def test_fetch_single_read(self):
b = BamCache(get_data('mini_mock_reads_for_events.sorted.bam'))
s = b.fetch_from_bins('reference3', 1382, 1383, read_limit=1, sample_bins=1)
self.assertEqual(1, len(s))
r = list(s)[0]
self.assertEqual('HISEQX1_11:4:2122:14275:37717:split', r.qname)
b.close()
def test_genome_bam_stats(self):
bamfh = BamCache(get_data('mock_reads_for_events.sorted.bam'))
stats = compute_genome_bam_stats(
bamfh, 1000, 100, min_mapping_quality=1, sample_cap=10000, distribution_fraction=0.99
)
self.assertGreaterEqual(50, abs(stats.median_fragment_size - 420))
self.assertEqual(150, stats.read_length)
bamfh.close()
def test_fetch_single_read(self):
b = BamCache(BAM_INPUT)
s = b.fetch_from_bins('reference3',
1382,
1383,
read_limit=1,
sample_bins=1)
self.assertEqual(1, len(s))
r = list(s)[0]
self.assertEqual('HISEQX1_11:4:2122:14275:37717:split', r.qname)
b.close()
def test_genome_bam_stats(self):
bamfh = BamCache(FULL_BAM_INPUT)
stats = compute_genome_bam_stats(bamfh,
1000,
100,
min_mapping_quality=1,
sample_cap=10000,
distribution_fraction=0.99)
self.assertGreaterEqual(50, abs(stats.median_fragment_size - 420))
self.assertEqual(150, stats.read_length)
bamfh.close()
def test_trans_bam_stats(self):
bamfh = BamCache(TRANSCRIPTOME_BAM_INPUT)
annotations = load_reference_genes(
FULL_REFERENCE_ANNOTATIONS_FILE_JSON)
stats = compute_transcriptome_bam_stats(bamfh,
annotations,
100,
min_mapping_quality=1,
stranded=True,
sample_cap=10000,
distribution_fraction=0.99)
self.assertTrue(abs(stats.median_fragment_size - 185) < 5)
self.assertEqual(75, stats.read_length)
self.assertTrue(stats.stdev_fragment_size < 50)
bamfh.close()
def test_trans_bam_stats(self):
bamfh = BamCache(get_data('mock_trans_reads_for_events.sorted.bam'))
annotations = load_reference_genes(get_data('mock_annotations.json'))
stats = compute_transcriptome_bam_stats(
bamfh,
annotations,
100,
min_mapping_quality=1,
stranded=True,
sample_cap=10000,
distribution_fraction=0.99,
)
self.assertTrue(abs(stats.median_fragment_size - 185) < 5)
self.assertEqual(75, stats.read_length)
self.assertTrue(stats.stdev_fragment_size < 50)
bamfh.close()