def test_basic(self): """Basic smoke test""" output_dir = tempfile.mkdtemp() report = to_report(self.ccs_set, output_dir) validate_report_complete(self, report) d = report.to_dict() self.assertIsNotNone(d)
def test_ccs_mulitple_movies_single_bam(self): """ Check that the report doesn't crash when a single BAM file contains reads from multiple movies """ ds = ConsensusReadSet(self.CCS_BAM) r = to_report(ds, tempfile.mkdtemp())
def test_ccs_barcodes_table_asymmetric(self): CCS_DS = op.join(ROOT_DATA_DIR, "ccs", "asym_barcodes", "ccs.consensusreadset.xml") ds = ConsensusReadSet(CCS_DS) r = to_report(ds, tempfile.mkdtemp()) self.assertEqual(r.tables[1].columns[0].values, ['F5, R5', 'F8, R8', 'F20, R20', 'F29, R29', 'F30, R30'])
def test_ccs_barcodes_table_asymmetric(self): CCS_DS = op.join(ROOT_DATA_DIR, "ccs", "asym_barcodes", "ccs.consensusreadset.xml") ds = ConsensusReadSet(CCS_DS) r = to_report(ds, tempfile.mkdtemp()) self.assertEqual(r.tables[1].columns[0].values, ['F5--R5', 'F8--R8', 'F20--R20', 'F29--R29', 'F30--R30'])
def test_ccs_barcodes_table(self): ds = ConsensusReadSet(self.CCS_DS) r = to_report(ds, tempfile.mkdtemp()) self.assertEqual([c.values for c in r.tables[1].columns[0:4]], [["lbc1", "lbc3"], [1,1], [1958,1954], [1958,1954]]) self.assertAlmostEqual(r.tables[1].columns[4].values[0], 0.9724, places=4) self.assertAlmostEqual(r.tables[1].columns[4].values[1], 0.9926, places=4)
def test_ccs_barcodes_table(self): CCS_DS = pbtestdata.get_file("ccs-barcoded") ds = ConsensusReadSet(CCS_DS) r = to_report(ds, tempfile.mkdtemp()) self.assertEqual([c.values for c in r.tables[1].columns[0:4]], [["lbc1--lbc1", "lbc3--lbc3"], [1, 1], [1958, 1954], [1958, 1954]]) self.assertAlmostEqual(r.tables[1].columns[4].values[0], 0.9724, places=4) self.assertAlmostEqual(r.tables[1].columns[4].values[1], 0.9926, places=4)
def setUpClass(cls): cls.output_dir = tempfile.mkdtemp() cls.ccs_set = ConsensusReadSet(cls.XML_FILE) cls.report = to_report(cls.ccs_set, cls.output_dir)
def setUpClass(cls): cls.setUpData() output_dir = tempfile.mkdtemp() cls.ccs_set = ConsensusReadSet(cls.xml_file_name) cls.report = to_report(cls.ccs_set, output_dir) cls.output_dir = output_dir