text: #!/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__()
  