code: def agp(args):
      
      p = OptionParser(agp.__doc__)
      p.set_outfile()
      opts, args = p.parse_args(args)
  
      if len(args) != 2:
          sys.exit(not p.print_help())
  
      odir, contigsfasta = args
      fwagp = must_open(opts.outfile, 'w')
      orderingfiles = natsorted(iglob(odir, "*.ordering"))
      sizes = Sizes(contigsfasta).mapping
      contigs = set(sizes.keys())
      anchored = set()
  
      for ofile in orderingfiles:
          co = ContigOrdering(ofile)
          anchored |= set([x.contig_name for x in co])
          obj = op.basename(ofile).split('.')[0]
          co.write_agp(obj, sizes, fwagp)
  
      singletons = contigs - anchored
      logging.debug('Anchored: {}, Singletons: {}'.
                    format(len(anchored), len(singletons)))
  
      for s in natsorted(singletons):
          order_to_agp(s, [(s, "?")], sizes, fwagp)
docs: %prog agp main_results/ contigs.fasta
  
      Generate AGP file based on LACHESIS output.