Annotate miRNAs using miRBase database with seqbuster tool

def sample_annotation(data):
    """
    Annotate miRNAs using miRBase database with seqbuster tool
    """
    names = data["rgnames"]['sample']
    tools = dd.get_expression_caller(data)
    work_dir = os.path.join(dd.get_work_dir(data), "mirbase")
    out_dir = os.path.join(work_dir, names)
    utils.safe_makedir(out_dir)
    out_file = op.join(out_dir, names)
    if dd.get_mirbase_hairpin(data):
        mirbase = op.abspath(op.dirname(dd.get_mirbase_hairpin(data)))
        if utils.file_exists(data["collapse"]):
            data['transcriptome_bam'] = _align(data["collapse"],
                                               dd.get_mirbase_hairpin(data),
                                               out_file,
                                               data)
            data['seqbuster'] = _miraligner(data["collapse"], out_file,
                                            dd.get_species(data),
                                            mirbase,
                                            data['config'])
            data["mirtop"] = _mirtop(data['seqbuster'],
                                     dd.get_species(data),
                                     mirbase,
                                     out_dir,
                                     data['config'])
        else:
            logger.debug("Trimmed collapsed file is empty for %s." % names)
    else:
        logger.debug("No annotation file from miRBase.")

    sps = dd.get_species(data) if dd.get_species(data) else "None"
    logger.debug("Looking for mirdeep2 database for %s" % names)
    if file_exists(op.join(dd.get_work_dir(data), "mirdeep2", "novel", "hairpin.fa")):
        data['seqbuster_novel'] = _miraligner(data["collapse"], "%s_novel" % out_file, sps,
                                              op.join(dd.get_work_dir(data),
                                                      "mirdeep2", "novel"),
                                              data['config'])

    if "trna" in tools:
        data['trna'] = _mint_trna_annotation(data)

    data = spikein.counts_spikein(data)
    return [[data]]