def test_set_fuzzy(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
f.fuzzy = [(False, False), (False, False)]
self.assertEqual(f.fuzzy, [(False, False), (False, False)])
def test_get_metadata(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
f.metadata['name'] = 'sagB'
self.assertEqual(f.metadata, {'name': 'sagB', 'function': 'transport'})
def test_set_fuzzy(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
f.fuzzy = [(False, False), (False, False)]
self.assertEqual(f.fuzzy, [(False, False), (False, False)])
def test_get_metadata(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
f.metadata['name'] = 'sagB'
self.assertEqual(f.metadata, {'name': 'sagB', 'function': 'transport'})
def test_set_metadata_bad(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
for value in [1, '', None]:
with self.assertRaises(TypeError):
f.metadata = value
def test_set_metadata_bad(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
for value in [1, '', None]:
with self.assertRaises(TypeError):
f.metadata = value
def test_set_bounds(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
f.bounds = [(4, 7), (1, 3)]
self.assertEqual(f.bounds, [(1, 3), (4, 7)])
self.assertEqual(f.fuzzy, [(False, False), (False, False)])
self.assertEqual(self.im._is_stale_tree, True)
def test_set_bounds(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
f.bounds = [(4, 7), (1, 3)]
self.assertEqual(f.bounds, [(1, 3), (4, 7)])
self.assertEqual(f.fuzzy, [(False, False), (False, False)])
self.assertEqual(self.im._is_stale_tree, True)
def test_get_on_dropped(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2)],
fuzzy=[(True, False)],
metadata={'name': 'sagA'})
f.drop()
self.assertEqual(f.fuzzy, [(True, False)])
self.assertEqual(f.bounds, [(1, 2)])
self.assertEqual(f.metadata, {'name': 'sagA'})
def test_get_on_dropped(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2)],
fuzzy=[(True, False)],
metadata={'name': 'sagA'})
f.drop()
self.assertEqual(f.fuzzy, [(True, False)])
self.assertEqual(f.bounds, [(1, 2)])
self.assertEqual(f.metadata, {'name': 'sagA'})
def test_reverse(self):
self.im_2._reverse()
Interval(
interval_metadata=self.im_empty,
bounds=[(0, 6), (8, 9)],
metadata={'gene': 'sagA', 'bound': 0})
Interval(
interval_metadata=self.im_empty,
bounds=[(5, 7)],
metadata={'gene': 'sagB', 'bound': 0, 'spam': [0]})
self.assertEqual(self.im_2, self.im_empty)
def test_init_out_of_bounds(self):
with self.assertRaises(ValueError):
Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 101)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
with self.assertRaises(ValueError):
Interval(interval_metadata=self.im,
bounds=[(-1, 2), (4, 6)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
def test_repr(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2)],
metadata={'name': 'sagA'})
exp = (r"Interval\(interval_metadata=<[0-9]+>, bounds=\[\(1, 2\)\],"
" fuzzy=\[\(False, False\)\], metadata={'name': 'sagA'}\)")
obs = repr(f)
self.assertRegex(obs, exp)
# test for dropped
f.drop()
exp = (r"Interval\(dropped=True, bounds=\[\(1, 2\)\],"
" fuzzy=\[\(False, False\)\], metadata={'name': 'sagA'}\)")
obs = repr(f)
self.assertRegex(obs, exp)
def test_repr(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2)],
metadata={'name': 'sagA'})
exp = (r"Interval\(interval_metadata=<[0-9]+>, bounds=\[\(1, 2\)\],"
" fuzzy=\[\(False, False\)\], metadata={'name': 'sagA'}\)")
obs = repr(f)
self.assertRegex(obs, exp)
# test for dropped
f.drop()
exp = (r"Interval\(dropped=True, bounds=\[\(1, 2\)\],"
