root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/EGG-INFO/scripts/maf_div_sites.py @ 3

#!/usr/bin/python2.6
"""
Create a bed file listing all the divergent sites between two specific species 
in a maf.

usage: %prog maf_file reference_species_name other_species_name
"""

import sys
import bx.align.maf
import bx.bitset
from bx.bitset_builders import *
from itertools import *

def main():
        bitsets = {}
        maf = sys.argv[1]
        reference_sp, other_sp = sys.argv[2], sys.argv[3]

        for block in bx.align.maf.Reader( open(maf) ):
                ref = block.get_component_by_src_start( reference_sp )
                other = block.get_component_by_src_start( other_sp )

                if not ref or not other: continue
                ref_chrom = ref.src.split( '.' )[1]
                ref_start = ref.start
                ref_end = ref.end
                chrom_size = ref.get_src_size()

                if ref_chrom not in bitsets: bitsets[ ref_chrom ] = bx.bitset.BinnedBitSet( chrom_size )

                pos = ref_start
                for i,j in izip( ref.text.upper(), other.text.upper() ):
                        if i != '-':
                                if i != j: # mismatch
                                        if i != 'N' and j != 'N' and j != '-': 
                                                # set if all valid chars
                                                bitsets[ ref_chrom ].set( pos )
                                pos += 1

        
        # bits --> bed file
        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 )


main()