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 split_demultiplexed_sampledata(data, demultiplexed): """ splits demultiplexed samples into separate entries in the global sample datadict """ datadicts = [] samplename = dd.get_sample_name(data) for fastq in demultiplexed: barcode = os.path.basename(fastq).split(".")[0] datadict = copy.deepcopy(data) datadict = dd.set_sample_name(datadict, samplename + "-" + barcode) datadict = dd.set_description(datadict, samplename + "-" + barcode) datadict["rgnames"]["rg"] = samplename + "-" + barcode datadict["name"] = ["", samplename + "-" + barcode] datadict["files"] = [fastq] datadicts.append(datadict) return datadicts
def split_demultiplexed_sampledata(data, demultiplexed): """ splits demultiplexed samples into separate entries in the global sample datadict """ datadicts = [] samplename = dd.get_sample_name(data) for fastq in demultiplexed: barcode = os.path.basename(fastq).split(".")[0] datadict = copy.deepcopy(data) datadict = dd.set_sample_name(datadict, samplename + "-" + barcode) datadict = dd.set_description(datadict, samplename + "-" + barcode) datadict["rgnames"]["rg"] = samplename + "-" + barcode datadict["name"]= ["", samplename + "-" + barcode] datadict["files"] = [fastq] datadicts.append(datadict) return datadicts