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#!/usr/bin/env python

Find regions of first bed file that overlap regions in a second bed file. The
output preserves all fields from the input. 

NOTE: -u and -d options are currently not functional!

usage: %prog bed_file_1 bed_file_2
    -m, --mincols=N: Require this much overlap (default 1bp)
    -u, --upstream_pad=N: upstream interval padding (default 0bp)
    -d, --downstream_pad=N: downstream interval padding (default 0bp)
    -v, --reverse: Print regions that DO NOT overlap
    -b, --booleans: Just print '1' if interval overlaps or '0' otherwise

import sys
from warnings import warn

from bx.bitset import *
from bx.bitset_builders import *

from bx.cookbook import doc_optparse

mincols = 1
upstream_pad = 0
downstream_pad = 0

options, args = doc_optparse.parse( __doc__ )
    if options.mincols: mincols = int( options.mincols )
    if options.upstream_pad: upstream_pad = int( options.upstream_pad )
    if options.downstream_pad: downstream_pad = int( options.downstream_pad )
    reverse = bool( options.reverse )
    booleans = bool( options.booleans )
    in_fname, in2_fname = args

# Read first bed into some bitsets

bitsets = binned_bitsets_from_file( open( in2_fname ) )

# Read second BED and intersect

for line in open( in_fname ):
    if line.startswith("#") or line.isspace(): 
    fields = line.split()
    start, end = int( fields[1] ), int( fields[2] )
    if start > end: 
        warn( "Bed interval start after end!" )
    if fields[0] in bitsets and bitsets[fields[0]].count_range( start, end-start ) >= mincols:
        if booleans:
            if reverse: 
                print 0
                print 1
        elif not reverse:
            print line,
        if booleans:
            if reverse:
                print 1
                print 0
        elif reverse:
            print line,