def METHOD_NAME(input_file, output, settings):
    sorted_scores, accum_hits, accum_decoys = _accum_decoys(input_file, settings)
    fdr_array = compute_fdr(sorted_scores, accum_hits, accum_decoys, settings)
    index = 0
    for line in __read_lines(input_file):
        if not line or line.startswith('#'):
            continue
        entry = Entry(line, settings, index)
        this_fdr = fdr_array[entry.score]
        new_line = "%s%s%f" % (line, settings["separator"], this_fdr)
        print >> output, new_line
        index += 1