#!/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1724774845760/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python

"""

Reads a maf file from stdin and applies the mapping file specified by
`mapping_file` to produce a sequence of integers. Then for each possible word
of length `motif_len` in this integer alphabet print the number of times
that word occurs in the block.

usage: %prog motif_len mapping_file < maf_file > counts
"""

import sys

from numpy import zeros

import bx.align.maf
from bx import seqmapping


def main():
    word_length = int(sys.argv[1])
    with open(sys.argv[2]) as f:
        align_count, alpha_map = seqmapping.alignment_mapping_from_file(f)

    for maf in bx.align.maf.Reader(sys.stdin):
        assert len(maf.components) == align_count
        # Translate alignment to ints
        ints = seqmapping.DNA.translate_list([c.text for c in maf.components])
        # Apply mapping
        ints = alpha_map.translate(ints)
        # Count words
        radix = alpha_map.get_out_size()
        counts = zeros(radix**word_length, int)
        total = 0
        for i in range(word_length, len(ints)):
            index = 0
            factor = 1
            skip = False
            for j in range(word_length):
                assert 0 < i - j < len(ints)
                letter = ints[i - j]
                if letter < 0:
                    skip = True
                    break
                index += letter * factor
                factor *= radix
            if skip:
                continue
            else:
                counts[index] += 1
                total += 1
        # Write ints separated by tabs
        print("\t".join([str(total)] + [str(_) for _ in counts]))


if __name__ == "__main__":
    main()
