def test_to_series_4x4(self):
dm = DistanceMatrix([[0.0, 0.2, 0.3, 0.4], [0.2, 0.0, 0.5, 0.6],
[0.3, 0.5, 0.0, 0.7], [0.4, 0.6, 0.7, 0.0]],
['a', 'b', 'c', 'd'])
series = dm.to_series()
exp = pd.Series([0.2, 0.3, 0.4, 0.5, 0.6, 0.7],
index=pd.Index([('a', 'b'), ('a', 'c'), ('a', 'd'),
('b', 'c'), ('b', 'd'), ('c', 'd')]))
assert_series_almost_equal(series, exp)
def test_to_series_4x4(self):
dm = DistanceMatrix([
[0, 0.25, 0.75, 0.75],
[0.25, 0.0, 0.5, 0.5],
[0.75, 0.5, 0.0, 0.0],
[0.75, 0.5, 0.0, 0.0]], ['a', 'b', 'c', 'd'])
series = dm.to_series()
exp = pd.Series([0.25, 0.75, 0.75, 0.25, 0.5, 0.5, 0.75, 0.5, 0.75, 0.5],
index = [('a', 'b'), ('a', 'c'), ('a', 'd'), ('b', 'a'), ('b', 'c'), ('b', 'd'),
('c', 'a'), ('c', 'b'), ('d', 'a'), ('d', 'b')])
assert_series_almost_equal(series, exp)
def test_to_series_4x4(self):
dm = DistanceMatrix([
[0.0, 0.2, 0.3, 0.4],
[0.2, 0.0, 0.5, 0.6],
[0.3, 0.5, 0.0, 0.7],
[0.4, 0.6, 0.7, 0.0]], ['a', 'b', 'c', 'd'])
series = dm.to_series()
exp = pd.Series([0.2, 0.3, 0.4, 0.5, 0.6, 0.7],
index=pd.Index([('a', 'b'), ('a', 'c'), ('a', 'd'),
('b', 'c'), ('b', 'd'), ('c', 'd')]))
assert_series_almost_equal(series, exp)
class DistanceMatrixTests(DissimilarityMatrixTestData):
def setUp(self):
super(DistanceMatrixTests, self).setUp()
self.dm_1x1 = DistanceMatrix(self.dm_1x1_data, ['a'])
self.dm_2x2 = DistanceMatrix(self.dm_2x2_data, ['a', 'b'])
self.dm_3x3 = DistanceMatrix(self.dm_3x3_data, ['a', 'b', 'c'])
self.dms = [self.dm_1x1, self.dm_2x2, self.dm_3x3]
self.dm_condensed_forms = [
np.array([]),
np.array([0.123]),
np.array([0.01, 4.2, 12.0])
]
def test_init_from_condensed_form(self):
data = [1, 2, 3]
exp = DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['0', '1', '2'])
res = DistanceMatrix(data)
self.assertEqual(exp, res)
def test_init_invalid_input(self):
# Asymmetric.
data = [[0.0, 2.0], [1.0, 0.0]]
with self.assertRaises(DistanceMatrixError):
DistanceMatrix(data, ['a', 'b'])
# Non-hollow
data = [[1.0, 2.0], [2.0, 1.0]]
with self.assertRaises(DistanceMatrixError):
DistanceMatrix(data, ['a', 'b'])
