def est_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.assertEquals(total, 10.0)
self.assertEquals(p, 0.2)
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.assertEquals(total, 10.0)
self.assertEquals(p, 0.2)
def est_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)
self.assertFloatEqual(matrix1, matrix2)
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)
self.assertFloatEqual(matrix1, matrix2)
def est_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)
self.assertEquals(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_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)
self.assertEquals(
matrix,
numpy.array(
[[2, 0, 0, 0], [1, 2, 0, 0], [0, 0, 2, 1], [0, 0, 0, 2]],
float))
def est_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)
self.assertEquals(matrix.sum(), len(s1))
self.assertEquals(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)
self.assertEquals(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)
self.assertEquals(matrix.sum(), len(s1))
self.assertEquals(
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)
self.assertEquals(
matrix,
numpy.array(
[[2, 0, 0, 0], [1, 2, 0, 0], [0, 0, 2, 1], [0, 0, 0, 2]],
float))
