Compute effective genome size for genome.

def effective_genome_size(fasta, read_length, nb_cores, tmpdir="/tmp"):
    # type: (str, int, int, str) -> None
    """Compute effective genome size for genome."""

    idx = Fasta(fasta)

    genome_length = sum([len(c) for c in idx])

    logging.info("Temporary directory: " + tmpdir)
    logging.info("File analyzed: " + fasta)
    logging.info("Genome length: " + str(genome_length))
    print("File analyzed: ", fasta)
    print("Genome length: ", genome_length)

    chromosomes = ", ".join([c.name for c in idx])

    if "_" in chromosomes:
        print("Warning. The following chromosomes are part of your genome:\n",
              chromosomes.replace(">", "") + "\n",
              file=sys.stderr)
        print(
            "You probably want to remove all chromosomes in your fasta containing '_' for the effective genome size computation to be accurate.",
            file=sys.stderr)

    # if tmpdir is None:
    #     try:
    #         tmpdir = os.environ['TMPDIR']
    #     except KeyError:
    #         tmpdir = '/tmp'
    output_file = os.path.join(tmpdir, '{1}.jf'.format(read_length,
                                                       basename(fasta)))
    atexit.register(
        lambda: call("rm {output_file}".format(output_file=output_file), shell=True))

    call(
        "jellyfish count -t {nb_cores} -m {read_length} -s {genome_length} -L 1 -U 1 --out-counter-len 1 --counter-len 1 {fasta} -o {output_file}".format(
            **vars()),
        shell=True)

    stats = check_output("jellyfish stats {output_file}".format(
        output_file=output_file),
                         shell=True)

    unique_kmers = int(stats.split()[1])

    effective_genome_size = unique_kmers / genome_length

    logging.info("Number unique {read_length}-mers: ".format(
        read_length=read_length) + str(unique_kmers))
    logging.info("Effective genome size: " + str(effective_genome_size))
    print("Number unique {read_length}-mers: ".format(read_length=read_length),
          unique_kmers)
    print("Effective genome size: ", effective_genome_size)
    assert effective_genome_size < 1, "Something wrong happened, effective genome size over 1!"