ragtag_delta2paf.py

#!/usr/bin/env python

"""
MIT License

Copyright (c) 2021 Michael Alonge <malonge11@gmail.com>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
"""

import gzip
import argparse


def delta2paf():
    """
    Essentially a translation of paftools.js delta2paf

    https://github.com/lh3/minimap2/tree/master/misc
    """
    parser = argparse.ArgumentParser(description="Convert a Nucmer delta file to a PAF file.", usage="ragtag.py delta2paf <alns.delta>")
    parser.add_argument("delta_file", metavar="<alns.delta>", type=str, help="delta file to convert.")

    args = parser.parse_args()
    delta_file = args.delta_file

    seen_gt = False

    if delta_file[-3:] == ".gz":
        f = gzip.open(delta_file)
    else:
        f = open(delta_file, "r")

    for line in f:
        if not isinstance(line, str):
            line = line.decode("utf-8")

        t = line.rstrip().split(" ")

        # Check to see if we have started a new ref/query pair
        if line.startswith(">"):
            rname, qname, rlen, qlen = t[0][1:], t[1], int(t[2]), int(t[3])
            seen_gt = True
            continue

        # Continue if we haven't reached alignments yet
        if not seen_gt:
            continue

        if len(t) == 7:
            for i in range(5):
                t[i] = int(t[i])

            strand = True if (t[0] < t[1] and t[2] < t[3]) or (t[0] > t[1] and t[2] > t[3]) else False

            # Reference/query start/end
            rs = (t[0] - 1) if t[0] < t[1] else (t[1] - 1)
            re = t[1] if t[1] > t[0] else t[0]
            qs = (t[2] - 1) if t[2] < t[3] else (t[3] - 1)
            qe = t[3] if t[3] > t[2] else t[2]
            x, y = 0, 0
            NM = t[4]
            cigar = []

        elif len(t) == 1:
            d = int(t[0])
            if d == 0:
                blen, cigar_str = 0, []
                if re - rs - x != qe - qs - y:
                    print(re, rs, x)
                    print(qe, qs, y)
                    raise RuntimeError("inconsistent alignment")

                cigar.append((re - rs - x) << 4)
                for i in cigar:
                    blen += i >> 4
                    cigar_str.append(str((i >> 4)) + "MID"[i & 0xf])
                out_strand = "+" if strand > 0 else "-"
                print("\t".join([
                    qname,
                    str(qlen),
                    str(qs),
                    str(qe),
                    out_strand,
                    rname,
                    str(rlen),
                    str(rs),
                    str(re),
                    str(blen - NM),
                    str(blen),
                    "0",
                    "NM:i:" + str(NM),
                    "cg:Z:" + "".join(cigar_str)
                ]))
            elif d > 0:
                l = d - 1
                x += l + 1
                y += l
                if l:
                    cigar.append(l << 4)
                if len(cigar) > 0 and (cigar[-1] & 0xf) == 2:
                    cigar[-1] += 1 << 4
                else:
                    cigar.append(1 << 4 | 2)  # deletion
            else:
                l = -d - 1
                x += l
                y += l + 1
                if l:
                    cigar.append(l << 4)
                if len(cigar) > 0 and (cigar[-1] & 0xf) == 1:
                    cigar[-1] += 1 << 4
                else:
                    cigar.append(1 << 4 | 1)  # insertion

    f.close()


if __name__ == "__main__":
    delta2paf()