code: def computeFrequencyOfSignificantSNPs(options):
      
      # The plink command
      plinkCommand = ["plink", "--noweb", "--bfile", options.bfile, "--extract",
                      options.out + ".significant_SNPs.txt", "--freq", "--out",
                      options.out + ".significant_SNPs"]
      runCommand(plinkCommand)
  
      # Reading the frequency file
      maf = {}
      with open(options.out + ".significant_SNPs.frq", "r") as i_file:
          header = {
              name: i for i, name in
              enumerate(createRowFromPlinkSpacedOutput(i_file.readline()))
          }
          for required_col in ("SNP", "MAF"):
              if required_col not in header:
                  msg = "{}: missing column {}".format(
                      script_prefix + ".significant_SNPs.frq",
                      required_col,
                  )
                  raise ProgramError(msg)
  
          for line in i_file:
              row = createRowFromPlinkSpacedOutput(line)
              maf[row[header["SNP"]]] = row[header["MAF"]]
  
      return maf
docs: Computes the frequency of the significant markers.
  
      :param options: the options.
  
      :type options: argparse.Namespace
  
      Extract a list of markers (significant after plate bias analysis) and
      computes their frequencies.