#!/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1733805827733/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python

"""
'Tile' the blocks of a maf file over each of a set of intervals. The
highest scoring block that covers any part of a region will be used, and
pieces not covered by any block filled with "-" or optionally "*". The list
of species to tile is specified by `tree` (either a tree or just a comma
separated list). The `seq_db` is a lookup table mapping chromosome names
to nib file for filling in the reference species. Maf files must be indexed.

NOTE: See maf_tile_2.py for a more sophisticated version of this program, I
      think this one will be eliminated in the future.

usage: %prog tree maf_files...
    -m, --missingData: Inserts wildcards for missing block rows instead of '-'
"""

import sys

import bx.align as align
import bx.align.maf
import bx.seq.nib
from bx.cookbook import doc_optparse

tree_tx = str.maketrans("(),", "   ")


def main():
    options, args = doc_optparse.parse(__doc__)
    try:
        sources = args[0].translate(tree_tx).split()
        seq_db = load_seq_db(args[1])
        index = bx.align.maf.MultiIndexed(args[2:])

        out = bx.align.maf.Writer(sys.stdout)
        missing_data = bool(options.missingData)
    except Exception:
        doc_optparse.exception()

    for line in sys.stdin:
        ref_src, start, end = line.split()[0:3]
        do_interval(sources, index, out, ref_src, int(start), int(end), seq_db, missing_data)

    out.close()


def load_seq_db(fname):
    db = {}
    for line in open(fname):
        fields = line.split(",")
        src = fields[1] + "." + fields[2]
        seq = fields[4]
        db[src] = seq.strip()
    return db


def do_interval(sources, index, out, ref_src, start, end, seq_db, missing_data):
    assert sources[0].split(".")[0] == ref_src.split(".")[0], "{} != {}".format(
        sources[0].split(".")[0], ref_src.split(".")[0]
    )

    base_len = end - start

    blocks = index.get(ref_src, start, end)
    # From low to high score
    blocks.sort(key=lambda _: _.score)

    mask = [-1] * base_len

    ref_src_size = None
    for i, block in enumerate(blocks):
        ref = block.get_component_by_src_start(ref_src)
        ref_src_size = ref.src_size
        assert ref.strand == "+"
        slice_start = max(start, ref.start)
        slice_end = min(end, ref.end)
        for j in range(slice_start, slice_end):
            mask[j - start] = i

    tiled = []
    for i in range(len(sources)):
        tiled.append([])

    for ss, ee, index in intervals_from_mask(mask):
        if index < 0:
            tiled[0].append(bx.seq.nib.NibFile(open(seq_db[ref_src])).get(start + ss, ee - ss))
            for row in tiled[1:]:
                if missing_data:
                    row.append("*" * (ee - ss))
                else:
                    row.append("-" * (ee - ss))
        else:
            slice_start = start + ss
            slice_end = start + ee
            block = blocks[index]
            ref = block.get_component_by_src_start(ref_src)
            sliced = block.slice_by_component(ref, slice_start, slice_end)
            sliced = sliced.limit_to_species(sources)
            sliced.remove_all_gap_columns()
            for i, src in enumerate(sources):
                comp = sliced.get_component_by_src_start(src)
                if comp:
                    tiled[i].append(comp.text)
                else:
                    if missing_data:
                        tiled[i].append("*" * sliced.text_size)
                    else:
                        tiled[i].append("-" * sliced.text_size)

    a = align.Alignment()
    for i, name in enumerate(sources):
        text = "".join(tiled[i])
        size = len(text) - text.count("-")
        if i == 0:
            if ref_src_size is None:
                ref_src_size = bx.seq.nib.NibFile(open(seq_db[ref_src])).length
            c = align.Component(ref_src, start, end - start, "+", ref_src_size, text)
        else:
            c = align.Component(name + ".fake", 0, size, "?", size, text)
        a.add_component(c)

    out.write(a)


def intervals_from_mask(mask):
    start = 0
    last = mask[0]
    for i in range(1, len(mask)):
        if mask[i] != last:
            yield start, i, last
            start = i
            last = mask[i]
    yield start, len(mask), last


main()
