bx-python / scripts /

#!/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

import psyco_full

import string
import sys

import bx.intervals.intersection

def main():

    intersecters = {}

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

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

if __name__ == "__main__":