#!/opt/conda/conda-bld/bx-python_1720643340496/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/python

"""
FIXME!

usage: %prog feature.bed ar.bed snp.bed div_directory [options]
    -m, --mask=M: Mask AR and features with this file
    -s, --suffix=S: append suffix to chromosomes to get filenames from div_directory
    -l, --lens=l: Set chromosome ends using LEN file
"""

import sys

from bx.bitset import BinnedBitSet
from bx.bitset_builders import binned_bitsets_from_file
from bx.cookbook import doc_optparse


def main():
    options, args = doc_optparse.parse(__doc__)
    try:
        lens = {}
        if options.lens:
            for line in open(options.lens):
                chrom, length = line.split()
                lens[chrom] = int(length)

        if options.suffix:
            suffix = options.suffix
        else:
            suffix = ""

        print("\nReading feature", end=" ", file=sys.stderr)
        interval_file = open(args[0])
        feature = binned_bitsets_from_file(interval_file, lens=lens)
        interval_file.close()
        # reuse interval file
        intervals = {}
        interval_file = open(args[0])
        for line in interval_file:
            fields = line.split()
            chrom, start, end = fields[0], int(fields[1]), int(fields[2])
            if chrom not in intervals:
                intervals[chrom] = []
            intervals[chrom].append([start, end])
        interval_file.close()

        print("\nReading ar", end=" ", file=sys.stderr)
        ar = binned_bitsets_from_file(open(args[1]), lens=lens)

        print("\nReading snps", end=" ", file=sys.stderr)
        snp = binned_bitsets_from_file(open(args[2]), lens=lens)
        snp_mask = clone_inverted(snp)
        snp_copy = clone(snp)

        print("\nMasking AR", end=" ", file=sys.stderr)
        ar_mask = clone_inverted(ar)
        print(file=sys.stderr)

        dirname = args[3]

        if options.mask:
            mask = binned_bitsets_from_file(open(options.mask), lens=lens)
        else:
            mask = None
    except Exception:
        doc_optparse.exit()

    if mask:
        for chrom in mask.keys():
            if chrom in feature:
                feature[chrom].iand(mask[chrom])
            if chrom in ar:
                ar[chrom].iand(mask[chrom])

    # divergence and snp counts for all features
    feature_div_count = 0
    feature_snp_count = 0
    ar_div_count = 0
    ar_snp_count = 0

    # collect snp and div
    for chr in feature.keys():
        if chr not in snp:
            continue
        if chr not in ar:
            continue

        print("reading %s ..." % chr, end=" ", file=sys.stderr)
        try:
            div = binned_bitsets_from_file(open(dirname + "/%s.bed" % (chr + suffix)), lens=lens)
        except Exception:
            print("%s.bed not found" % chr, file=sys.stderr)
            continue

        div[chr].iand(snp_mask[chr])  # div/snp sites count snp-only
        div_copy = clone(div)

        print("AR:", chr, end=" ", file=sys.stderr)
        snp[chr].iand(ar[chr])
        div[chr].iand(ar[chr])
        snp_count = snp[chr].count_range(0, snp[chr].size)
        ar_snp_count += snp_count
        print(snp_count, end=" ", file=sys.stderr)
        try:
            div_count = div[chr].count_range(0, div[chr].size)
            ar_div_count += div_count
            print(div_count, file=sys.stderr)
        except Exception:
            print(chr, "failed", file=sys.stderr)

        div = div_copy
        snp[chr] = snp_copy[chr]
        print("feature:", chr, end=" ", file=sys.stderr)
        feature[chr].iand(ar_mask[chr])  # clip to non-AR only
        snp[chr].iand(feature[chr])
        div[chr].iand(feature[chr])
        feature_snp_count += snp[chr].count_range(0, snp[chr].size)
        print(snp[chr].count_range(0, snp[chr].size), div[chr].count_range(0, div[chr].size), file=sys.stderr)
        feature_div_count += div[chr].count_range(0, div[chr].size)
        print(snp[chr].count_range(0, snp[chr].size), div[chr].count_range(0, div[chr].size), file=sys.stderr)

        # Note: can loop over feature intervals here for individual counts
        if chr in intervals:
            for start, end in intervals[chr]:
                ind_div_count = div[chr].count_range(start, end - start)
                ind_snp_count = snp[chr].count_range(start, end - start)
                print(chr, start, end, ind_div_count, ind_snp_count)

    print("feature snp\t%d" % feature_snp_count)
    print("feature div\t%d" % feature_div_count)
    print("ar snp\t%d" % ar_snp_count)
    print("ar div\t%d" % ar_div_count)


# copies a dictionary of bitsets
def copybits(binnedbits):
    bitset = BinnedBitSet(binnedbits.size)
    bitset.ior(binnedbits)
    return bitset


def clone(bitsets):
    r = {}
    for k, b in bitsets.items():
        r[k] = copybits(b)
    return r


def clone_inverted(bitsets):
    r = {}
    for k, b in bitsets.items():
        r[k] = copybits(b)
        r[k].invert()
    return r


main()
