view filter_multihit_paf.py @ 135:21bb464c1d53 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 78bf7abb931bf3d348837c7211cd3cff32486691

# idea from https://github.com/marbl/MashMap/blob/master/scripts/denovo_repeat_annotation.py
# adds filter for more than minMatch denovo repeated paf read locations: >1 gives ~13%, >3 gives 3% of all hits in testing a big and small paf.
# A haplotype paf filtered of denovo repeats might give cleaner dotplots, because they add visual noise and repeats are less informative for sequence similarity.
# Alternative to use repeatmasked haplotype as the mashmap reference might also be useful.
# Also outputs a bed with the multimatch regions filtered from the paf with their repeat count as the score
# ross lazarus october 6 2024

import argparse

from collections import OrderedDict


def pafDeDupe(inPaf, outDeNovoBed, outPaf, minMatch):
    """
    Usage notes:
    if a segment appears more than once on the left of a paf row, it can be considered a denovo repeat!
    Contig and start offset are used as the id so approximate-ish.
    Seems a consistent 13% 1+ denovo repeats with different levels of identity and match length
    3+ finds a much lower 3% of hits

    With a 181217 row squirrelhaps1k.paf at 1k 99%, get about 13% denovo repeat rows
    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ python filter_multihit_paf.py --inpaf squirrelhaps1k.paf --outbed sh1k.bed --outpaf sh1kdedupe.paf --minMatch 1
    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l sh1kdedupe.paf
    109179 sh1kdedupe.paf
    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l sh1k.bed
    23015 sh1k.bed

    venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ python filter_multihit_paf.py --inpaf squirrelhaps1k.paf --outbed sh1k.bed --outpaf sh1kdedupe.paf --minMatch 3
    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l sh1k.bed
    7996 sh1k.bed

    with a smaller 26610 10k 95%, get about
    (venv3row 11) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l squirrelhaps.paf
    26610 squirrelhaps.paf
    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ python filter_multihit_paf.py squirrelhaps.paf sh.bed shdedupe.paf
    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l shdedupe.paf
    18332 shdedupe.paf
    (venv311) ross@pn50:~/rossgit/galaxytools/tools/jbrowse2$ wc -l sh.bed
    3663 sh.bed
    """

    CHROMOSOMECOL1 = 0
    STARTCOL1 = 2
    ENDCOL1 = 3
    hitTable1 = OrderedDict()
    hitTable1_lens = {}
    filterLen = minMatch
    minMatch = int(minMatch)
    filterMe = {}

    with open(inPaf) as f:
        for i, line in enumerate(f):
            rowElements = line.split()
            chromosome1 = rowElements[CHROMOSOMECOL1]
            start1 = int(rowElements[STARTCOL1])
            end1 = int(rowElements[ENDCOL1])
            h1key = "%s~%d" % (chromosome1, start1)
            if hitTable1.get(h1key, None):
                hitTable1[h1key].append(i)
                if len(hitTable1[h1key]) > minMatch:
                    filterMe[i] = i
            else:
                hitTable1[h1key] = [
                    i,
                ]
                hitTable1_lens[h1key] = abs(end1 - start1)
    with open(outDeNovoBed, "w") as f:
        for k in hitTable1.keys():
            # OrderedDict so input paf order preserved - if that's wrong so is the bed.
            nk = len(hitTable1[k])
            if nk > minMatch:
                (chr, start) = k.split("~")
                end = int(start) + hitTable1_lens.get(k, 0)
                name= '_'.join([chr,start])
                row = (chr, start, "%d" % end, name, "%d" % nk)
                f.write("\t".join(row))
                f.write("\n")
    with open(outPaf, "w") as f:
        f.writelines(
        line for i, line in enumerate(open(inPaf)) if not filterMe.get(i, None)
    )


if __name__ == "__main__":
    VERS = 0.01
    parser = argparse.ArgumentParser()
    a = parser.add_argument
    a("--inpaf", default=None)
    a("--outbed", default=None)
    a("--outpaf", default=None)
    a("--minmatch", default=1, type=int)
    a('--version', action='version', version='%(prog)s 0.1')
    args = parser.parse_args()
    pafDeDupe(args.inpaf, args.outbed, args.outpaf, args.minmatch)