def test_bcbio_dexseq(self):
data = dd.set_sample_name({}, "test")
data = dd.set_work_bam(data, test_data.BAM_FILE)
data = dd.set_work_dir(data, self.out_dir)
data = dd.set_dexseq_gff(data, test_data.DEXSEQ_GFF)
data = dd.set_strandedness(data, "unstranded")
out_file = dexseq.bcbio_run(data)
self.assertTrue(file_exists(out_file))
def generate_transcript_counts(data):
"""Generate counts per transcript and per exon from an alignment"""
data["count_file"] = featureCounts.count(data)
if dd.get_fusion_mode(data, False):
oncofuse_file = oncofuse.run(data)
if oncofuse_file:
data["oncofuse_file"] = oncofuse.run(data)
if dd.get_dexseq_gff(data, None):
data = dd.set_dexseq_counts(data, dexseq.bcbio_run(data))
# if RSEM was run, stick the transcriptome BAM file into the datadict
if dd.get_aligner(data).lower() == "star" and dd.get_rsem(data):
base, ext = os.path.splitext(dd.get_work_bam(data))
data = dd.set_transcriptome_bam(data, base + ".transcriptome" + ext)
return [[data]]
def run_dexseq(data):
"""Quantitate exon-level counts with DEXSeq"""
if dd.get_dexseq_gff(data, None):
data = dexseq.bcbio_run(data)
return [[data]]
