code: def fromovl(args):
      
      p = OptionParser(fromovl.__doc__)
      opts, args = p.parse_args(args)
  
      if len(args) != 2:
          sys.exit(not p.print_help())
  
      ovlfile, fastafile = args
      ovl = OVL(ovlfile)
      g = ovl.graph
  
      fw = open("contained.ids", "w")
      print("\n".join(sorted(ovl.contained)), file=fw)
  
      graph_to_agp(g, ovlfile, fastafile, exclude=ovl.contained, verbose=False)
docs: %prog graph nucmer2ovl.ovl fastafile
  
      Build overlap graph from ovl file which is converted using NUCMER2OVL.