse.ArgumentParser(
        description= "Compute blastx coverage\n",
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument(
        "-i","--input",
        help="the blastx formatted input file\n",
        required=True)
    parser.add_argument(
        "--coverage-threshold",
        type=float,
        help="the subject coverage threshold\n[ DEFAULT : "+str(config.translated_subject_coverage_threshold)+" ]", 
        default=config.translated_subject_coverage_threshold)
    parser.add_argument(
        "--print-protein-list",
        action="store_true",
        help="print the list of proteins that meet the coverage threshold")
    
    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= "Compute blastx coverage\n",
        formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument(
        "-i","--input",
        help="the blastx formatted input file\n",
        required=True)
    parser.add_argument(
        "--coverage-threshold",
        type=float,
        help="the subject coverage threshold\n[ DEFAULT : "+str(config.translated_subject_coverage_threshold)+" ]", 
        default=config.translated_subject_coverage_threshold)
    parser.add_argument(
        "--print-protein-list",
        action="store_true",
        help="print the list of proteins that meet the coverage threshold")
    return parser.parse_args()
def parse_arguments ( args ) : parser = argparse . ArgumentParser ( description = "Compute blastx coverage\n" , formatter_class = argparse . RawTextHelpFormatter ) parser . add_argument ( "-i" , "--input" , help = "the blastx formatted input file\n" , required = True ) parser . add_argument ( "--coverage-threshold" , type = float , help = "the subject coverage threshold\n[ DEFAULT : " + str ( config . translated_subject_coverage_threshold ) + " ]" , default = config . translated_subject_coverage_threshold ) parser . add_argument ( "--print-protein-list" , action = "store_true" , help = "print the list of proteins that meet the coverage threshold" ) return parser . parse_args ( )
Parse the arguments from the user
Parse the arguments from the user
""" 
    Parse the arguments from the user
    """
args