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()