genomes.py 文件源码

def get_effective_genome_length(genome, read_length):
    # type: (str, int) -> float

    genome_names = pkg_resources.resource_listdir("epic",
                                                  "scripts/effective_sizes")
    name_dict = {n.split("_")[0]: "".join(n.split("_")[:-1])
                 for n in genome_names}

    try:
        genome_exact = name_dict[genome.lower()]
        egf = pkg_resources.resource_string( # type: ignore
            "epic", "scripts/effective_sizes/{}_{}.txt".format(
                genome_exact, read_length)).split()[-1].decode()
    except KeyError:
        genome_list = "\n".join(list(name_dict.keys()))
        logging.error(
            "Genome " + genome +
            " not found.\n These are the available genomes: " + genome_list +
            "\nIf yours is not there, please request it at github.com/endrebak/epic .")

    genome_length = sum(create_genome_size_dict(genome).values())

    logging.info("Using an effective genome fraction of {}.".format(egf))

    assert float(
        egf) < 1, "Something wrong happened, effective genome fraction over 1!"

    egs = float(egf) * genome_length

    return egs