def test_add_read(self):
fh = MockBamFileHandle()
b = BamCache(fh)
r = MockRead('name')
b.add_read(r)
self.assertEqual(1, len(b.cache.values()))
self.assertEqual(set([r]), b.cache['name'])
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_add_invalid_read(self, log_patcher):
bad_read = mock.Mock(
is_unmapped=False, reference_start=0, reference_end=0, query_name='BAD_READ'
)
cache = BamCache(MockBamFileHandle())
cache.add_read(bad_read)
assert len(cache.cache) == 0
log_patcher.method_calls[0].assert_called_with('ignoring invalid read: BAD_READ')
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_add_invalid_read(self, log_patcher):
bad_read = mock.Mock(
is_unmapped=False, reference_start=0, reference_end=0, query_name='BAD_READ'
)
cache = BamCache(MockBamFileHandle())
cache.add_read(bad_read)
self.assertEqual(0, len(cache.cache))
log_patcher.assert_called_with('ignoring invalid read', 'BAD_READ', level=logging.DEBUG)
def test_bin_fetch_invalid_read(self, log_patcher):
bad_read = mock.Mock(is_unmapped=False, reference_start=0, reference_end=0, query_name='BAD_READ')
fh = mock.Mock(references=['chr'], spec=['references', 'fetch'])
fh.configure_mock(**{'fetch.return_value': [bad_read]})
cache = BamCache(fh)
cache.fetch_from_bins('chr', 1, 10)
self.assertEqual(0, len(cache.cache))
log_patcher.assert_called_with('ignoring invalid read', 'BAD_READ', level=logging.DEBUG)
def test_generate_fetch_bins_multi(self):
assert BamCache._generate_fetch_bins(1, 100, 2, 1) == [(1, 50), (51, 100)]
assert BamCache._generate_fetch_bins(1, 100, 5, 1) == [
(1, 20),
(21, 40),
(41, 60),
(61, 80),
(81, 100),
]
def test_fetch_invalid_read(self, log_patcher):
bad_read = mock.Mock(
is_unmapped=False, reference_start=0, reference_end=0, query_name='BAD_READ'
)
fh = mock.Mock(references=['chr'], spec=['references', 'fetch'])
fh.configure_mock(**{'fetch.return_value': [bad_read]})
cache = BamCache(fh)
cache.fetch('chr', 1, 10)
assert len(cache.cache) == 0
log_patcher.method_calls[0].assert_called_with('ignoring invalid read: BAD_READ')
def test_get_mate(self):
# dependant on fetch working
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)
o = b.get_mate(r, allow_file_access=True)
self.assertEqual(1, len(o))
self.assertEqual('HISEQX1_11:4:2122:14275:37717:split', o[0].qname)
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 setUpModule():
global REFERENCE_GENOME
REFERENCE_GENOME = load_reference_genome(get_data('mock_reference_genome.fa'))
if 'CTCCAAAGAAATTGTAGTTTTCTTCTGGCTTAGAGGTAGATCATCTTGGT' != REFERENCE_GENOME['fake'].seq[0:50].upper():
raise AssertionError('fake genome file does not have the expected contents')
global BAM_CACHE
BAM_CACHE = BamCache(get_data('mini_mock_reads_for_events.sorted.bam'))
def setUp(self):
self.cache = BamCache(
MockBamFileHandle({
'Y': 23,
'fake': 0,
'reference3': 3
}))
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()
def cache():
return BamCache(
MockBamFileHandle({
'Y': 23,
'fake': 0,
'reference3': 3,
'14': 13
}))
def setUpModule():
global REFERENCE_GENOME
REFERENCE_GENOME = load_reference_genome(REFERENCE_GENOME_FILE)
if 'CTCCAAAGAAATTGTAGTTTTCTTCTGGCTTAGAGGTAGATCATCTTGGT' != REFERENCE_GENOME[
'fake'].seq[0:50].upper():
