bin/merge_kraken_res.py
def _get_args():
    '''This function parses and return arguments passed in'''
    parser = argparse.ArgumentParser(
        prog='merge_kraken_res',
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description='Merging csv count files in one table')
    parser.add_argument(
        '-or',
        dest="readout",
        default="kraken_read_count_table.csv",
        help="Read count output file. Default = kraken_read_count_table.csv")
    parser.add_argument(
        '-ok',
        dest="kmerout",
        default="kraken_kmer_unicity_table.csv",
        help="Kmer unicity output file. Default = kraken_kmer_unicity_table.csv")

    args = parser.parse_args()

    readout = args.readout
    kmerout = args.kmerout

    return(readout, kmerout)
This function parses and return arguments passed in
This function parses and return arguments passed in
This function parses and return arguments passed in
def _get_args():
    parser = argparse.ArgumentParser(
        prog='merge_kraken_res',
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description='Merging csv count files in one table')
    parser.add_argument(
        '-or',
        dest="readout",
        default="kraken_read_count_table.csv",
        help="Read count output file. Default = kraken_read_count_table.csv")
    parser.add_argument(
        '-ok',
        dest="kmerout",
        default="kraken_kmer_unicity_table.csv",
        help="Kmer unicity output file. Default = kraken_kmer_unicity_table.csv")
    args = parser.parse_args()
    readout = args.readout
    kmerout = args.kmerout
    return(readout, kmerout)
def _get_args ( ) : parser = argparse . ArgumentParser ( prog = 'merge_kraken_res' , formatter_class = argparse . RawDescriptionHelpFormatter , description = 'Merging csv count files in one table' ) parser . add_argument ( '-or' , dest = "readout" , default = "kraken_read_count_table.csv" , help = "Read count output file. Default = kraken_read_count_table.csv" ) parser . add_argument ( '-ok' , dest = "kmerout" , default = "kraken_kmer_unicity_table.csv" , help = "Kmer unicity output file. Default = kraken_kmer_unicity_table.csv" ) args = parser . parse_args ( ) readout = args . readout kmerout = args . kmerout return ( readout , kmerout )
This function parses and return arguments passed in
This function parses and return arguments passed in
'''This function parses and return arguments passed in'''