def test_basic(self): cmd = _to_cmd(self.ALIGNMENTS, self.report_json) rcode = run_backticks(cmd) self.assertEqual(rcode, 0) with open(self.report_json, 'r') as f: s = json.load(f) log.info("JsonReport: ") log.info(pprint.pformat(s, indent=4)) report = dict_to_report(s) self.assertIsNotNone(report) self.assertEqual(len(report.tables), 1) log.info(str(report.tables[0])) validate_report_metadata(self, report, meta_rpt)
def run_after(self, rtc, output_dir): r = load_report_from_json(rtc.task.output_files[0]) with ConsensusAlignmentSet(self.INPUT_FILES[0]) as ds: self.assertEqual(r._dataset_uuids, [ds.uuid]) self.assertEqual(len(r.plotGroups), 4) validate_report_metadata(self, r, mapping_stats_ccs.ccs_spec)
def run_after(self, rtc, output_dir): r = load_report_from_json(rtc.task.output_files[0]) with AlignmentSet(self.INPUT_FILES[0]) as ds: self.assertEqual(r._dataset_uuids, [ds.uuid]) validate_report_metadata(self, r, spec)
def test_report_metadata(self): validate_report_metadata(self, self.report, mapping_stats_ccs.ccs_spec)
def test_report_metadata(self): validate_report_metadata(self, self.report, spec)
def test_report_metadata(self): validate_report_metadata(self, self.report, meta_rpt)
def run_after(self, rtc, output_dir): r = load_report_from_json(rtc.task.output_files[0]) with ConsensusAlignmentSet(self.INPUT_FILES[0]) as ds: self.assertEqual(r._dataset_uuids, [ds.uuid]) self.assertEqual(len(r.plotGroups), 4) validate_report_metadata(self, r, mapping_stats_ccs.meta_rpt)
def run_after(self, rtc, output_dir): r = load_report_from_json(rtc.task.output_files[0]) with AlignmentSet(self.INPUT_FILES[0]) as ds: self.assertEqual(r._dataset_uuids, [ds.uuid]) validate_report_metadata(self, r, meta_rpt)
def test_report_metadata(self): validate_report_metadata(self, self.report, mapping_stats_ccs.meta_rpt)