# Ensure that the superclass validation is still being performed.
with self.assertRaises(DissimilarityMatrixError):
DistanceMatrix([[1, 2, 3]], ['a'])
def test_init_nans(self):
with self.assertRaisesRegex(DistanceMatrixError, r'NaNs'):
DistanceMatrix([[0.0, np.nan], [np.nan, 0.0]], ['a', 'b'])
def test_from_iterable_no_key(self):
iterable = (x for x in range(4))
exp = DistanceMatrix([[0, 1, 2, 3], [1, 0, 1, 2], [2, 1, 0, 1],
[3, 2, 1, 0]])
res = DistanceMatrix.from_iterable(iterable, lambda a, b: abs(b - a))
self.assertEqual(res, exp)
def test_from_iterable_validate_equal_valid_data(self):
validate_true = DistanceMatrix.from_iterable((x for x in range(4)),
lambda a, b: abs(b - a),
validate=True)
validate_false = DistanceMatrix.from_iterable((x for x in range(4)),
lambda a, b: abs(b - a),
validate=False)
self.assertEqual(validate_true, validate_false)
def test_from_iterable_validate_false(self):
iterable = (x for x in range(4))
exp = DistanceMatrix([[0, 1, 2, 3], [1, 0, 1, 2], [2, 1, 0, 1],
[3, 2, 1, 0]])
res = DistanceMatrix.from_iterable(iterable,
lambda a, b: abs(b - a),
validate=False)
self.assertEqual(res, exp)
def test_from_iterable_validate_non_hollow(self):
iterable = (x for x in range(4))
with self.assertRaises(DistanceMatrixError):
DistanceMatrix.from_iterable(iterable, lambda a, b: 1)
def test_from_iterable_validate_false_non_symmetric(self):
exp = DistanceMatrix([[0, 1, 2, 3], [1, 0, 1, 2], [2, 1, 0, 1],
[3, 2, 1, 0]])
res = DistanceMatrix.from_iterable((x for x in range(4)),
lambda a, b: a - b,
validate=False)
self.assertEqual(res, exp)
def test_from_iterable_validate_asym(self):
iterable = (x for x in range(4))
with self.assertRaises(DistanceMatrixError):
DistanceMatrix.from_iterable(iterable, lambda a, b: b - a)
def test_from_iterable_with_key(self):
iterable = (x for x in range(4))
exp = DistanceMatrix(
[[0, 1, 2, 3], [1, 0, 1, 2], [2, 1, 0, 1], [3, 2, 1, 0]],
['0', '1', '4', '9'])
res = DistanceMatrix.from_iterable(iterable,
lambda a, b: abs(b - a),
key=lambda x: str(x**2))
self.assertEqual(res, exp)
def test_from_iterable_empty(self):
with self.assertRaises(DissimilarityMatrixError):
DistanceMatrix.from_iterable([], lambda x: x)
def test_from_iterable_single(self):
exp = DistanceMatrix([[0]])
res = DistanceMatrix.from_iterable(["boo"], lambda a, b: 0)
self.assertEqual(res, exp)
def test_from_iterable_with_keys(self):
iterable = (x for x in range(4))
exp = DistanceMatrix(
[[0, 1, 2, 3], [1, 0, 1, 2], [2, 1, 0, 1], [3, 2, 1, 0]],
['0', '1', '4', '9'])
res = DistanceMatrix.from_iterable(iterable,
lambda a, b: abs(b - a),
keys=iter(['0', '1', '4', '9']))
self.assertEqual(res, exp)
def test_from_iterable_with_key_and_keys(self):
iterable = (x for x in range(4))
with self.assertRaises(ValueError):
DistanceMatrix.from_iterable(iterable,
lambda a, b: abs(b - a),
key=str,
keys=['1', '2', '3', '4'])
def test_from_iterable_scipy_hamming_metric_with_metadata(self):
# test for #1254
seqs = [
Sequence('ACGT'),
Sequence('ACGA', metadata={'id': 'seq1'}),
Sequence('AAAA', metadata={'id': 'seq2'}),
Sequence('AAAA', positional_metadata={'qual': range(4)})
]
exp = DistanceMatrix([[0, 0.25, 0.75, 0.75], [0.25, 0.0, 0.5, 0.5],
[0.75, 0.5, 0.0, 0.0], [0.75, 0.5, 0.0, 0.0]],
['a', 'b', 'c', 'd'])
dm = DistanceMatrix.from_iterable(
seqs,
metric=scipy.spatial.distance.hamming,
keys=['a', 'b', 'c', 'd'])
self.assertEqual(dm, exp)
def test_from_iterable_skbio_hamming_metric_with_metadata(self):
# test for #1254
seqs = [
Sequence('ACGT'),
Sequence('ACGA', metadata={'id': 'seq1'}),
Sequence('AAAA', metadata={'id': 'seq2'}),
Sequence('AAAA', positional_metadata={'qual': range(4)})
]
exp = DistanceMatrix([[0, 0.25, 0.75, 0.75], [0.25, 0.0, 0.5, 0.5],
[0.75, 0.5, 0.0, 0.0], [0.75, 0.5, 0.0, 0.0]],
['a', 'b', 'c', 'd'])
dm = DistanceMatrix.from_iterable(
seqs,
metric=skbio.sequence.distance.hamming,
keys=['a', 'b', 'c', 'd'])
self.assertEqual(dm, exp)
def test_condensed_form(self):
for dm, condensed in zip(self.dms, self.dm_condensed_forms):
obs = dm.condensed_form()
self.assertTrue(np.array_equal(obs, condensed))
def test_permute_condensed(self):