" fuzzy=\[\(False, False\)\], metadata={'name': 'sagA'}\)")
obs = repr(f)
self.assertRegex(obs, exp)
def test_set_bounds_bad(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
for value in [1, 's']:
with self.assertRaises(TypeError):
f.bounds = value
for value in [[(-1, 2)], # start < lower_bound
[(1, 101)], # end > upper_bound
[(3, 1)], # start < end
[('s', 1)], (), None]: # invalid values
with self.assertRaises(ValueError):
f.bounds = value
def test_drop(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2)],
metadata={'name': 'sagA'})
f.drop()
self.assertTrue(f._interval_metadata is None)
self.assertTrue(f.dropped)
self.assertTrue(f.bounds, [(1, 2)])
self.assertTrue(f.metadata, {'name': 'sagA'})
# test the idempotence
f.drop()
self.assertTrue(f._interval_metadata is None)
self.assertTrue(f.dropped)
self.assertTrue(f.bounds, [(1, 2)])
self.assertTrue(f.metadata, {'name': 'sagA'})
def test_init_default(self):
f = Interval(self.im, bounds=[(0, 2), (4, self.upper_bound)])
self.assertTrue(f._interval_metadata is not None)
self.assertListEqual(f.bounds, [(0, 2), (4, self.upper_bound)])
self.assertListEqual(f.fuzzy, [(False, False), (False, False)])
self.assertDictEqual(f.metadata, {})
def test_set_bounds_bad(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={'name': 'sagA', 'function': 'transport'})
for value in [1, 's']:
with self.assertRaises(TypeError):
f.bounds = value
for value in [[(-1, 2)], # start < lower_bound
[(1, 101)], # end > upper_bound
[(3, 1)], # start < end
[(1, 1)], # start == end
[('s', 1)], (), None]: # invalid values
with self.assertRaises(ValueError):
f.bounds = value
def test_init_no_interval_metadata(self):
with self.assertRaises(TypeError):
Interval(interval_metadata=None,
bounds=[(4, 7)],
metadata={
'name': 'sagA',
'function': 'transport'
})
def setUp(self):
self.upper_bound = 10
self.im_empty = IntervalMetadata(self.upper_bound)
self.im_1 = IntervalMetadata(self.upper_bound)
self.im_1_1 = Interval(
interval_metadata=self.im_1,
bounds=[(1, 2), (4, self.upper_bound)],
metadata={'gene': 'sagA', 'bound': 0})
self.im_2 = IntervalMetadata(self.upper_bound)
self.im_2_1 = Interval(
interval_metadata=self.im_2,
bounds=[(1, 2), (4, self.upper_bound)],
metadata={'gene': 'sagA', 'bound': 0})
self.im_2_2 = Interval(
interval_metadata=self.im_2,
bounds=[(3, 5)],
metadata={'gene': 'sagB', 'bound': 0, 'spam': [0]})
def test_init_bad_fuzzy(self):
with self.assertRaises(ValueError):
Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(False, False)],
metadata={
'name': 'sagA',
'function': 'transport'
})
def test_init_iterables(self):
f = Interval(interval_metadata=self.im,
bounds=((1, 2), (4, 7)),
fuzzy=((True, False), (False, False)),
metadata={'name': 'sagA', 'function': 'transport'})
self.assertTrue(f._interval_metadata is not None)
self.assertListEqual(f.bounds, [(1, 2), (4, 7)])
self.assertListEqual(f.fuzzy, [(True, False), (False, False)])
self.assertDictEqual(f.metadata, {'name': 'sagA',
'function': 'transport'})
def test_init_bounds_scrambled(self):
f = Interval(interval_metadata=self.im,
bounds=[(4, 7), (1, 2)],
fuzzy=[(True, False), (False, True)],
metadata={'name': 'sagA', 'function': 'transport'})
self.assertTrue(f._interval_metadata is not None)
self.assertListEqual(f.bounds, [(1, 2), (4, 7)])
self.assertListEqual(f.fuzzy, [(False, True), (True, False)])
self.assertDictEqual(f.metadata, {'name': 'sagA',
'function': 'transport'})
def test_eq(self):
f0 = Interval(interval_metadata=self.im,
bounds=[(4, 7), (1, 2)],
