tigmint-ntlink-map

#!/usr/bin/env python3
"""
Helper script for running ntLink, followed by creation of the molecule extents file
@author: Lauren Coombe
"""
import argparse
import shlex
import subprocess


def run_ntlink_pair(args):
    "Run ntLink pair stage to obtain PAF-formatted mappings"
    command = f"ntLink pair target={args.target}.fa reads={args.reads} " \
              f"paf=True k={args.k} w={args.w} t={args.t} sensitive=True"
    command_shlex = shlex.split(command)
    return_code = subprocess.call(command_shlex)
    assert return_code == 0

def run_tigmint_filter_paf(args):
    "Run tigmint-filter-paf to filter and convert PAF file to BED format"
    script_loc = "tigmint-filter-paf"
    if args.path:
        script_loc = f"{args.path}/{script_loc}"

    command_1_shlex = shlex.split(f"{script_loc} -m {args.m} {args.target}.fa.k{args.k}.w{args.w}.z1000.paf")
    command_2_shlex = shlex.split("sort -k1,1 -k2,2n -k3,3n")

    with open(args.bed, "wb") as outfile:
        process_1 = subprocess.Popen(command_1_shlex, stdout=subprocess.PIPE)
        process_2 = subprocess.Popen(command_2_shlex, stdin=process_1.stdout, stdout=outfile)
        process_1.wait()
        process_2.wait()

    assert process_1.returncode == 0
    assert process_2.returncode == 0

def main():
    "Run ntLink mapping, then output filtered, sorted BED file with mapping extents"
    parser = argparse.ArgumentParser(description="Run ntLink mapping, then output a filtered "
                                                 "and sorted BED file with mapping extents")
    parser.add_argument("target", help="Draft assembly to scaffold")
    parser.add_argument("reads", help="Long reads file")
    parser.add_argument("--bed", help="Name for output BED file with mapping extents",
                        required=True, type=str)
    parser.add_argument("-k", help="K-mer size (bp)", required=True, type=int)
    parser.add_argument("-w", help="Window size", required=True, type=int)
    parser.add_argument("-t", help="Number of threads [4]", default=4, type=int)
    parser.add_argument("--path", help="Path to directory with tigmint-fiter-paf executable, "
                                       "if not in PATH", type=str)
    parser.add_argument("-m", help="Minimum size for mapping block (bp) [2000]", default=2000, type=int)
    parser.add_argument("--span", help="Span value specified for tigmint-cut", required=True)
    parser.add_argument('--version', action='version', version='tigmint-ntlink-map 1.2.9')

    args = parser.parse_args()

    if args.span == "auto":
        raise ValueError("Error: span=auto is currently not compatible with using ntLink for mapping. " \
            "Please specify an integer value for span. " \
            "When using ntLink for mapping, we recommend the span value to be between 2-10.")

    run_ntlink_pair(args)
    run_tigmint_filter_paf(args)

if __name__ == "__main__":
    main()