This module will run transgene on the input vcf file from the aggregator and produce the
    peptides for MHC prediction

    ARGUMENTS
    1. snpeffed_file: <JSid for snpeffed vcf>
    2. univ_options: Dict of universal arguments used by almost all tools
         univ_options
                +- 'dockerhub': <dockerhub to use>
    3. transgene_options: Dict of parameters specific to transgene
         transgene_options
                +- 'gencode_peptide_fasta': <JSid for the gencode protein fasta>

    RETURN VALUES
    1. output_files: Dict of transgened n-mer peptide fastas
         output_files
                |- 'transgened_tumor_9_mer_snpeffed.faa': <JSid>
                |- 'transgened_tumor_10_mer_snpeffed.faa': <JSid>
                +- 'transgened_tumor_15_mer_snpeffed.faa': <JSid>

    This module corresponds to node 17 on the tree

def run_transgene(job, snpeffed_file, univ_options, transgene_options):
    """
    This module will run transgene on the input vcf file from the aggregator and produce the
    peptides for MHC prediction

    ARGUMENTS
    1. snpeffed_file: <JSid for snpeffed vcf>
    2. univ_options: Dict of universal arguments used by almost all tools
         univ_options
                +- 'dockerhub': <dockerhub to use>
    3. transgene_options: Dict of parameters specific to transgene
         transgene_options
                +- 'gencode_peptide_fasta': <JSid for the gencode protein fasta>

    RETURN VALUES
    1. output_files: Dict of transgened n-mer peptide fastas
         output_files
                |- 'transgened_tumor_9_mer_snpeffed.faa': <JSid>
                |- 'transgened_tumor_10_mer_snpeffed.faa': <JSid>
                +- 'transgened_tumor_15_mer_snpeffed.faa': <JSid>

    This module corresponds to node 17 on the tree
    """
    job.fileStore.logToMaster('Running transgene on %s' % univ_options['patient'])
    work_dir = job.fileStore.getLocalTempDir()
    input_files = {
        'snpeffed_muts.vcf': snpeffed_file,
        'pepts.fa': transgene_options['gencode_peptide_fasta']}
    input_files = get_files_from_filestore(job, input_files, work_dir, docker=True)
    parameters = ['--peptides', input_files['pepts.fa'],
                  '--snpeff', input_files['snpeffed_muts.vcf'],
                  '--prefix', 'transgened',
                  '--pep_lens', '9,10,15']
    docker_call(tool='transgene', tool_parameters=parameters, work_dir=work_dir,
                dockerhub=univ_options['dockerhub'])
    output_files = defaultdict()
    for peplen in ['9', '10', '15']:
        peptfile = '_'.join(['transgened_tumor', peplen, 'mer_snpeffed.faa'])
        mapfile = '_'.join(['transgened_tumor', peplen, 'mer_snpeffed.faa.map'])
        output_files[peptfile] = job.fileStore.writeGlobalFile(os.path.join(work_dir, peptfile))
        output_files[mapfile] = job.fileStore.writeGlobalFile(os.path.join(work_dir, mapfile))
    return output_files