# Can't really permute a 1x1 or 2x2...
for _ in range(2):
obs = self.dm_1x1.permute(condensed=True)
npt.assert_equal(obs, np.array([]))
for _ in range(2):
obs = self.dm_2x2.permute(condensed=True)
npt.assert_equal(obs, np.array([0.123]))
dm_copy = self.dm_3x3.copy()
np.random.seed(0)
obs = self.dm_3x3.permute(condensed=True)
npt.assert_equal(obs, np.array([12.0, 4.2, 0.01]))
obs = self.dm_3x3.permute(condensed=True)
npt.assert_equal(obs, np.array([4.2, 12.0, 0.01]))
# Ensure dm hasn't changed after calling permute() on it a couple of
# times.
self.assertEqual(self.dm_3x3, dm_copy)
def test_permute_not_condensed(self):
obs = self.dm_1x1.permute()
self.assertEqual(obs, self.dm_1x1)
self.assertFalse(obs is self.dm_1x1)
obs = self.dm_2x2.permute()
self.assertEqual(obs, self.dm_2x2)
self.assertFalse(obs is self.dm_2x2)
np.random.seed(0)
exp = DistanceMatrix([[0, 12, 4.2], [12, 0, 0.01], [4.2, 0.01, 0]],
self.dm_3x3.ids)
obs = self.dm_3x3.permute()
self.assertEqual(obs, exp)
exp = DistanceMatrix([[0, 4.2, 12], [4.2, 0, 0.01], [12, 0.01, 0]],
self.dm_3x3.ids)
obs = self.dm_3x3.permute()
self.assertEqual(obs, exp)
def test_eq(self):
# Compare DistanceMatrix to DissimilarityMatrix, where both have the
# same data and IDs.
eq_dm = DissimilarityMatrix(self.dm_3x3_data, ['a', 'b', 'c'])
self.assertTrue(self.dm_3x3 == eq_dm)
self.assertTrue(eq_dm == self.dm_3x3)
def test_to_series_1x1(self):
series = self.dm_1x1.to_series()
exp = pd.Series([], index=[])
assert_series_almost_equal(series, exp)
def test_to_series_2x2(self):
series = self.dm_2x2.to_series()
exp = pd.Series([0.123], index=pd.Index([('a', 'b')]))
assert_series_almost_equal(series, exp)
def test_to_series_4x4(self):
dm = DistanceMatrix([[0.0, 0.2, 0.3, 0.4], [0.2, 0.0, 0.5, 0.6],
[0.3, 0.5, 0.0, 0.7], [0.4, 0.6, 0.7, 0.0]],
['a', 'b', 'c', 'd'])
series = dm.to_series()
exp = pd.Series([0.2, 0.3, 0.4, 0.5, 0.6, 0.7],
index=pd.Index([('a', 'b'), ('a', 'c'), ('a', 'd'),
('b', 'c'), ('b', 'd'), ('c', 'd')]))
assert_series_almost_equal(series, exp)
def test_to_series_default_ids(self):
series = DistanceMatrix(self.dm_2x2_data).to_series()
exp = pd.Series([0.123], index=pd.Index([('0', '1')]))
assert_series_almost_equal(series, exp)
def test_validate_asym_shape(self):
# first check it actually likes good matrices
data_good = np.array([[0., 42.], [42., 0.]])
