#!/usr/bin/env python

#Reads a LAV file and writes two BED files.

import sys

from galaxy import eggs

import pkg_resources

pkg_resources.require( "bx-python" )

import bx.align.lav



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



def stop_err( msg ):

    sys.stderr.write( msg )

    sys.exit()



def main():

    try:

        lav_file = open(sys.argv[1],'r')

        bed_file1 = open(sys.argv[2],'w')

        bed_file2 = open(sys.argv[3],'w')

    except Exception, e:

        stop_err( str( e ) )

        

    lavsRead = 0

    bedsWritten = 0

    species = {}

    # TODO: this is really bad since everything is read into memory.  Can we eliminate this tool?

    for lavBlock in bx.align.lav.Reader( lav_file ):

        lavsRead += 1

        for c in lavBlock.components:

            spec, chrom = bx.align.lav.src_split( c.src )

            if bedsWritten < 1:

                if len( species )==0:

                    species[spec]=bed_file1

                elif len( species )==1:

                    species[spec]=bed_file2

                else:

                    continue #this is a pairwise alignment...

            if spec in species:

                species[spec].write( "%s\t%i\t%i\t%s_%s\t%i\t%s\n" % ( chrom, c.start, c.end, spec, str( bedsWritten ), 0, c.strand ) )

        bedsWritten += 1

        



    for spec,file in species.items():

        print "#FILE\t%s\t%s" % (file.name, spec)

    

    lav_file.close()

    bed_file1.close()

    bed_file2.close()

    

    print "%d lav blocks read, %d regions written\n" % (lavsRead,bedsWritten)







if __name__ == "__main__": main()