raise AssertionError(
'fake genome file does not have the expected contents')
global BAM_CACHE
BAM_CACHE = BamCache(BAM_INPUT)
def test_add_read(self):
fh = MockBamFileHandle()
b = BamCache(fh)
r = mock.MagicMock(query_name='name', query_sequence='')
b.add_read(r)
self.assertEqual(1, len(b.cache.values()))
b.add_read(r)
self.assertEqual(1, len(b.cache.values()))
r.reference_start = 0
b.add_read(r)
self.assertEqual(1, len(b.cache.values()))
def setUpModule():
global REFERENCE_GENOME
REFERENCE_GENOME = load_reference_genome(get_data('mock_reference_genome.fa'))
if 'CTCCAAAGAAATTGTAGTTTTCTTCTGGCTTAGAGGTAGATCATCTTGGT' != REFERENCE_GENOME['fake'].seq[0:50].upper():
raise AssertionError('fake genome file does not have the expected contents')
global BAM_CACHE
BAM_CACHE = BamCache(get_data('mini_mock_reads_for_events.sorted.bam'))
global FULL_BAM_CACHE
FULL_BAM_CACHE = BamCache(get_data('mock_reads_for_events.sorted.bam'))
global READS
READS = {}
for read in BAM_CACHE.fetch('reference3', 1, 8000):
if read.qname not in READS:
READS[read.qname] = [None, None]
if read.is_supplementary:
continue
if read.is_read1:
READS[read.qname][0] = read
else:
READS[read.qname][1] = read
def flanking_ge(read_length):
return GenomeEvidence(
Breakpoint('1', 1500, orient=ORIENT.LEFT),
Breakpoint('1', 6001, orient=ORIENT.RIGHT),
BamCache(MockBamFileHandle({'1': 0})),
None, # reference_genome
opposing_strands=False,
read_length=150,
stdev_fragment_size=500,
median_fragment_size=100,
config={'validate.stdev_count_abnormal': 1, 'validate.call_error': 0},
)
def setUp(self):
self.ge = GenomeEvidence(
Breakpoint('1', 1500, orient=ORIENT.LEFT),
Breakpoint('1', 6001, orient=ORIENT.RIGHT),
BamCache(MockBamFileHandle({'1': 0})),
None, # reference_genome
opposing_strands=False,
read_length=150,
stdev_fragment_size=500,
median_fragment_size=100,
call_error=0,
stdev_count_abnormal=1)
def test___init__(self):
fh = MockBamFileHandle()
b = BamCache(fh)
self.assertEqual(fh, b.fh)
def test___init__(self):
fh = MockBamFileHandle()
b = BamCache(fh)
assert b.fh == fh
def test_reference_id(self):
fh = MockBamFileHandle({'1': 0})
b = BamCache(fh)
assert b.reference_id('1') == 0
with pytest.raises(KeyError):
b.reference_id('2')
def test_generate_fetch_bins_multi(self):
self.assertEqual([(1, 50), (51, 100)], BamCache._generate_fetch_bins(1, 100, 2, 1))
self.assertEqual(
[(1, 20), (21, 40), (41, 60), (61, 80), (81, 100)],
BamCache._generate_fetch_bins(1, 100, 5, 1),
)
def test_generate_fetch_bins_single(self):
self.assertEqual([(1, 100)], BamCache._generate_fetch_bins(1, 100, 1, 1))
def test_get_read_reference_name(self):
fh = MockBamFileHandle({'1': 0})
b = BamCache(fh)
r = MockRead('name', 0)
self.assertEqual('1', b.get_read_reference_name(r))
def test_generate_fetch_bins_large_min_size(self):
self.assertEqual([(1, 50), (51, 100)], BamCache._generate_fetch_bins(1, 100, 5, 50))
def test_reference_id(self):
fh = MockBamFileHandle({'1': 0})
b = BamCache(fh)
self.assertEqual(0, b.reference_id('1'))
with self.assertRaises(KeyError):
b.reference_id('2')
def test_get_read_reference_name(self):
fh = MockBamFileHandle({'1': 0})
b = BamCache(fh)
r = MockRead('name', 0)
assert b.get_read_reference_name(r) == '1'