7645a5a90740ad0f9222620d8eda5c9a6544011c,chiron/chiron_eval.py,,,#,377

Before Change

if __name__ == "__main__":
    parser = argparse.ArgumentParser(prog="chiron",
                                     description="A deep neural network basecaller.")
    parser.add_argument("-i", "--input", default="example_data/output/raw",
                        help="File path or Folder path to the fast5 file.")
    parser.add_argument("-o", "--output", default="example_data/output",
                        help="Output Folder name")
    parser.add_argument("-m", "--model", default="model/DNA_default",
                        help="model folder")
    parser.add_argument("-s", "--start", type=int, default=0,
                        help="Start index of the signal file.")
    parser.add_argument("-b", "--batch_size", type=int, default=1100,
                        help="Batch size for run, bigger batch_size will increase the processing speed and give a slightly better accuracy but require larger RAM load")
    parser.add_argument("-l", "--segment_len", type=int, default=300,
                        help="Segment length to be divided into.")
    parser.add_argument("-j", "--jump", type=int, default=30,
                        help="Step size for segment")
    parser.add_argument("-t", "--threads", type=int, default=0,
                        help="Threads number")
    parser.add_argument("-e", "--extension", default="fastq",
                        help="Output file extension.")
    parser.add_argument("--beam", type=int, default=0,
                        help="Beam width used in beam search decoder, default is 0, in which a greedy decoder is used. Recommend width:100, Large beam width give better decoding result but require longer decoding time.")
    parser.add_argument("--concise", action="store_true",
                        help="Concisely output the result, the meta and segments files will not be output.")
    parser.add_argument("--mode", default = "dna",
                        help="Output mode, can be chosen from dna or rna.")
    args = parser.parse_args(sys.argv[1:])
    run(args)

After Change

            time_dict["real"], time_dict["sys"], time_dict["user"], time_dict["sys"] + time_dict["user"]))


if __name__ == "__main__":
    from .entry import main
    print("This calling method is deprecated, use entry", file=sys.stderr)
    main(["call"] + sys.argv[1:])

Instances