bx-python / scripts /

#!/usr/bin/env python

Find regions of first bed file that overlap regions in a second bed file. This
program performs a base-by-base intersection, so only runs of bases that are
covered in both of the inputs will be output.

usage: %prog bed_file_1 bed_file_2

import sys
from warnings import warn
from bx.bitset import *
from bx.bitset_builders import *
from bx.cookbook import doc_optparse

options, args = doc_optparse.parse( __doc__ )
    in_fname, in2_fname = args

bits1 = binned_bitsets_from_file( open( in_fname ) )
bits2 = binned_bitsets_from_file( open( in2_fname ) )

bitsets = dict()

for key in bits1:
    if key in bits2:
        bits1[key].iand( bits2[key] )
        bitsets[key] = bits1[key]

for chrom in bitsets:
    bits = bitsets[chrom]
    end = 0
    while 1:
        start = bits.next_set( end )
        if start == bits.size: break
        end = bits.next_clear( start )
        print "%s\t%d\t%d" % ( chrom, start, end )
Tip: Filter by directory path e.g. /media app.js to search for public/media/app.js.
Tip: Use camelCasing e.g. ProjME to search for
Tip: Filter by extension type e.g. /repo .js to search for all .js files in the /repo directory.
Tip: Separate your search with spaces e.g. /ssh pom.xml to search for src/ssh/pom.xml.
Tip: Use ↑ and ↓ arrow keys to navigate and return to view the file.
Tip: You can also navigate files with Ctrl+j (next) and Ctrl+k (previous) and view the file with Ctrl+o.
Tip: You can also navigate files with Alt+j (next) and Alt+k (previous) and view the file with Alt+o.