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)
