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]]