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)