data_sym, data_hollow = is_symmetric_and_hollow(data_good)
self.assertEqual(data_sym, True)
del data_sym
self.assertEqual(data_hollow, True)
del data_hollow
data_sym = skbio.stats.distance._utils.is_symmetric(data_good)
self.assertEqual(data_sym, True)
del data_sym
data_hollow = skbio.stats.distance._utils.is_hollow(data_good)
self.assertEqual(data_hollow, True)
del data_hollow
self.dm_3x3._validate_shape(data_good)
del data_good
# _validate_shap checks just the shape, not the content
bad_data = np.array([[1., 2.], [3., 4.]])
data_sym, data_hollow = is_symmetric_and_hollow(bad_data)
self.assertEqual(data_sym, False)
del data_sym
self.assertEqual(data_hollow, False)
del data_hollow
data_sym = skbio.stats.distance._utils.is_symmetric(bad_data)
self.assertEqual(data_sym, False)
del data_sym
data_hollow = skbio.stats.distance._utils.is_hollow(bad_data)
self.assertEqual(data_hollow, False)
del data_hollow
self.dm_3x3._validate_shape(bad_data)
del bad_data
# re-try with partially bad data
bad_data = np.array([[0., 2.], [3., 0.]])
data_sym, data_hollow = is_symmetric_and_hollow(bad_data)
self.assertEqual(data_sym, False)
del data_sym
self.assertEqual(data_hollow, True)
del data_hollow
data_sym = skbio.stats.distance._utils.is_symmetric(bad_data)
self.assertEqual(data_sym, False)
del data_sym
data_hollow = skbio.stats.distance._utils.is_hollow(bad_data)
self.assertEqual(data_hollow, True)
del data_hollow
self.dm_3x3._validate_shape(bad_data)
del bad_data
class DistanceMatrixTests(DissimilarityMatrixTestData):
def setUp(self):
super(DistanceMatrixTests, self).setUp()
self.dm_1x1 = DistanceMatrix(self.dm_1x1_data, ['a'])
self.dm_2x2 = DistanceMatrix(self.dm_2x2_data, ['a', 'b'])
self.dm_3x3 = DistanceMatrix(self.dm_3x3_data, ['a', 'b', 'c'])
self.dms = [self.dm_1x1, self.dm_2x2, self.dm_3x3]
self.dm_condensed_forms = [np.array([]), np.array([0.123]),
np.array([0.01, 4.2, 12.0])]
def test_init_from_condensed_form(self):
data = [1, 2, 3]
exp = DistanceMatrix([[0, 1, 2],
[1, 0, 3],
[2, 3, 0]], ['0', '1', '2'])
res = DistanceMatrix(data)
self.assertEqual(exp, res)
def test_init_invalid_input(self):
# Asymmetric.
data = [[0.0, 2.0], [1.0, 0.0]]
with self.assertRaises(DistanceMatrixError):
DistanceMatrix(data, ['a', 'b'])
# Non-hollow
data = [[1.0, 2.0], [2.0, 1.0]]
with self.assertRaises(DistanceMatrixError):
DistanceMatrix(data, ['a', 'b'])
