if there are genomes to be disambiguated, create a FASTA file of
    all of the transcripts for all genomes

def create_combined_fasta(data):
    """
    if there are genomes to be disambiguated, create a FASTA file of
    all of the transcripts for all genomes
    """
    out_dir = os.path.join(dd.get_work_dir(data), "inputs", "transcriptome")
    items = disambiguate.split([data])
    fasta_files = []
    for i in items:
        odata = i[0]
        gtf_file = dd.get_gtf_file(odata)
        ref_file = dd.get_ref_file(odata)
        out_file = os.path.join(out_dir, dd.get_genome_build(odata) + ".fa")
        if file_exists(out_file):
            fasta_files.append(out_file)
        else:
            out_file = gtf.gtf_to_fasta(gtf_file, ref_file, out_file=out_file)
            fasta_files.append(out_file)
    out_stem = os.path.join(out_dir, dd.get_genome_build(data))
    if dd.get_disambiguate(data):
        out_stem = "-".join([out_stem] + (dd.get_disambiguate(data) or []))
    combined_file = out_stem + ".fa"
    if file_exists(combined_file):
        return combined_file

    fasta_file_string = " ".join(fasta_files)
    cmd = "cat {fasta_file_string} > {tx_out_file}"
    with file_transaction(data, combined_file) as tx_out_file:
        do.run(cmd.format(**locals()), "Combining transcriptome FASTA files.")
    return combined_file