def test_distances(self):
s1 = SequenceCollection([DNA("ACGT", "d1"), DNA("ACGG", "d2")])
expected = [[0, 0.25], [0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(hamming)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.], [42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
def test_distances(self):
s1 = SequenceCollection([DNA("ACGT", "d1"), DNA("ACGG", "d2")])
expected = [[0, 0.25],
[0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(hamming)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.],
[42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
def test_distances(self):
s1 = SequenceCollection([DNA("ACGT", metadata={'id': "d1"}),
DNA("ACGG", metadata={'id': "d2"})])
expected = [[0, 0.25],
[0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
def h(s1, s2):
return hamming(s1.values, s2.values)
actual = s1.distances(h)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.],
[42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
def test_distances(self):
s1 = SequenceCollection([
DNA("ACGT", metadata={'id': "d1"}),
DNA("ACGG", metadata={'id': "d2"})
])
expected = [[0, 0.25], [0.25, 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
def h(s1, s2):
return hamming(s1.values, s2.values)
actual = s1.distances(h)
self.assertEqual(actual, expected)
# alt distance function provided
def dumb_distance(s1, s2):
return 42.
expected = [[0, 42.], [42., 0]]
expected = DistanceMatrix(expected, ['d1', 'd2'])
actual = s1.distances(dumb_distance)
self.assertEqual(actual, expected)
