INNER CODE UNIT · Python

main

steineggerlab/Metabuli · util/gtdb_to_taxdump.py:311

def main(args):
    # creating DAG
    graph = Graph()
    graph.add_vertex('root')
    for F in args.tax_file:
        logging.info('Loading: {}'.format(F))
        load_gtdb_tax(F, graph)
    # transversing DAG and writing node.dmp & names.dmp
    names_file, nodes_file = graph.write_dmp(args.outdir,
                                             embl_code=args.embl_code)
    logging.info('File written: {}'.format(names_file))
    logging.info('File written: {}'.format(nodes_file))
    # writing standard table of taxIDs
    graph.to_tbl()
    # appending to table
    if args.table is not None:
        graph.append_tbl(args.table, args.column)
    # writing "blank" delnodes.dmp & merged.dmp files

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