only estimate expression the Stringtie, do not assemble new transcripts

def _stringtie_expression(bam, data, out_dir="."):
    """
    only estimate expression the Stringtie, do not assemble new transcripts
    """
    gtf_file = dd.get_gtf_file(data)
    num_cores = dd.get_num_cores(data)
    error_message = "The %s file for %s is missing. StringTie has an error."
    stringtie = config_utils.get_program("stringtie", data, default="stringtie")
    # don't assemble transcripts unless asked
    exp_flag = ("-e" if "stringtie" not in dd.get_transcript_assembler(data)
                else "")
    base_cmd = ("{stringtie} {exp_flag} -b {out_dir} -p {num_cores} -G {gtf_file} "
                "-o {out_gtf} {bam}")
    transcript_file = os.path.join(out_dir, "t_data.ctab")
    exon_file = os.path.join(out_dir, "e_data.ctab")
    out_gtf = os.path.join(out_dir, "stringtie-assembly.gtf")
    if file_exists(transcript_file):
        return exon_file, transcript_file, out_gtf
    cmd = base_cmd.format(**locals())
    do.run(cmd, "Running Stringtie on %s." % bam)
    assert file_exists(exon_file), error_message % ("exon", exon_file)
    assert file_exists(transcript_file), error_message % ("transcript", transcript_file)
    return transcript_file