def test_summarize_blank(self): records = [] expected_summary = {} summary = {} summarize_quality_records(records, summary) self.assertEqual(expected_summary, summary)
def test_summarize_ignores_index_reads(self): read_lengths = [95, 5, 95] records = [dict(cycle=96, quality_bins=[0] * 50), dict(cycle=100, quality_bins=[0] * 50)] records[0]['quality_bins'][29] = 1 records[1]['quality_bins'][29] = 1 expected_summary = {} summary = {} summarize_quality_records(records, summary, read_lengths) self.assertEqual(expected_summary, summary)
def test_summarize(self): records = [dict(cycle=1, quality_bins=[0] * 50), dict(cycle=101, quality_bins=[0] * 50)] records[0]['quality_bins'][28] = 1 records[0]['quality_bins'][29] = 1 records[1]['quality_bins'][29] = 1 expected_summary = dict(q30_fwd=2/3.0) summary = {} summarize_quality_records(records, summary) self.assertEqual(expected_summary, summary)
def test_summarize_reverse(self): read_lengths = [95, 5, 95] records = [dict(cycle=1, quality_bins=[0] * 50), dict(cycle=101, quality_bins=[0] * 50)] records[0]['quality_bins'][28] = 1 records[0]['quality_bins'][29] = 1 records[1]['quality_bins'][29] = 1 expected_summary = dict(q30_fwd=0.5, q30_rev=1.0) summary = {} summarize_quality_records(records, summary, read_lengths) self.assertEqual(expected_summary, summary)