def test_get_column_data(self): """ Test: Assert array equals when getting column data """ try: log.info(TestFilteredSummaryReader.test_count_records.__doc__) fsr = FilteredSummaryReader( os.path.join(BaseTestCase.get_data_dir(), 'loading', 'filtered_summary_small.csv')) fsr.load() ri_exp = [ 'm120128_025832_42129_c100277632550000001523007907041250_s2_p0/0', 'm120128_025832_42129_c100277632550000001523007907041250_s2_p0/1' ] ri_act = [] data = fsr.data_as_numpy_array() for row in data: ri_act.append(row['ReadId']) self.assertSequenceEqual(ri_exp, ri_act) except: log.error(traceback.format_exc()) raise
def test_count_records(self): """ Test: Count num csv records """ try: log.info(TestFilteredSummaryReader.test_count_records.__doc__) fsr = FilteredSummaryReader(os.path.join(BaseTestCase.get_data_dir(), 'loading', 'filtered_summary_small.csv')) fsr.load() self.assertEqual(2, fsr.num_records) except: log.error(traceback.format_exc()) raise
def test_num_reads(self): """ Test: get num reads from csv """ try: log.info(TestFilteredSummaryReader.test_num_reads.__doc__) fsr = FilteredSummaryReader( os.path.join(BaseTestCase.get_data_dir(), 'loading', 'filtered_summary_small.csv')) fsr.load() self.assertEqual(1, fsr.num_reads) except: log.error(traceback.format_exc()) raise
def test_get_column_data(self): """ Test: Assert array equals when getting column data """ try: log.info(TestFilteredSummaryReader.test_count_records.__doc__) fsr = FilteredSummaryReader(os.path.join(BaseTestCase.get_data_dir(), 'loading', 'filtered_summary_small.csv')) fsr.load() ri_exp = ['m120128_025832_42129_c100277632550000001523007907041250_s2_p0/0', 'm120128_025832_42129_c100277632550000001523007907041250_s2_p0/1'] ri_act = [] data = fsr.data_as_numpy_array() for row in data: ri_act.append(row['ReadId']) self.assertSequenceEqual(ri_exp, ri_act) except: log.error(traceback.format_exc()) raise
def _create_adapter_report(self): """ Creates and returns an Adapter Report """ from pbreports.report.adapter import make_adapter_report from test_pbreports_report_adapters import DataCache as d BaseTestCase.setUpClass() d.data_dir = BaseTestCase.get_data_dir() log.info( 'Creating adapter report using datadir {d}'.format(d=d.data_dir)) fofn = os.path.join(self._output_dir, 'test.fofn') d.write_fofn(fofn) dpi = 60 dumpdata = False output_json = os.path.join(self._output_dir, 'adapter.json') make_adapter_report(fofn, 'adapter.json', self._output_dir, dpi, dumpdata) return self._deserialize_report(output_json)
def _create_adapter_report(self): """ Creates and returns an Adapter Report """ from pbreports.report.adapter import make_adapter_report from test_pbreports_report_adapters import DataCache as d BaseTestCase.setUpClass() d.data_dir = BaseTestCase.get_data_dir() log.info( 'Creating adapter report using datadir {d}'.format(d=d.data_dir)) fofn = os.path.join(self._output_dir, 'test.fofn') d.write_fofn(fofn) dpi = 60 dumpdata = False output_json = os.path.join(self._output_dir, 'adapter.json') make_adapter_report( fofn, 'adapter.json', self._output_dir, dpi, dumpdata) return self._deserialize_report(output_json)