create_inference_graphs.py

import argparse
import pickle
import os
import graph_parser
import dgl


def create_inference_graph(gfa_path, reads_path, out_dir, assembler, paf_path):
    assert os.path.isfile(gfa_path), "GFA not found!"
    assert os.path.isfile(reads_path), "Reads not found!"

    print(f'Starting to parse assembler output')
    graph, auxiliary = graph_parser.only_from_gfa(gfa_path, training=False, reads_path=reads_path, get_similarities=True, paf_path=paf_path)
    print(f'Parsed assembler output! Saving files...')

    out_dir = os.path.join(out_dir, assembler)
    if not os.path.isdir(out_dir):
        os.makedirs(out_dir)
    processed_dir = f'{out_dir}/processed'
    info_dir = f'{out_dir}/info'
    if not os.path.isdir(processed_dir):
        os.mkdir(processed_dir)
    if not os.path.isdir(info_dir):
        os.mkdir(info_dir)

    processed_path = f'{processed_dir}/0.dgl'
    dgl.save_graphs(processed_path, graph)
    for name, data in auxiliary.items():
        pickle.dump(data, open(f'{info_dir}/0_{name}.pkl', 'wb'))
    print(f'Processing of graph done!\n')


if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('--gfa', type=str, help='Path to the GFA graph file')
    parser.add_argument('--reads', type=str, help='Path to the FASTA/Q reads file')
    parser.add_argument('--asm', type=str, help='Assembler used')
    parser.add_argument('--out', type=str, help='Output directory')
    parser.add_argument('--paf', type=str, help='Path to the PAF file')
    args = parser.parse_args()

    gfa = args.gfa
    reads = args.reads
    out = args.out
    asm = args.asm
    paf = args.paf
    
    create_inference_graph(gfa, reads, out, asm, paf)