def test_concat_empty(self):
for i in 0, 1, 2:
obs = IntervalMetadata.concat([self.im_empty] * i)
exp = IntervalMetadata(self.upper_bound * i)
self.assertEqual(obs, exp)
obs = IntervalMetadata.concat([])
self.assertEqual(obs, IntervalMetadata(0))
def test_concat_empty(self):
for i in 0, 1, 2:
obs = IntervalMetadata.concat([self.im_empty] * i)
exp = IntervalMetadata(self.upper_bound * i)
self.assertEqual(obs, exp)
obs = IntervalMetadata.concat([])
self.assertEqual(obs, IntervalMetadata(0))
def test_upper_bound_is_none(self):
im = IntervalMetadata(None)
# should not raise error
im.add([(0, 1000000000)])
self.assertIsNone(im.upper_bound)
with self.assertRaisesRegex(TypeError, 'upper bound is `None`'):
im._reverse()
with self.assertRaisesRegex(TypeError, 'upper bound is `None`'):
IntervalMetadata.concat([self.im_1, im])
def test_upper_bound_is_none(self):
im = IntervalMetadata(None)
# should not raise error
im.add([(0, 1000000000)])
self.assertIsNone(im.upper_bound)
with self.assertRaisesRegex(
TypeError, r'upper bound is `None`'):
im._reverse()
with self.assertRaisesRegex(
TypeError, r'upper bound is `None`'):
IntervalMetadata.concat([self.im_1, im])
def test_concat(self):
im1 = IntervalMetadata(3)
im2 = IntervalMetadata(4)
im3 = IntervalMetadata(5)
im1.add([(0, 2)], [(True, True)])
im2.add([(0, 3)], [(True, False)], {'gene': 'sagA'})
im2.add([(2, 4)], metadata={'gene': 'sagB'})
im3.add([(1, 5)], [(False, True)], {'gene': 'sagC'})
obs = IntervalMetadata.concat([im1, im2, im3])
exp = IntervalMetadata(12)
exp.add(bounds=[(0, 2)], fuzzy=[(True, True)])
exp.add(bounds=[(3, 6)], fuzzy=[(True, False)],
metadata={'gene': 'sagA'})
exp.add(bounds=[(5, 7)], metadata={'gene': 'sagB'})
exp.add(bounds=[(8, 12)], fuzzy=[(False, True)],
metadata={'gene': 'sagC'})
self.assertEqual(obs, exp)
def test_concat(self):
im1 = IntervalMetadata(3)
im2 = IntervalMetadata(4)
im3 = IntervalMetadata(5)
im1.add([(0, 2)], [(True, True)])
im2.add([(0, 3)], [(True, False)], {'gene': 'sagA'})
im2.add([(2, 4)], metadata={'gene': 'sagB'})
im3.add([(1, 5)], [(False, True)], {'gene': 'sagC'})
obs = IntervalMetadata.concat([im1, im2, im3])
exp = IntervalMetadata(12)
exp.add(bounds=[(0, 2)], fuzzy=[(True, True)])
exp.add(bounds=[(3, 6)], fuzzy=[(True, False)],
metadata={'gene': 'sagA'})
exp.add(bounds=[(5, 7)], metadata={'gene': 'sagB'})
exp.add(bounds=[(8, 12)], fuzzy=[(False, True)],
metadata={'gene': 'sagC'})
self.assertEqual(obs, exp)
