def test_case3(self):
# case 3: longer >= 2 x len shorter and < 50% shorter overlaps longer, remove shorter
starts_ends = [(7000, 8000), (7501, 8000)]
expected = [(7000, 8000)]
alignments = [
TruthAlignment(MockAlignment(start, end, end - start))
for start, end in starts_ends
]
filtered = [
(f.start, f.end)
for f in TruthAlignment._filter_alignments(alignments, full_region)
]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
# case 3 (contained): shorter contained within longer, shorter should be removed
starts_ends = [(0, 1000), (100, 200)]
expected = [(0, 1000)]
alignments = [
TruthAlignment(MockAlignment(start, end, end - start))
for start, end in starts_ends
]
filtered = [
(f.start, f.end)
for f in TruthAlignment._filter_alignments(alignments, full_region)
]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
def test_many(self):
starts_ends = [(0, 1000), (100, 200),
(3000, 4000), (3800, 4299),
(7000, 8000), (7501, 8000),
(2000, 2999), (2500, 3000),
(5000, 5999), (5900, 6401),]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=1)]
expected = [(0, 1000), (3000, 4000), (4000, 4299), (5000, 5900), (5999, 6401), (7000, 8000)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
starts_ends_m = starts_ends + [(0, 5000)]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends_m]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=1)]
expected = [(0, 5000), (5000, 5900), (5999, 6401), (7000, 8000)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
starts_ends_m = starts_ends + [(0, 5200)]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends_m]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=1)]
expected = [(0, 5200), (5200, 5900), (5999, 6401), (7000, 8000)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
starts_ends_m = starts_ends + [(0, 10000)]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends_m]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=1)]
expected = [(0, 10000)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
def test_case2(self):
# case 2: longer < 2 x len shorter and < 50% shorter overlaps longer, trim both
starts_ends = [(5000, 5999), (5900, 6401)]
alignments = [
TruthAlignment(MockAlignment(start, end, end - start))
for start, end in starts_ends
]
filtered = [(f.start, f.end)
for f in TruthAlignment._filter_alignments(
alignments, full_region, min_length=401)]
expected = [(5000, 5900), (5999, 6401)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
filtered = [(f.start, f.end)
for f in TruthAlignment._filter_alignments(
alignments, full_region, min_length=899)]
expected = [(5000, 5900)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
filtered = [(f.start, f.end)
for f in TruthAlignment._filter_alignments(
alignments, full_region, min_length=1000)]
expected = []
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(
filtered, expected))
def test_case4(self):
# case 4: longer >= 2 x len shorter and < 50% shorter overlaps longer, trim shorter
starts_ends = [(3000, 4000), (3800, 4299)]
expected = [(3000, 4000), (4000, 4299)]
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments, min_length=298)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))
def test_case1(self):
# case 1: longer < 2 x len shorter and >= 50% of shorter overlaps longer both should be removed
starts_ends = [(2000, 2999), (2500, 3000)]
expected = []
alignments = [TruthAlignment(MockAlignment(start, end, end-start)) for start, end in starts_ends]
filtered = [(f.start, f.end) for f in TruthAlignment.filter_alignments(alignments)]
if filtered != expected:
raise AssertionError('got {}, expected {}'.format(filtered, expected))