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