def test_overlaps_variant_with_ranges(self):
variant = variants_pb2.Variant(reference_name='chr2', start=10, end=11)
range_set = ranges.RangeSet([ranges.make_range('chr1', 0, 5)])
with mock.patch.object(range_set, 'overlaps') as mock_overlaps:
mock_overlaps.return_value = True
self.assertEqual(range_set.variant_overlaps(variant), True)
mock_overlaps.assert_called_once_with('chr2', 10)
def test_detector_ranges(self):
test_ranges = [
ranges.make_range('chr1', 0, 5),
ranges.make_range('chr1', 8, 10),
ranges.make_range('chr1', 12, 13),
ranges.make_range('chr2', 2, 5),
]
range_set = ranges.RangeSet(test_ranges)
self.assertEqual(bool(range_set), True)
self.assertEqual(len(range_set), 4)
self.assertEqual(range_set.overlaps('chr1', 0), True)
self.assertEqual(range_set.overlaps('chr1', 1), True)
self.assertEqual(range_set.overlaps('chr1', 2), True)
self.assertEqual(range_set.overlaps('chr1', 3), True)
self.assertEqual(range_set.overlaps('chr1', 4), True)
self.assertEqual(range_set.overlaps('chr1', 5), False)
self.assertEqual(range_set.overlaps('chr1', 6), False)
self.assertEqual(range_set.overlaps('chr1', 7), False)
self.assertEqual(range_set.overlaps('chr1', 8), True)
self.assertEqual(range_set.overlaps('chr1', 9), True)
self.assertEqual(range_set.overlaps('chr1', 10), False)
self.assertEqual(range_set.overlaps('chr1', 11), False)
self.assertEqual(range_set.overlaps('chr1', 12), True)
self.assertEqual(range_set.overlaps('chr1', 13), False)
self.assertEqual(range_set.overlaps('chr1', 100), False)
self.assertEqual(range_set.overlaps('chr1', 1000), False)
self.assertEqual(range_set.overlaps('chr2', 0), False)
self.assertEqual(range_set.overlaps('chr2', 1), False)
self.assertEqual(range_set.overlaps('chr2', 2), True)
self.assertEqual(range_set.overlaps('chr2', 3), True)
self.assertEqual(range_set.overlaps('chr2', 4), True)
self.assertEqual(range_set.overlaps('chr2', 5), False)
self.assertEqual(range_set.overlaps('chr2', 6), False)
self.assertEqual(range_set.overlaps('chr3', 3), False)
def test_partition_of_multiple_intervals(self, interval_size, expected):
rangeset = ranges.RangeSet([
ranges.make_range('1', 0, 10),
ranges.make_range('1', 20, 40),
ranges.make_range('1', 45, 50),
])
self.assertCountEqual([ranges.make_range(*args) for args in expected],
rangeset.partition(interval_size))
def test_partitions(self, interval_size, expected):
rangeset = ranges.RangeSet([
ranges.make_range('chrM', 0, 100),
ranges.make_range('chr1', 0, 76),
ranges.make_range('chr2', 0, 121),
])
self.assertCountEqual([ranges.make_range(*args) for args in expected],
rangeset.partition(interval_size))
def test_intersection(self, regions, expected):
regions_list = [ranges.RangeSet.from_regions(r) for r in regions]
copies = [ranges.RangeSet(rs) for rs in regions_list]
# Check that the intersection is as expected.
self.assertCountEqual(
ranges.RangeSet.from_regions(expected),
regions_list[0].intersection(*regions_list[1:]))
# Check that no one was modified.
for pre, post in zip(copies, regions_list):
self.assertCountEqual(pre, post)
def test_regions_and_exclude_regions_flags(self):
FLAGS.mode = 'calling'
FLAGS.ref = test_utils.CHR20_FASTA
FLAGS.reads = test_utils.CHR20_BAM
FLAGS.regions = 'chr20:10,000,000-11,000,000'
FLAGS.examples = 'examples.tfrecord'
FLAGS.exclude_regions = 'chr20:10,010,000-10,100,000'
options = make_examples.default_options(add_flags=True)
self.assertCountEqual(
list(
ranges.RangeSet(
make_examples.processing_regions_from_options(options))),
_from_literals_list(
['chr20:10,000,000-10,009,999', 'chr20:10,100,001-11,000,000']))
def test_detector_no_ranges(self):
range_set = ranges.RangeSet()
# don't have any ranges by default
self.assertEqual(bool(range_set), False)
# make sure we can call overlaps without any ranges
self.assertFalse(range_set.overlaps('chr1', 10))
def test_partitions_bad_interval_size_raises(self):
# list() is necessary to force the generator to execute.
with self.assertRaisesRegexp(ValueError, 'max_size'):
list(ranges.RangeSet([ranges.make_range('chrM', 0, 100)]).partition(-10))
with self.assertRaisesRegexp(ValueError, 'max_size'):
list(ranges.RangeSet([ranges.make_range('chrM', 0, 100)]).partition(0))
def test_overlaps_variant_empty_range(self):
variant = variants_pb2.Variant(reference_name='chr2', start=10, end=11)
empty_set = ranges.RangeSet()
self.assertEqual(
empty_set.variant_overlaps(variant, empty_set_return_value='foo'),
'foo')
def setUp(self):
self.labeler = variant_labeler.VariantLabeler(
vcf_reader=mock_vcf_reader(self.variants),
confident_regions=ranges.RangeSet(
[ranges.make_range(self.snp.reference_name, 10, 100)]))