#!/usr/bin/env python
#Dan Blankenberg

import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.align.maf
from galaxy.tools.util import maf_utilities

assert sys.version_info[:2] >= ( 2, 4 )

def __main__():
    output_name = sys.argv.pop(1)
    input_name = sys.argv.pop(1)
    species = sys.argv.pop(1)
    out = open(output_name,'w')
    count = 0
    #write interval header line
    out.write( "#chrom\tstart\tend\tstrand\n" )
    try:
        for block in bx.align.maf.Reader( open( input_name, 'r' ) ):
            for c in maf_utilities.iter_components_by_src_start( block, species ):
                if c is not None:
                    out.write( "%s\t%i\t%i\t%s\n" %  ( maf_utilities.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) )
                    count += 1
    except Exception, e:
        print >> sys.stderr, "There was a problem processing your input: %s" % e
    out.close()
    print "%i MAF blocks converted to Genomic Intervals for species %s." % ( count, species )


if __name__ == "__main__": __main__()