code: def sort(args):
      
      p = OptionParser(sort.__doc__)
      p.add_option("-i", "--inplace", dest="inplace",
              default=False, action="store_true",
              help="Sort bed file in place [default: %default]")
      p.add_option("-u", dest="unique",
              default=False, action="store_true",
              help="Uniqify the bed file")
      p.add_option("--accn", default=False, action="store_true",
              help="Sort based on the accessions [default: %default]")
      p.set_outfile(outfile=None)
      p.set_tmpdir()
      opts, args = p.parse_args(args)
  
      if len(args) != 1:
          sys.exit(not p.print_help())
  
      bedfile, = args
      inplace = opts.inplace
  
      if not inplace and ".sorted." in bedfile:
          return bedfile
  
      sortedbed = opts.outfile
      if inplace:
          sortedbed = bedfile
      elif opts.outfile is None:
          pf, sf = op.basename(bedfile).rsplit(".", 1)
          sortedbed = pf + ".sorted." + sf
  
      sortopt = "-k1,1 -k2,2n -k3,3n -k4,4" if not opts.accn else \
                "-k4,4 -k1,1 -k2,2n -k3,3n"
      cmd = "sort"
      if opts.tmpdir:
          cmd += " -T {0}".format(opts.tmpdir)
      if opts.unique:
          cmd += " -u"
      cmd += " {0} {1} -o {2}".format(sortopt, bedfile, sortedbed)
  
      if inplace or need_update(bedfile, sortedbed):
          sh(cmd)
  
      return sortedbed
docs: %prog sort bedfile
  
      Sort bed file to have ascending order of seqid, then start. It uses the
      `sort` command.