def test_from_iterable_with_key_and_keys(self):
iterable = (x for x in range(4))
with self.assertRaises(ValueError):
DissimilarityMatrix.from_iterable(iterable,
lambda a, b: abs(b - a),
key=str,
keys=['1', '2', '3', '4'])
def test_from_iterable_with_key_and_keys(self):
iterable = (x for x in range(4))
with self.assertRaises(ValueError):
DissimilarityMatrix.from_iterable(iterable,
lambda a, b: abs(b - a),
key=str,
keys=['1', '2', '3', '4'])
def test_from_iterable_asymmetric_data(self):
iterable = (x for x in range(4))
exp = DissimilarityMatrix([[0, 1, 2, 3], [-1, 0, 1, 2], [-2, -1, 0, 1],
[-3, -2, -1, 0]])
res = DissimilarityMatrix.from_iterable(iterable, lambda a, b: b - a)
self.assertEqual(res, exp)
def test_from_iterable_non_hollow_data(self):
iterable = (x for x in range(4))
exp = DissimilarityMatrix([[1, 1, 1, 1], [1, 1, 1, 1], [1, 1, 1, 1],
[1, 1, 1, 1]])
res = DissimilarityMatrix.from_iterable(iterable, lambda a, b: 1)
self.assertEqual(res, exp)
def test_from_iterable_no_key(self):
iterable = (x for x in range(4))
exp = DissimilarityMatrix([[0, 1, 2, 3], [1, 0, 1, 2], [2, 1, 0, 1],
[3, 2, 1, 0]])
res = DissimilarityMatrix.from_iterable(iterable,
lambda a, b: abs(b - a))
self.assertEqual(res, exp)
def test_from_iterable_asymmetric_data(self):
iterable = (x for x in range(4))
exp = DissimilarityMatrix([[0, 1, 2, 3],
[-1, 0, 1, 2],
[-2, -1, 0, 1],
[-3, -2, -1, 0]])
res = DissimilarityMatrix.from_iterable(iterable, lambda a, b: b - a)
self.assertEqual(res, exp)
def test_from_iterable_non_hollow_data(self):
iterable = (x for x in range(4))
exp = DissimilarityMatrix([[1, 1, 1, 1],
[1, 1, 1, 1],
[1, 1, 1, 1],
[1, 1, 1, 1]])
res = DissimilarityMatrix.from_iterable(iterable, lambda a, b: 1)
self.assertEqual(res, exp)
def test_from_iterable_with_key(self):
iterable = (x for x in range(4))
exp = DissimilarityMatrix(
[[0, 1, 2, 3], [1, 0, 1, 2], [2, 1, 0, 1], [3, 2, 1, 0]],
['0', '1', '4', '9'])
res = DissimilarityMatrix.from_iterable(iterable,
lambda a, b: abs(b - a),
key=lambda x: str(x**2))
self.assertEqual(res, exp)
def test_from_iterable_no_key(self):
iterable = (x for x in range(4))
exp = DissimilarityMatrix([[0, 1, 2, 3],
[1, 0, 1, 2],
[2, 1, 0, 1],
[3, 2, 1, 0]])
res = DissimilarityMatrix.from_iterable(iterable,
lambda a, b: abs(b - a))
self.assertEqual(res, exp)
def test_from_iterable_with_key(self):
iterable = (x for x in range(4))
exp = DissimilarityMatrix([[0, 1, 2, 3],
[1, 0, 1, 2],
[2, 1, 0, 1],
[3, 2, 1, 0]], ['0', '1', '4', '9'])
res = DissimilarityMatrix.from_iterable(iterable,
lambda a, b: abs(b - a),
key=lambda x: str(x ** 2))
self.assertEqual(res, 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 = DissimilarityMatrix(
[[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 = DissimilarityMatrix.from_iterable(
seqs,
metric=skbio.sequence.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 = DissimilarityMatrix([
[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 = DissimilarityMatrix.from_iterable(
seqs,
metric=skbio.sequence.distance.hamming,
keys=['a', 'b', 'c', 'd'])
self.assertEqual(dm, exp)
def test_from_iterable_single(self):
exp = DissimilarityMatrix([[100]])
res = DissimilarityMatrix.from_iterable(["boo"], lambda a, b: 100)
self.assertEqual(res, exp)
def test_from_iterable_empty(self):
with self.assertRaises(DissimilarityMatrixError):
DissimilarityMatrix.from_iterable([], lambda x: x)
def test_from_iterable_single(self):
exp = DissimilarityMatrix([[100]])
res = DissimilarityMatrix.from_iterable(["boo"], lambda a, b: 100)
self.assertEqual(res, exp)
def test_from_iterable_empty(self):
with self.assertRaises(DissimilarityMatrixError):
DissimilarityMatrix.from_iterable([], lambda x: x)