# Ensure that the superclass validation is still being performed.
with self.assertRaises(DissimilarityMatrixError):
DistanceMatrix([[1, 2, 3]], ['a'])
def test_init_nans(self):
with self.assertRaisesRegex(DistanceMatrixError, 'NaNs'):
DistanceMatrix([[0.0, np.nan], [np.nan, 0.0]], ['a', 'b'])
def test_from_iterable_no_key(self):
iterable = (x for x in range(4))
exp = DistanceMatrix([[0, 1, 2, 3],
[1, 0, 1, 2],
[2, 1, 0, 1],
[3, 2, 1, 0]])
res = DistanceMatrix.from_iterable(iterable, lambda a, b: abs(b - a))
self.assertEqual(res, exp)
def test_from_iterable_validate_equal_valid_data(self):
validate_true = DistanceMatrix.from_iterable((x for x in range(4)),
lambda a, b: abs(b - a),
validate=True)
validate_false = DistanceMatrix.from_iterable((x for x in range(4)),
lambda a, b: abs(b - a),
validate=False)
self.assertEqual(validate_true, validate_false)
def test_from_iterable_validate_false(self):
iterable = (x for x in range(4))
exp = DistanceMatrix([[0, 1, 2, 3],
[1, 0, 1, 2],
[2, 1, 0, 1],
[3, 2, 1, 0]])
res = DistanceMatrix.from_iterable(iterable, lambda a, b: abs(b - a),
validate=False)
self.assertEqual(res, exp)
def test_from_iterable_validate_non_hollow(self):
iterable = (x for x in range(4))
with self.assertRaises(DistanceMatrixError):
DistanceMatrix.from_iterable(iterable, lambda a, b: 1)
def test_from_iterable_validate_false_non_symmetric(self):
exp = DistanceMatrix([[0, 1, 2, 3],
[1, 0, 1, 2],
[2, 1, 0, 1],
[3, 2, 1, 0]])
res = DistanceMatrix.from_iterable((x for x in range(4)),
lambda a, b: a - b,
validate=False)
self.assertEqual(res, exp)
def test_from_iterable_validate_asym(self):
iterable = (x for x in range(4))
with self.assertRaises(DistanceMatrixError):
DistanceMatrix.from_iterable(iterable, lambda a, b: b - a)
def test_from_iterable_with_key(self):
iterable = (x for x in range(4))
exp = DistanceMatrix([[0, 1, 2, 3],
[1, 0, 1, 2],
[2, 1, 0, 1],
[3, 2, 1, 0]], ['0', '1', '4', '9'])
res = DistanceMatrix.from_iterable(iterable, lambda a, b: abs(b - a),
key=lambda x: str(x**2))
self.assertEqual(res, exp)
def test_from_iterable_empty(self):
with self.assertRaises(DissimilarityMatrixError):
DistanceMatrix.from_iterable([], lambda x: x)
def test_from_iterable_single(self):
exp = DistanceMatrix([[0]])
res = DistanceMatrix.from_iterable(["boo"], lambda a, b: 0)
self.assertEqual(res, exp)
def test_from_iterable_with_keys(self):
iterable = (x for x in range(4))
exp = DistanceMatrix([[0, 1, 2, 3],
[1, 0, 1, 2],
[2, 1, 0, 1],
[3, 2, 1, 0]], ['0', '1', '4', '9'])
res = DistanceMatrix.from_iterable(iterable, lambda a, b: abs(b - a),
keys=iter(['0', '1', '4', '9']))
self.assertEqual(res, exp)
def test_from_iterable_with_key_and_keys(self):
iterable = (x for x in range(4))
with self.assertRaises(ValueError):
DistanceMatrix.from_iterable(iterable, lambda a, b: abs(b - a),
key=str, keys=['1', '2', '3', '4'])
def test_from_iterable_scipy_hamming_metric_with_metadata(self):
# test for #1254
seqs = [
Sequence('ACGT'),
Sequence('ACGA', metadata={'id': 'seq1'}),
Sequence('AAAA', metadata={'id': 'seq2'}),
Sequence('AAAA', positional_metadata={'qual': range(4)})
]
exp = DistanceMatrix([
[0, 0.25, 0.75, 0.75],
[0.25, 0.0, 0.5, 0.5],
[0.75, 0.5, 0.0, 0.0],
[0.75, 0.5, 0.0, 0.0]], ['a', 'b', 'c', 'd'])
dm = DistanceMatrix.from_iterable(
seqs,
metric=scipy.spatial.distance.hamming,
keys=['a', 'b', 'c', 'd'])
self.assertEqual(dm, exp)
def test_from_iterable_skbio_hamming_metric_with_metadata(self):
# test for #1254
seqs = [
Sequence('ACGT'),
Sequence('ACGA', metadata={'id': 'seq1'}),
Sequence('AAAA', metadata={'id': 'seq2'}),
Sequence('AAAA', positional_metadata={'qual': range(4)})
]
exp = DistanceMatrix([
[0, 0.25, 0.75, 0.75],
[0.25, 0.0, 0.5, 0.5],
[0.75, 0.5, 0.0, 0.0],
[0.75, 0.5, 0.0, 0.0]], ['a', 'b', 'c', 'd'])
dm = DistanceMatrix.from_iterable(
seqs,
metric=skbio.sequence.distance.hamming,
keys=['a', 'b', 'c', 'd'])
self.assertEqual(dm, exp)
def test_condensed_form(self):
for dm, condensed in zip(self.dms, self.dm_condensed_forms):
obs = dm.condensed_form()
self.assertTrue(np.array_equal(obs, condensed))
def test_permute_condensed(self):
