#!/usr/bin/env python



"""

Reads a MAF file. Produces a MAF file containing

the reverse complement for each block in the source file.



usage: %prog input_maf_file output_maf_file

"""

#Dan Blankenberg

from galaxy import eggs

import pkg_resources; pkg_resources.require( "bx-python" )

import bx.align.maf

from galaxy.tools.util import maf_utilities

import sys



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



def __main__():

    #Parse Command Line

    input_file = sys.argv.pop( 1 )

    output_file = sys.argv.pop( 1 )

    species = maf_utilities.parse_species_option( sys.argv.pop( 1 ) )

    

    try:

        maf_writer = bx.align.maf.Writer( open( output_file, 'w' ) )

    except:

        print sys.stderr, "Unable to open output file"

        sys.exit()

    try:

        count = 0

        for count, maf in enumerate( bx.align.maf.Reader( open( input_file ) ) ):

            maf = maf.reverse_complement()

            if species:

                maf = maf.limit_to_species( species )

            maf_writer.write( maf )

    except:

        print >>sys.stderr, "Your MAF file appears to be malformed."

        sys.exit()

    print "%i regions were reverse complemented." % count

    maf_writer.close()



if __name__ == "__main__": __main__()