code: def batchoverlap(args):
      
      p = OptionParser(batchoverlap.__doc__)
      p.set_cpus()
      opts, args = p.parse_args(args)
  
      if len(args) != 2:
          sys.exit(not p.print_help())
  
      pairsfile, outdir = args
      fp = open(pairsfile)
      cmds = []
      mkdir("overlaps")
      for row in fp:
          a, b = row.split()[:2]
          oa = op.join(outdir, a + ".fa")
          ob = op.join(outdir, b + ".fa")
          cmd = "python -m jcvi.assembly.goldenpath overlap {0} {1}".format(oa, ob)
          cmd += " -o overlaps/{0}_{1}.ov".format(a, b)
          cmds.append(cmd)
  
      print("\n".join(cmds))
docs: %prog batchoverlap pairs.txt outdir
  
      Check overlaps between pairs of sequences.