def test_char_to_index(self):
"""should correctly recode a DNA & RNA seqs into indices"""
seq = "TCAGRNY?-"
expected = [0, 1, 2, 3, -9, -9, -9, -9, -9]
indices = seq_to_indices(seq, self.dna_char_indices)
assert_equal(indices, expected)
seq = "UCAGRNY?-"
indices = seq_to_indices(seq, self.rna_char_indices)
assert_equal(indices, expected)
def test_python_vs_cython_fill_matrix(self):
"""python & cython fill_diversity_matrix give same answer"""
s1 = seq_to_indices("RACGTACGTACN", self.dna_char_indices)
s2 = seq_to_indices("AGTGTACGTACA", self.dna_char_indices)
matrix1 = numpy.zeros((4, 4), float)
_fill_diversity_matrix(matrix1, s1, s2)
matrix2 = numpy.zeros((4, 4), float)
pyx_fill_diversity_matrix(matrix2, s1, s2)
assert_allclose(matrix1, matrix2)
def test_jc69_from_matrix(self):
"""compute JC69 from diversity matrix"""
s1 = seq_to_indices("ACGTACGTAC", self.dna_char_indices)
s2 = seq_to_indices("GTGTACGTAC", self.dna_char_indices)
matrix = numpy.zeros((4, 4), float)
_fill_diversity_matrix(matrix, s1, s2)
total, p, dist, var = _jc69_from_matrix(matrix)
self.assertEqual(total, 10.0)
self.assertEqual(p, 0.2)
def test_fill_diversity_matrix_some(self):
"""make correct diversity matrix when not all chars valid"""
s1 = seq_to_indices("RACGTACGTACN", self.dna_char_indices)
s2 = seq_to_indices("AGTGTACGTACA", self.dna_char_indices)
matrix = numpy.zeros((4, 4), float)
# small diffs
matrix.fill(0)
_fill_diversity_matrix(matrix, s1, s2)
assert_equal(
matrix,
numpy.array(
[[2, 0, 0, 0], [1, 2, 0, 0], [0, 0, 2, 1], [0, 0, 0, 2]],
float),
)
def test_fill_diversity_matrix_all(self):
"""make correct diversity matrix when all chars valid"""
s1 = seq_to_indices("ACGTACGTAC", self.dna_char_indices)
s2 = seq_to_indices("GTGTACGTAC", self.dna_char_indices)
matrix = numpy.zeros((4, 4), float)
# self-self should just be an identity matrix
_fill_diversity_matrix(matrix, s1, s1)
assert_equal(matrix.sum(), len(s1))
assert_equal(
matrix,
numpy.array(
[[2, 0, 0, 0], [0, 3, 0, 0], [0, 0, 3, 0], [0, 0, 0, 2]],
float),
)
# small diffs
matrix.fill(0)
_fill_diversity_matrix(matrix, s1, s2)
assert_equal(
matrix,
numpy.array(
[[2, 0, 0, 0], [1, 2, 0, 0], [0, 0, 2, 1], [0, 0, 0, 2]],
float),
)
