#!/usr/bin/python3

"""
Complement the regions of a bed file. Requires a file that maps source names
to sizes. This should be in the simple LEN file format (each line contains
a source name followed by a size, separated by whitespace).

usage: %prog bed_file chrom_length_file
"""

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


def read_len(f):
    """Read a 'LEN' file and return a mapping from chromosome to length"""
    mapping = {}
    for line in f:
        fields = line.split()
        mapping[fields[0]] = int(fields[1])
    return mapping


options, args = doc_optparse.parse(__doc__)
try:
    in_fname, len_fname = args
except Exception:
    doc_optparse.exit()

bitsets = binned_bitsets_from_file(open(in_fname))

lens = read_len(open(len_fname))

for chrom in lens:
    if chrom in bitsets:
        bits = bitsets[chrom]
        bits.invert()
        len = lens[chrom]
        end = 0
        while True:
            start = bits.next_set(end)
            if start == bits.size:
                break
            end = bits.next_clear(start)
            if end > len:
                end = len
            print("%s\t%d\t%d" % (chrom, start, end))
            if end == len:
                break
    else:
        print("%s\t%d\t%d" % (chrom, 0, lens[chrom]))