code: def paste(args):
      
      from jcvi.formats.bed import uniq
  
      p = OptionParser(paste.__doc__)
      p.add_option("--maxsize", default=300000, type="int",
              help="Maximum size of patchers to be replaced [default: %default]")
      p.add_option("--prefix", help="Prefix of the new object [default: %default]")
      p.set_rclip(rclip=1)
      opts, args = p.parse_args(args)
  
      if len(args) != 3:
          sys.exit(not p.print_help())
  
      pbed, blastfile, bbfasta = args
      maxsize = opts.maxsize  # Max DNA size to replace gap
      order = Bed(pbed).order
  
      beforebed, afterbed = blast_to_twobeds(blastfile, order, log=True,
                                             rclip=opts.rclip, maxsize=maxsize,
                                             flipbeds=True)
      beforebed = uniq([beforebed])
  
      afbed = Bed(beforebed)
      bfbed = Bed(afterbed)
  
      shuffle_twobeds(afbed, bfbed, bbfasta, prefix=opts.prefix)
docs: %prog paste flanks.bed flanks_vs_assembly.blast backbone.fasta
  
      Paste in good sequences in the final assembly.