def count(args):
    """
    %prog count fastafile jf.db

    Run dump - jellyfish - bin - bincount in serial.
    """
    from bitarray import bitarray

    p = OptionParser(count.__doc__)
    opts, args = p.parse_args(args)

    if len(args) != 2:
        sys.exit(not p.print_help())

    fastafile, jfdb = args
    K = get_K(jfdb)
    cmd = "jellyfish query {0} -C | cut -d' ' -f 2".format(jfdb)
    t = must_open("tmp", "w")
    proc = Popen(cmd, stdin=PIPE, stdout=t)
    t.flush()

    f = Fasta(fastafile, lazy=True)
    for name, rec in f.iteritems_ordered():
        kmers = list(make_kmers(rec.seq, K))
        print("\n".join(kmers), file=proc.stdin)
    proc.stdin.close()
    logging.debug(cmd)
    proc.wait()

    a = bitarray()
    binfile = ".".join((fastafile, jfdb, "bin"))
    fw = open(binfile, "w")
    t.seek(0)
    for row in t:
        c = row.strip()
        a.append(int(c))
    a.tofile(fw)
    logging.debug("Serialize {0} bits to `{1}`.".format(len(a), binfile))
    fw.close()
    sh("rm {0}".format(t.name))

    logging.debug("Shared K-mers (K={0}) between `{1}` and `{2}` written to `{3}`.".\
                    format(K, fastafile, jfdb, binfile))
    cntfile = ".".join((fastafile, jfdb, "cnt"))
    bincount([fastafile, binfile, "-o", cntfile, "-K {0}".format(K)])
    logging.debug("Shared K-mer counts written to `{0}`.".format(cntfile))
%prog count fastafile jf.db

    Run dump - jellyfish - bin - bincount in serial.