Convert to GFF3 standard format

def _mirtop(input_fn, sps, db, out_dir, config):
    """
    Convert to GFF3 standard format
    """
    hairpin = os.path.join(db, "hairpin.fa")
    gtf = os.path.join(db, "mirbase.gff3")
    if not file_exists(hairpin) or not file_exists(gtf):
        logger.warning("%s or %s are not installed. Skipping." % (hairpin, gtf))
        return None
    out_gtf_fn = "%s.gtf" % utils.splitext_plus(os.path.basename(input_fn))[0]
    out_gff_fn = "%s.gff" % utils.splitext_plus(os.path.basename(input_fn))[0]
    export = _get_env()
    cmd = ("{export} mirtop gff  --sps {sps} --hairpin {hairpin} "
           "--gtf {gtf} --format seqbuster -o {out_tx} {input_fn}")
    if not file_exists(os.path.join(out_dir, out_gtf_fn)) and \
       not file_exists(os.path.join(out_dir, out_gff_fn)):
        with tx_tmpdir() as out_tx:
            do.run(cmd.format(**locals()), "Do miRNA annotation for %s" % input_fn)
            with utils.chdir(out_tx):
                out_fn = out_gtf_fn if utils.file_exists(out_gtf_fn) \
                                    else out_gff_fn
                if utils.file_exists(out_fn):
                    shutil.move(os.path.join(out_tx, out_fn),
                                os.path.join(out_dir, out_fn))
    out_fn = out_gtf_fn if utils.file_exists(os.path.join(out_dir, out_gtf_fn)) \
                        else os.path.join(out_dir, out_gff_fn)
    if utils.file_exists(os.path.join(out_dir, out_fn)):
        return os.path.join(out_dir, out_fn)