INNER CODE UNIT · Python
main
MariaNattestad/assemblytics · assemblytics/dot_prep.py:159
def main():
parser=argparse.ArgumentParser(description="Take a delta file, apply Assemblytics unique anchor filtering, and prepare coordinates input files for Dot")
parser.add_argument("--delta",help="delta file" ,dest="delta", type=str, required=True)
parser.add_argument("--out",help="output file prefix" ,dest="out", type=str, default="output")
parser.add_argument("--unique-length",help="The total length of unique sequence an alignment must have on the query side to be retained. Default: 10000" ,dest="unique_length",type=int, default=10000)
parser.add_argument("--overview",help="The number of alignments to include in the coords.idx output file. Default: 1000" ,dest="overview",type=int, default=1000)
args=parser.parse_args()
import os
from .uniq_anchor import run as run_uniq_anchor
out_dir = os.path.dirname(args.out) or "."
reference_lengths, fields_by_query = run_uniq_anchor(
argparse.Namespace(delta=args.delta, out=out_dir, unique_length=args.unique_length, keep_small_uniques=True)
)
index_for_dot(reference_lengths, fields_by_query, args.out, args.overview)
if __name__=="__main__":