# Can't really permute a 1x1 or 2x2...
for _ in range(2):
obs = self.dm_1x1.permute(condensed=True)
npt.assert_equal(obs, np.array([]))
for _ in range(2):
obs = self.dm_2x2.permute(condensed=True)
npt.assert_equal(obs, np.array([0.123]))
dm_copy = self.dm_3x3.copy()
np.random.seed(0)
obs = self.dm_3x3.permute(condensed=True)
npt.assert_equal(obs, np.array([12.0, 4.2, 0.01]))
obs = self.dm_3x3.permute(condensed=True)
npt.assert_equal(obs, np.array([4.2, 12.0, 0.01]))
# Ensure dm hasn't changed after calling permute() on it a couple of
# times.
self.assertEqual(self.dm_3x3, dm_copy)
def test_permute_not_condensed(self):
obs = self.dm_1x1.permute()
self.assertEqual(obs, self.dm_1x1)
self.assertFalse(obs is self.dm_1x1)
obs = self.dm_2x2.permute()
self.assertEqual(obs, self.dm_2x2)
self.assertFalse(obs is self.dm_2x2)
np.random.seed(0)
exp = DistanceMatrix([[0, 12, 4.2],
[12, 0, 0.01],
[4.2, 0.01, 0]], self.dm_3x3.ids)
obs = self.dm_3x3.permute()
self.assertEqual(obs, exp)
exp = DistanceMatrix([[0, 4.2, 12],
[4.2, 0, 0.01],
[12, 0.01, 0]], self.dm_3x3.ids)
obs = self.dm_3x3.permute()
self.assertEqual(obs, exp)
def test_eq(self):
# Compare DistanceMatrix to DissimilarityMatrix, where both have the
# same data and IDs.
eq_dm = DissimilarityMatrix(self.dm_3x3_data, ['a', 'b', 'c'])
self.assertTrue(self.dm_3x3 == eq_dm)
self.assertTrue(eq_dm == self.dm_3x3)
def test_to_series_1x1(self):
series = self.dm_1x1.to_series()
exp = pd.Series([], index=[])
assert_series_almost_equal(series, exp)
def test_to_series_2x2(self):
series = self.dm_2x2.to_series()
exp = pd.Series([0.123], index=pd.Index([('a', 'b')]))
assert_series_almost_equal(series, exp)
def test_to_series_4x4(self):
dm = DistanceMatrix([
[0.0, 0.2, 0.3, 0.4],
[0.2, 0.0, 0.5, 0.6],
[0.3, 0.5, 0.0, 0.7],
[0.4, 0.6, 0.7, 0.0]], ['a', 'b', 'c', 'd'])
series = dm.to_series()
exp = pd.Series([0.2, 0.3, 0.4, 0.5, 0.6, 0.7],
index=pd.Index([('a', 'b'), ('a', 'c'), ('a', 'd'),
('b', 'c'), ('b', 'd'), ('c', 'd')]))
assert_series_almost_equal(series, exp)
def test_to_series_default_ids(self):
series = DistanceMatrix(self.dm_2x2_data).to_series()
exp = pd.Series([0.123], index=pd.Index([('0', '1')]))
assert_series_almost_equal(series, exp)