def cscore(args):
    """
    %prog cscore blastfile > cscoreOut

    See supplementary info for sea anemone genome paper, C-score formula:

        cscore(A,B) = score(A,B) /
             max(best score for A, best score for B)

    A C-score of one is the same as reciprocal best hit (RBH).

    Output file will be 3-column (query, subject, cscore). Use --cutoff to
    select a different cutoff.
    """
    from jcvi.utils.cbook import gene_name

    p = OptionParser(cscore.__doc__)
    p.add_option("--cutoff", default=.9999, type="float",
            help="Minimum C-score to report [default: %default]")
    p.add_option("--pct", default=False, action="store_true",
            help="Also include pct as last column [default: %default]")
    p.add_option("--writeblast", default=False, action="store_true",
            help="Also write filtered blast file [default: %default]")
    p.set_stripnames()
    p.set_outfile()

    opts, args = p.parse_args(args)
    ostrip = opts.strip_names
    writeblast = opts.writeblast
    outfile = opts.outfile

    if len(args) != 1:
        sys.exit(not p.print_help())

    blastfile, = args

    blast = Blast(blastfile)
    logging.debug("Register best scores ..")
    best_score = defaultdict(float)
    for b in blast:
        query, subject = b.query, b.subject
        if ostrip:
            query, subject = gene_name(query), gene_name(subject)

        score = b.score
        if score > best_score[query]:
            best_score[query] = score
        if score > best_score[subject]:
            best_score[subject] = score

    blast = Blast(blastfile)
    pairs = {}
    cutoff = opts.cutoff
    for b in blast:
        query, subject = b.query, b.subject
        if ostrip:
            query, subject = gene_name(query), gene_name(subject)

        score = b.score
        pctid = b.pctid
        s = score / max(best_score[query], best_score[subject])
        if s > cutoff:
            pair = (query, subject)
            if pair not in pairs or s > pairs[pair][0]:
                pairs[pair] = (s, pctid, b)

    fw = must_open(outfile, "w")
    if writeblast:
        fwb = must_open(outfile + ".filtered.blast", "w")
    pct = opts.pct
    for (query, subject), (s, pctid, b) in sorted(pairs.items()):
        args = [query, subject, "{0:.2f}".format(s)]
        if pct:
            args.append("{0:.1f}".format(pctid))
        print("\t".join(args), file=fw)
        if writeblast:
            print(b, file=fwb)
    fw.close()
    if writeblast:
        fwb.close()
%prog cscore blastfile > cscoreOut

    See supplementary info for sea anemone genome paper, C-score formula:

        cscore(A,B) = score(A,B) /
             max(best score for A, best score for B)

    A C-score of one is the same as reciprocal best hit (RBH).

    Output file will be 3-column (query, subject, cscore). Use --cutoff to
    select a different cutoff.