def test_sam_query(self):
reader = genomics_io.make_sam_reader(
test_utils.genomics_core_testdata('test.bam'))
expected = [(ranges.parse_literal('chr20:10,000,000-10,000,100'), 106),
(ranges.parse_literal('chr20:10,000,000-10,000,000'), 45)]
with reader:
for interval, n_expected in expected:
with reader.query(interval) as iterable:
self.assertEqual(test_utils.iterable_len(iterable), n_expected)
def test_bam_query(self):
reader = sam_reader.SamReader.from_file(self.bam, self.indexed_options)
expected = [(ranges.parse_literal('chr20:10,000,000-10,000,100'), 106),
(ranges.parse_literal('chr20:10,000,000-10,000,000'), 45)]
with reader:
for interval, n_expected in expected:
with reader.query(interval) as iterable:
self.assertIsInstance(iterable,
clif_postproc.WrappedCppIterable)
self.assertEqual(test_utils.iterable_len(iterable),
n_expected)
def test_downsampling(self, method, maybe_range, fraction, expected_n_reads):
reader = genomics_io.make_sam_reader(
test_utils.genomics_core_testdata('test.bam'),
downsample_fraction=fraction,
random_seed=12345)
with reader:
if method == 'iterate':
reads_iter = reader.iterate()
elif method == 'query':
reads_iter = reader.query(ranges.parse_literal(maybe_range))
else:
self.fail('Unexpected method', method)
self.assertEqual(test_utils.iterable_len(reads_iter), expected_n_reads)
def test_vcf_query(self):
range1 = ranges.parse_literal('chr3:100,000-500,000')
iterable = self.samples_reader.query(range1)
self.assertEqual(test_utils.iterable_len(iterable), 4)
def test_vcf_iterate(self): iterable = self.sites_reader.iterate() self.assertEqual(test_utils.iterable_len(iterable), 5)
def test_bam_iterate(self):
reader = sam_reader.SamReader.from_file(self.bam, self.options)
with reader:
iterable = reader.iterate()
self.assertIsInstance(iterable, clif_postproc.WrappedCppIterable)
self.assertEqual(test_utils.iterable_len(iterable), 106)
def test_bam_iterate(self):
reader = genomics_io.make_sam_reader(
test_utils.genomics_core_testdata('test.bam'), use_index=False)
with reader:
self.assertEqual(test_utils.iterable_len(reader.iterate()), 106)