fuzzy=[(False, False), (True, False)],
metadata={
'name': 'sagA',
'function': 'transport'
})
f1 = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={
'name': 'sagA',
'function': 'transport'
})
f2 = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={
'name': 'sagA',
'function': 'transport'
})
f3 = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, True), (False, False)],
metadata={
'name': 'sagA',
'function': 'transport'
})
f4 = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 8)],
fuzzy=[(True, False), (False, False)],
metadata={
'name': 'sagA',
'function': 'transport'
})
f5 = Interval(interval_metadata=self.im,
bounds=[(1, 2), (4, 7)],
fuzzy=[(True, False), (False, False)],
metadata={
'name': 'sagB',
'function': 'transport'
})
# scramble bounds/fuzzy
self.assertReallyEqual(f0, f1)
self.assertReallyEqual(f2, f1)
# diff fuzzy
self.assertReallyNotEqual(f1, f3)
# diff bounds
self.assertReallyNotEqual(f1, f4)
# diff metadata
self.assertReallyNotEqual(f1, f5)
def test_init_generator(self):
def gen():
for x in [(1, 2), (4, 7)]:
yield x
f = Interval(interval_metadata=self.im,
bounds=gen(),
fuzzy=((True, False), (False, False)),
metadata={'name': 'sagA', 'function': 'transport'})
self.assertTrue(f._interval_metadata is not None)
self.assertListEqual(f.bounds, [(1, 2), (4, 7)])
self.assertListEqual(f.fuzzy, [(True, False), (False, False)])
self.assertDictEqual(f.metadata, {'name': 'sagA',
'function': 'transport'})
def test_set_delete_on_dropped(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2)],
fuzzy=[(True, False)],
metadata={'name': 'sagA'})
f.drop()
with self.assertRaises(RuntimeError):
f.fuzzy = None
with self.assertRaises(RuntimeError):
f.bounds = [(1, 2)]
with self.assertRaises(RuntimeError):
f.metadata = {}
with self.assertRaises(RuntimeError):
del f.fuzzy
with self.assertRaises(RuntimeError):
del f.metadata
def test_sort(self):
interval = Interval(
self.im_2,
[(1, 2), (3, 8)],
metadata={'gene': 'sagA', 'bound': 0})
im = deepcopy(self.im_2)
self.im_2.sort(False)
# check sorting does not have other side effects
self.assertEqual(im, self.im_2)
self.assertEqual(self.im_2._intervals,
[self.im_2_2, self.im_2_1, interval])
self.im_2.sort()
self.assertEqual(im, self.im_2)
self.assertEqual(self.im_2._intervals,
[interval, self.im_2_1, self.im_2_2])
self.im_empty.sort()
self.assertEqual(self.im_empty, IntervalMetadata(self.upper_bound))
def test_drop(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2)],
metadata={'name': 'sagA'})
f.drop()
self.assertTrue(f._interval_metadata is None)
self.assertTrue(f.dropped)
self.assertTrue(f.bounds, [(1, 2)])
self.assertTrue(f.metadata, {'name': 'sagA'})
# test the idempotence
f.drop()
self.assertTrue(f._interval_metadata is None)
self.assertTrue(f.dropped)
self.assertTrue(f.bounds, [(1, 2)])
self.assertTrue(f.metadata, {'name': 'sagA'})
def test_set_delete_on_dropped(self):
f = Interval(interval_metadata=self.im,
bounds=[(1, 2)],
fuzzy=[(True, False)],
metadata={'name': 'sagA'})
f.drop()
with self.assertRaises(RuntimeError):
f.fuzzy = None
with self.assertRaises(RuntimeError):
f.bounds = [(1, 2)]
with self.assertRaises(RuntimeError):
f.metadata = {}
with self.assertRaises(RuntimeError):
del f.fuzzy
with self.assertRaises(RuntimeError):
del f.metadata
def test_init_empty_metadata(self):
for i in 0, 1:
# test that no exception is raised
Interval(interval_metadata=self.im, bounds=[(i, i)])
def test_init_empty(self):
for i in 0, 1:
with self.assertRaises(ValueError):
Interval(interval_metadata=self.im, bounds=[(i, i)])