#!/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1753187629420/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python

from optparse import OptionParser

from rpy import r

import bx.align.maf
import bx.bitset
from bx.bitset_builders import binned_bitsets_from_file


def main():
    parser = OptionParser(usage="usage: %prog [options] maf_file snp_file neutral_file window_size step_size")
    parser.add_option("-o", "--outfile", help="Specify file for output")
    parser.add_option("-s", "--species", type="string", default="panTro2")
    parser.add_option("-b", "--build", type="string", default="hg18")
    (options, args) = parser.parse_args()

    if len(args) != 5:
        parser.error("Incorrect number of arguments")
    else:
        maf_filename = args[0]
        snp_filename = args[1]
        neutral_filename = args[2]
        window_size = int(args[3])
        step_size = int(args[4])

    if options.outfile is not None:
        out_file = open(options.outfile, "w")

    # Generate snp and neutral bitsets
    AR_snp_bitsets = binned_bitsets_from_file(open(snp_filename))
    neutral_bitsets = binned_bitsets_from_file(open(neutral_filename))

    # Generate divergence bitset from maf file
    AR_div_bitsets = {}
    chr_lens = {}
    reader = bx.align.maf.Reader(open(maf_filename))

    for block in reader:
        comp1 = block.get_component_by_src_start(options.build)
        comp2 = block.get_component_by_src_start(options.species)

        if comp1 is None or comp2 is None:
            continue

        # Chromosome, start, and stop of reference species alignment
        chr = comp1.src.split(".")[1]
        start = comp1.start

        # Get or create bitset for this chromosome
        if chr in AR_div_bitsets:
            bitset = AR_div_bitsets[chr]
        else:
            bitset = AR_div_bitsets[chr] = bx.bitset.BinnedBitSet()
            chr_lens[chr] = comp1.get_src_size()

        # Iterate over text and set diverged bit
        pos = start
        for ch1, ch2 in zip(comp1.text.upper(), comp2.text.upper()):
            if ch1 == "-":
                continue
            if ch2 == "-":
                pos += 1
                continue

            if ch1 != ch2 and not AR_snp_bitsets[chr][pos]:
                bitset.set(pos)
            pos += 1

    # Copy div and snp bitsets
    nonAR_snp_bitsets = {}
    for chr in AR_snp_bitsets:
        nonAR_snp_bitsets[chr] = bx.bitset.BinnedBitSet()
        nonAR_snp_bitsets[chr].ior(AR_snp_bitsets[chr])

    nonAR_div_bitsets = {}
    for chr in AR_div_bitsets:
        nonAR_div_bitsets[chr] = bx.bitset.BinnedBitSet()
        nonAR_div_bitsets[chr].ior(AR_div_bitsets[chr])

    # Generates AR snps by intersecting with neutral intervals
    for chr in AR_snp_bitsets:
        AR_snp_bitsets[chr].iand(neutral_bitsets[chr])

    # Generates AR divs by intersecting with neutral intervals
    for chr in AR_div_bitsets:
        AR_div_bitsets[chr].iand(neutral_bitsets[chr])

    # Inverts the neutral intervals so now represents nonAR
    for chr in neutral_bitsets:
        neutral_bitsets[chr].invert()

    # Generates nonAR snps by intersecting with masked neutral intervals
    for chr in nonAR_snp_bitsets:
        nonAR_snp_bitsets[chr].iand(neutral_bitsets[chr])
    # Generates nonAR divs by intersecting with masked neutral intervals
    for chr in nonAR_div_bitsets:
        nonAR_div_bitsets[chr].iand(neutral_bitsets[chr])

    for chr in AR_div_bitsets:
        for window in range(0, chr_lens[chr] - window_size, step_size):
            # neutral_size = neutral_bitsets[chr].count_range(window, window_size)
            # if neutral_size < 9200: continue
            AR_snp = AR_snp_bitsets[chr].count_range(window, window_size)
            AR_div = AR_div_bitsets[chr].count_range(window, window_size)
            nonAR_snp = nonAR_snp_bitsets[chr].count_range(window, window_size)
            nonAR_div = nonAR_div_bitsets[chr].count_range(window, window_size)

            if nonAR_snp >= 6 and nonAR_div >= 6 and AR_snp >= 6 and AR_div >= 6:
                MK_pval = MK_chi_pvalue(nonAR_snp, nonAR_div, AR_snp, AR_div)
            else:
                MK_pval = MK_fisher_pvalue(nonAR_snp, nonAR_div, AR_snp, AR_div)

            if options.outfile is not None:
                out_file.write(
                    "%s\t%d\t%d\t%d\t%d\t%d\t%d\t%1.15f\n"
                    % (chr, window, window + window_size, nonAR_snp, nonAR_div, AR_snp, AR_div, MK_pval)
                )
            else:
                print(
                    "%s\t%d\t%d\t%d\t%d\t%d\t%d\t%1.15f"
                    % (chr, window, window + window_size, nonAR_snp, nonAR_div, AR_snp, AR_div, MK_pval)
                )

    if options.outfile is not None:
        out_file.close()


def MK_fisher_pvalue(win_snp, win_div, AR_snp, AR_div):
    if win_snp == 0 and win_div == 0 and AR_snp == 0 and AR_div == 0:
        return 1.0

    fisher_result = r.fisher_test(r.matrix(r.c([win_snp, win_div, AR_snp, AR_div]), nr=2))

    return fisher_result["p.value"]


def MK_chi_pvalue(win_snp, win_div, AR_snp, AR_div):
    chi_result = r.chisq_test(r.matrix(r.c([win_snp, win_div, AR_snp, AR_div]), nr=2))

    return chi_result["p.value"]


main()
