#!/usr/bin/env python2.4

"""
Match up intersecting intervals from two files. This performs a "full join",
any pair of intervals with any basewise overlap will be printed side-by-side.

usage: %prog bed1 bed2
"""
from __future__ import division, print_function

import string
import sys

import bx.intervals.intersection
import bx.intervals.io
import psyco_full


def main():

    intersecters = {}

    # Read second set into intersecter
    for interval in bx.intervals.io.GenomicIntervalReader( open( sys.argv[2] ) ):
        if interval.chrom not in intersecters:
            intersecters[ interval.chrom ] = bx.intervals.Intersecter()
        intersecters[ interval.chrom ].add_interval( interval )

    # Join with first set
    for interval in bx.intervals.io.GenomicIntervalReader( open( sys.argv[1] ) ):
        if interval.chrom in intersecters:
            intersection = intersecters[ interval.chrom ].find( interval.start, interval.end )
            for interval2 in intersection:
                print("\t".join( [ str( interval ), str( interval2 ) ] ))


if __name__ == "__main__":
    main()