def test_validate_counts_vectors_suppress_cast(self):
# suppress_cast is passed through to _validate_counts_vector
obs_u, obs_v = _validate_counts_vectors(
[42.2, 42.1, 0], [42.2, 42.1, 1.0], suppress_cast=True)
npt.assert_array_equal(obs_u, np.array([42.2, 42.1, 0]))
npt.assert_array_equal(obs_v, np.array([42.2, 42.1, 1.0]))
self.assertEqual(obs_u.dtype, float)
self.assertEqual(obs_v.dtype, float)
with self.assertRaises(TypeError):
_validate_counts_vectors([0.0], [1], suppress_cast=False)
def test_validate_counts_vectors_suppress_cast(self):
# suppress_cast is passed through to _validate_counts_vector
obs_u, obs_v = _validate_counts_vectors([42.2, 42.1, 0],
[42.2, 42.1, 1.0],
suppress_cast=True)
npt.assert_array_equal(obs_u, np.array([42.2, 42.1, 0]))
npt.assert_array_equal(obs_v, np.array([42.2, 42.1, 1.0]))
self.assertEqual(obs_u.dtype, float)
self.assertEqual(obs_v.dtype, float)
with self.assertRaises(TypeError):
_validate_counts_vectors([0.0], [1], suppress_cast=False)
def test_validate_counts_vectors_invalid_input(self):
# checks that are caught by the calls to _validate_counts_vector
with self.assertRaises(ValueError):
_validate_counts_vectors([0, 1, 1, 0, 2], [0, 0, 2, -1, 3])
with self.assertRaises(ValueError):
_validate_counts_vectors([0, 0, 2, -1, 3], [0, 1, 1, 0, 2])
# len of vectors not equal
u_counts = [1, 2]
v_counts = [1, 1, 1]
self.assertRaises(ValueError, _validate_counts_vectors, u_counts,
v_counts)
u_counts = [1, 2, 3]
v_counts = [1, 1]
self.assertRaises(ValueError, _validate_counts_vectors, u_counts,
v_counts)
def test_validate_counts_vectors_invalid_input(self):
# checks that are caught by the calls to _validate_counts_vector
with self.assertRaises(ValueError):
_validate_counts_vectors([0, 1, 1, 0, 2], [0, 0, 2, -1, 3])
with self.assertRaises(ValueError):
_validate_counts_vectors([0, 0, 2, -1, 3], [0, 1, 1, 0, 2])
# len of vectors not equal
u_counts = [1, 2]
v_counts = [1, 1, 1]
self.assertRaises(ValueError, _validate_counts_vectors, u_counts,
v_counts)
u_counts = [1, 2, 3]
v_counts = [1, 1]
self.assertRaises(ValueError, _validate_counts_vectors, u_counts,
v_counts)
def test_validate_counts_vectors(self):
# basic valid input (n=2)
obs_u, obs_v = _validate_counts_vectors([0, 1, 1, 0, 2],
[0, 0, 2, 1, 3])
npt.assert_array_equal(obs_u, np.array([0, 1, 1, 0, 2]))
npt.assert_array_equal(obs_v, np.array([0, 0, 2, 1, 3]))
# basic valid input (n=3)
actual = _validate_counts_vectors([0, 1, 1, 0, 2], [0, 0, 2, 1, 3],
[1, 1, 1, 1, 1])
npt.assert_array_equal(actual[0], np.array([0, 1, 1, 0, 2]))
npt.assert_array_equal(actual[1], np.array([0, 0, 2, 1, 3]))
npt.assert_array_equal(actual[2], np.array([1, 1, 1, 1, 1]))
# empty counts vectors
obs_u, obs_v = _validate_counts_vectors(np.array([], dtype=int),
np.array([], dtype=int))
npt.assert_array_equal(obs_u, np.array([]))
npt.assert_array_equal(obs_v, np.array([]))
def test_validate_counts_vectors(self):
# basic valid input (n=2)
obs_u, obs_v = _validate_counts_vectors([0, 1, 1, 0, 2],
[0, 0, 2, 1, 3])
npt.assert_array_equal(obs_u, np.array([0, 1, 1, 0, 2]))
npt.assert_array_equal(obs_v, np.array([0, 0, 2, 1, 3]))
# basic valid input (n=3)
actual = _validate_counts_vectors([0, 1, 1, 0, 2],
[0, 0, 2, 1, 3],
[1, 1, 1, 1, 1])
npt.assert_array_equal(actual[0], np.array([0, 1, 1, 0, 2]))
npt.assert_array_equal(actual[1], np.array([0, 0, 2, 1, 3]))
npt.assert_array_equal(actual[2], np.array([1, 1, 1, 1, 1]))
# empty counts vectors
obs_u, obs_v = _validate_counts_vectors(np.array([], dtype=int),
np.array([], dtype=int))
npt.assert_array_equal(obs_u, np.array([]))
npt.assert_array_equal(obs_v, np.array([]))
def _validate(u_counts, v_counts, otu_ids, tree):
_validate_counts_vectors(u_counts, v_counts, suppress_cast=True)
_validate_otu_ids_and_tree(counts=u_counts, otu_ids=otu_ids, tree=tree)
def _validate(u_counts, v_counts, otu_ids, tree):
_validate_counts_vectors(u_counts, v_counts, suppress_cast=True)
_validate_otu_ids_and_tree(counts=u_counts, otu_ids=otu_ids, tree=tree)
