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 _get_all_filtered_read_ids(self): reader = FilteredSummaryReader(os.path.join( self.DATA_DIR, 'filtered_summary.csv'), CSV_COLUMN_MAP) reader.load() data = reader.data_as_numpy_array() ids = set([]) for row in data: ids.add(row['ReadId']) return ids
def _get_all_filtered_read_ids(self): reader = FilteredSummaryReader( os.path.join(self.DATA_DIR, 'filtered_summary.csv'), CSV_COLUMN_MAP) reader.load() data = reader.data_as_numpy_array() ids = set([]) for row in data: ids.add(row['ReadId']) return ids
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 _get_filtered_reads(filtered_subreads_csv): """ Return a numpy array of csv data filtered by PassedFilter > 0 :param filtered_subreads_csv: path to filtered_summary.csv f """ reader = FilteredSummaryReader(filtered_subreads_csv, CSV_COLUMN_MAP) reader.load() data = reader.data_as_numpy_array() data = data[data["PassedFilter"] > 0] log.info('Total # reads in {f}: {i}'.format( f=filtered_subreads_csv, i=reader.num_records)) log.info('# reads that passed filter: {i}'.format(i=len(data))) return data
def _get_filtered_reads(filtered_subreads_csv): """ Return a numpy array of csv data filtered by PassedFilter > 0 :param filtered_subreads_csv: path to filtered_summary.csv f """ reader = FilteredSummaryReader(filtered_subreads_csv, CSV_COLUMN_MAP) reader.load() data = reader.data_as_numpy_array() data = data[data["PassedFilter"] > 0] log.info('Total # reads in {f}: {i}'.format(f=filtered_subreads_csv, i=reader.num_records)) log.info('# reads that passed filter: {i}'.format(i=len(data))) return data
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_io_error(self): """ Test: Throws IOError in constructor """ log.info(TestFilteredSummaryReader.test_io_error.__doc__) try: FilteredSummaryReader('/i/dont/exits') self.fail('Should have thrown IOError') except IOError: pass 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