Source code for pmotools.scripts.pmo_to_tables.extract_insert_of_panels

#!/usr/bin/env python3
import argparse

from pmotools.pmo_engine.pmo_exporter import PMOExporter
from pmotools.pmo_engine.pmo_reader import PMOReader
from pmotools.utils.small_utils import Utils


def get_parser_extract_insert_of_panels() -> argparse.ArgumentParser:
    parser = argparse.ArgumentParser(
        prog="pmotools-python extract_insert_of_panels",
        description="Extract inserts of panels from a PMO",
    )
    parser.add_argument("--file", type=str, required=True, help="PMO file")
    parser.add_argument(
        "--output", type=str, default="STDOUT", required=False, help="output file"
    )
    parser.add_argument(
        "--overwrite", action="store_true", help="If output file exists, overwrite it"
    )
    parser.add_argument(
        "--add_ref_seqs",
        action="store_true",
        help="add ref seqs to the output as ref_seq",
    )
    return parser


def parse_args_extract_insert_of_panels():
    parser = get_parser_extract_insert_of_panels()
    return parser.parse_args()


def extract_insert_of_panels():
    args = parse_args_extract_insert_of_panels()

    # check files
    Utils.inputOutputFileCheck(args.file, args.output, args.overwrite)

    # read in PMO
    pmo = PMOReader.read_in_pmo(args.file)

    # get panel insert locations
    panel_bed_locs = PMOExporter.extract_panels_insert_bed_loc(pmo)

    # write
    with Utils.smart_open_write(args.output) as f:
        f.write(
            "\t".join(
                [
                    "#chrom",
                    "start",
                    "end",
                    "target_id",
                    "length",
                    "strand",
                    "extra_info",
                ]
            )
        )
        if args.add_ref_seqs:
            f.write("\tref_seq")
        f.write("\n")
        for loc in panel_bed_locs:
            f.write(
                "\t".join(
                    [
                        loc.chrom,
                        str(loc.start),
                        str(loc.end),
                        loc.name,
                        str(loc.score),
                        loc.strand,
                        loc.extra_info,
                    ]
                )
            )
            if args.add_ref_seqs:
                f.write("\t" + str(loc.ref_seq))
            f.write("\n")


if __name__ == "__main__":
    extract_insert_of_panels()