def test_should_call_variants_with_touching_and_unsorted_regions(self):
self.calls_variants_in_bed_region(
"ACGCCCCCTGCAAAAAAAAAA", ["......T...T.........."],
expected_variant_stubs=[(6, "CCTGC", "TCTGT")],
bed_regions=[Interval(7, 12),
Interval(2, 7),
Interval(4, 5)])
def test_should_return_reads_that_overlap_both_intervals_twice(self):
all_reads = [
make_read(0, 2),
make_read(1, 3),
]
iterator = BAMRegionIterator((read for read in all_reads))
self.assertEqual(all_reads[0:1], list(iterator(Interval(0, 1))))
self.assertEqual(all_reads[0:2], list(iterator(Interval(1, 2))))
def test_should_not_miss_any_reads_between_regions(self):
all_reads = [
make_read(0, 1),
make_read(1, 2),
make_read(2, 3),
make_read(3, 4),
make_read(4, 5),
make_read(5, 6),
]
iterator = BAMRegionIterator((read for read in all_reads))
self.assertEqual(all_reads[0:2], list(iterator(Interval(0, 2))))
self.assertEqual(all_reads[2:3], list(iterator(Interval(2, 3))))
def test_should_return_two_sets_of_values_for_intervals_in_correct_order(self):
all_reads = [
make_read(0, 1),
make_read(1, 2),
make_read(2, 3),
make_read(3, 4),
make_read(4, 5),
make_read(5, 6),
]
iterator = BAMRegionIterator((read for read in all_reads))
self.assertEqual(all_reads[0:2], list(iterator(Interval(0, 2))))
self.assertEqual(all_reads[3:5], list(iterator(Interval(3, 5))))
def test_should_fail_for_regions_in_incorrect_order(self):
all_reads = [
make_read(0, 1),
make_read(1, 2),
make_read(2, 3),
make_read(3, 4),
make_read(4, 5),
make_read(5, 6),
]
iterator = BAMRegionIterator((read for read in all_reads))
self.assertEqual(all_reads[3:5], list(iterator(Interval(3, 5))))
with self.assertRaises(Exception):
print((iterator(Interval(0, 2))))
def test_should_call_variants_when_whole_read_within_region_with_compressed_bed_file(
self):
self.calls_variants_in_bed_region(
"ACGCCCCCTGCAAAAAAAAAA",
[".T...................", "...........C........."],
[".T...................", "...........C........."],
bed_regions=[Interval(0, 12)],
compress=True)
def test_should_call_only_variant_that_is_within_region(self):
self.calls_variants_in_bed_region(
"AAAAAAAAACGCCCCCTGCAAAAAAAAAA",
[".........T...................", "..................T.........."],
[
".........T...................",
".............................",
],
bed_regions=[Interval(8, 15)],
)
def test_should_return_nothing_if_interval_does_not_overlap_any_reads(self):
all_reads = [
make_read(0, 1),
make_read(1, 2),
make_read(2, 3),
make_read(3, 4),
]
iterator = BAMRegionIterator((read for read in all_reads))
actual_results = list(iterator(Interval(4, 6)))
self.assertEqual([], actual_results)
def test_should_only_return_reads_with_end_overlapping_interval(self):
all_reads = [
make_read(0, 1),
make_read(1, 2),
make_read(2, 3),
make_read(3, 4),
]
iterator = BAMRegionIterator((read for read in all_reads))
actual_results = list(iterator(Interval(2, 4)))
self.assertEqual(all_reads[2:4], actual_results)
def test_should_return_all_reads_if_entire_fetch_region_requested(self):
all_reads = [
make_read(0, 1),
make_read(1, 2),
make_read(2, 3),
make_read(3, 4),
]
iterator = BAMRegionIterator((read for read in all_reads))
actual_results = list(iterator(Interval(0, 4)))
self.assertEqual(all_reads, actual_results)
def test_should_return_overlapping_reads_from_middle_of_query_region(self):
all_reads = [
make_read(0, 1),
make_read(1, 2),
make_read(2, 3),
make_read(3, 4),
make_read(4, 5),
make_read(5, 6),
]
iterator = BAMRegionIterator((read for read in all_reads))
actual_results = list(iterator(Interval(2, 4)))
self.assertEqual(all_reads[2:4], actual_results)
def __init__(self, fetch_iterator):
IntervalRegionIterator.__init__(
self, fetch_iterator, lambda read: Interval(read.pos, read.aend))