def run_rsem_postprocess(job, rsem_gene_id, rsem_isoform_id):
    """
    Parses RSEMs output to produce the separate .tab files (TPM, FPKM, counts) for both gene and isoform.
    These are two-column files: Genes and Quantifications.
    HUGO files are also provided that have been mapped from Gencode/ENSEMBLE names.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str rsem_gene_id: FileStoreID of rsem_gene_ids
    :param str rsem_isoform_id: FileStoreID of rsem_isoform_ids
    :return: FileStoreID from RSEM post process tarball
    :rytpe: str
    """
    work_dir = job.fileStore.getLocalTempDir()
    # I/O
    genes = job.fileStore.readGlobalFile(rsem_gene_id, os.path.join(work_dir, 'rsem_genes.results'))
    iso = job.fileStore.readGlobalFile(rsem_isoform_id, os.path.join(work_dir, 'rsem_isoforms.results'))
    # Perform HUGO gene / isoform name mapping
    command = ['-g', 'rsem_genes.results', '-i', 'rsem_isoforms.results']
    dockerCall(job=job, tool='quay.io/ucsc_cgl/gencode_hugo_mapping:1.0--cb4865d02f9199462e66410f515c4dabbd061e4d',
               parameters=command, workDir=work_dir)
    hugo_files = [os.path.join(work_dir, x) for x in ['rsem_genes.hugo.results', 'rsem_isoforms.hugo.results']]
    # Create tarballs for outputs
    tarball_files('rsem.tar.gz', file_paths=[os.path.join(work_dir, x) for x in [genes, iso]], output_dir=work_dir)
    tarball_files('rsem_hugo.tar.gz', file_paths=[os.path.join(work_dir, x) for x in hugo_files], output_dir=work_dir)
    rsem_id = job.fileStore.writeGlobalFile(os.path.join(work_dir, 'rsem.tar.gz'))
    hugo_id = job.fileStore.writeGlobalFile(os.path.join(work_dir, 'rsem_hugo.tar.gz'))
    return rsem_id, hugo_id
def run_rsem_postprocess(job, rsem_gene_id, rsem_isoform_id):
    """
    Parses RSEMs output to produce the separate .tab files (TPM, FPKM, counts) for both gene and isoform.
    These are two-column files: Genes and Quantifications.
    HUGO files are also provided that have been mapped from Gencode/ENSEMBLE names.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str rsem_gene_id: FileStoreID of rsem_gene_ids
    :param str rsem_isoform_id: FileStoreID of rsem_isoform_ids
    :return: FileStoreID from RSEM post process tarball
    :rytpe: str
    """
    work_dir = job.fileStore.getLocalTempDir()
    # I/O
    genes = job.fileStore.readGlobalFile(rsem_gene_id, os.path.join(work_dir, 'rsem_genes.results'))
    iso = job.fileStore.readGlobalFile(rsem_isoform_id, os.path.join(work_dir, 'rsem_isoforms.results'))
    # Perform HUGO gene / isoform name mapping
    command = ['-g', 'rsem_genes.results', '-i', 'rsem_isoforms.results']
    dockerCall(job=job, tool='quay.io/ucsc_cgl/gencode_hugo_mapping:1.0--cb4865d02f9199462e66410f515c4dabbd061e4d',
               parameters=command, workDir=work_dir)
    hugo_files = [os.path.join(work_dir, x) for x in ['rsem_genes.hugo.results', 'rsem_isoforms.hugo.results']]
    # Create tarballs for outputs
    tarball_files('rsem.tar.gz', file_paths=[os.path.join(work_dir, x) for x in [genes, iso]], output_dir=work_dir)
    tarball_files('rsem_hugo.tar.gz', file_paths=[os.path.join(work_dir, x) for x in hugo_files], output_dir=work_dir)
    rsem_id = job.fileStore.writeGlobalFile(os.path.join(work_dir, 'rsem.tar.gz'))
    hugo_id = job.fileStore.writeGlobalFile(os.path.join(work_dir, 'rsem_hugo.tar.gz'))
    return rsem_id, hugo_id
def run_rsem_postprocess ( job , rsem_gene_id , rsem_isoform_id ) : work_dir = job . fileStore . getLocalTempDir ( ) # I/O genes = job . fileStore . readGlobalFile ( rsem_gene_id , os . path . join ( work_dir , 'rsem_genes.results' ) ) iso = job . fileStore . readGlobalFile ( rsem_isoform_id , os . path . join ( work_dir , 'rsem_isoforms.results' ) ) # Perform HUGO gene / isoform name mapping command = [ '-g' , 'rsem_genes.results' , '-i' , 'rsem_isoforms.results' ] dockerCall ( job = job , tool = 'quay.io/ucsc_cgl/gencode_hugo_mapping:1.0--cb4865d02f9199462e66410f515c4dabbd061e4d' , parameters = command , workDir = work_dir ) hugo_files = [ os . path . join ( work_dir , x ) for x in [ 'rsem_genes.hugo.results' , 'rsem_isoforms.hugo.results' ] ] # Create tarballs for outputs tarball_files ( 'rsem.tar.gz' , file_paths = [ os . path . join ( work_dir , x ) for x in [ genes , iso ] ] , output_dir = work_dir ) tarball_files ( 'rsem_hugo.tar.gz' , file_paths = [ os . path . join ( work_dir , x ) for x in hugo_files ] , output_dir = work_dir ) rsem_id = job . fileStore . writeGlobalFile ( os . path . join ( work_dir , 'rsem.tar.gz' ) ) hugo_id = job . fileStore . writeGlobalFile ( os . path . join ( work_dir , 'rsem_hugo.tar.gz' ) ) return rsem_id , hugo_id
Parses RSEMs output to produce the separate .tab files (TPM, FPKM, counts) for both gene and isoform.
    These are two-column files: Genes and Quantifications.
    HUGO files are also provided that have been mapped from Gencode/ENSEMBLE names.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str rsem_gene_id: FileStoreID of rsem_gene_ids
    :param str rsem_isoform_id: FileStoreID of rsem_isoform_ids
    :return: FileStoreID from RSEM post process tarball
    :rytpe: str
Parses RSEMs output to produce the separate . tab files ( TPM FPKM counts ) for both gene and isoform . These are two - column files : Genes and Quantifications . HUGO files are also provided that have been mapped from Gencode / ENSEMBLE names .