def setUp(self):
self._alignment = MultipleAlignment()
class TestAlignment(unittest.TestCase):
def setUp(self):
self._alignment = MultipleAlignment()
def as_helper(self, seq):
self._alignment.add_sequence(seq)
self.assertEqual(len(self._alignment.sequence_matrix), len(seq))
self.assertEqual(len(self._alignment.sequence_matrix[0]), 1)
self.assertEqual(''.join(self._alignment.sequence_matrix), seq)
def ss_entropy_helper(self, expect):
actual = self._alignment.sum_aligned_char_scores(entropy)
self.assertLess(abs(actual - expect), SUM_ALIGN_EPSILON,
"Incorrect sum of entropy scores: {0} "
"(expected {1} to be within {2})".format(
actual,
expect,
SUM_ALIGN_EPSILON))
def ss_sp_helper(self, expect, matrix_wrapper):
actual = self._alignment.sum_aligned_char_scores(sum_of_pairs, matrix_wrapper)
self.assertLess(abs(actual - expect), SUM_ALIGN_EPSILON,
"Incorrect sum of SP scores: {0} "
"(expected {1} to be within {2})".format(
actual,
expect,
SUM_ALIGN_EPSILON))
def test_add_sequence_1(self):
self.as_helper('KMFPSTWY')
def test_add_sequence_2(self):
self.as_helper('K')
def test_add_sequence_3(self):
self.as_helper('KMFP----')
def test_add_sequence_4(self):
self.as_helper('---PSTWY')
def test_add_sequence_5(self):
self.as_helper('------')
def test_add_sequence_6(self):
self.as_helper('-')
def test_add_sequences_1(self):
seq_1 = 'BZXBZA'
seq_2 = 'TTTT'
seq_3 = 'XAXAXAXA'
self._alignment.add_sequence(seq_1)
self._alignment.add_sequence(seq_2)
self._alignment.add_sequence(seq_3)
self.assertEqual(len(self._alignment.sequence_matrix), len(seq_3))
self.assertEqual(len(self._alignment.sequence_matrix[0]), 3)
self.assertEqual(len(self._alignment.sequence_matrix[1]), 3)
self.assertEqual(len(self._alignment.sequence_matrix[2]), 3)
self.assertEqual(self._alignment.sequence_matrix[0], 'BTX')
self.assertEqual(self._alignment.sequence_matrix[1], 'ZTA')
self.assertEqual(self._alignment.sequence_matrix[2], 'XTX')
def test_add_sequences_2(self):
seq_1 = '-RRRRRRRRRRRRWWWWWWWWWWWWWWW-'
seq_2 = '----------T---------'
seq_3 = 'XZXZXZXZXZ------XZXZXZXZX'
self._alignment.add_sequence(seq_1)
self._alignment.add_sequence(seq_2)
self._alignment.add_sequence(seq_3)
self.assertEqual(len(self._alignment.sequence_matrix), len(seq_1))
self.assertEqual(len(self._alignment.sequence_matrix[0]), 3)
self.assertEqual(len(self._alignment.sequence_matrix[1]), 3)
self.assertEqual(len(self._alignment.sequence_matrix[2]), 3)
self.assertEqual(self._alignment.sequence_matrix[0], '--X')
self.assertEqual(self._alignment.sequence_matrix[1], 'R-Z')
self.assertEqual(self._alignment.sequence_matrix[2], 'R-X')
def test_add_sequences_3(self):
seq_1 = 'A'
seq_2 = 'BB'
seq_3 = 'CCC'
seq_4 = 'DDDD'
seq_5 = 'EEEEE'
seq_6 = 'FFFFFF'
self._alignment.add_sequence(seq_1)
self._alignment.add_sequence(seq_2)
self._alignment.add_sequence(seq_3)
self._alignment.add_sequence(seq_4)
self._alignment.add_sequence(seq_5)
self._alignment.add_sequence(seq_6)
self.assertEqual(len(self._alignment.sequence_matrix), len(seq_6))
self.assertEqual(len(self._alignment.sequence_matrix[0]), 6)
self.assertEqual(len(self._alignment.sequence_matrix[1]), 5)
self.assertEqual(len(self._alignment.sequence_matrix[2]), 4)
self.assertEqual(len(self._alignment.sequence_matrix[3]), 3)
self.assertEqual(len(self._alignment.sequence_matrix[4]), 2)
self.assertEqual(len(self._alignment.sequence_matrix[5]), 1)
self.assertEqual(self._alignment.sequence_matrix[0], 'ABCDEF')
self.assertEqual(self._alignment.sequence_matrix[1], 'BCDEF')
self.assertEqual(self._alignment.sequence_matrix[2], 'CDEF')
self.assertEqual(self._alignment.sequence_matrix[3], 'DEF')
self.assertEqual(self._alignment.sequence_matrix[4], 'EF')
self.assertEqual(self._alignment.sequence_matrix[5], 'F')
def test_sum_aligned_char_scores_1(self):
seq_1 = 'TWYV'
seq_2 = 'AWYA'
self._alignment.add_sequence(seq_1)
self._alignment.add_sequence(seq_2)
# -(-1 + 0 + 0 + -1)
self.ss_entropy_helper(2.0)
# 0 + 11 + 7 + 0
self.ss_sp_helper(18.0, blosum_62)
def test_sum_aligned_char_scores_2(self):
seq_1 = 'TWYV'
seq_2 = 'AW--'
self._alignment.add_sequence(seq_1)
self._alignment.add_sequence(seq_2)
# -(-1 + 0 + 0 + 0)
self.ss_entropy_helper(1.0)
# 0 + 11 + 0 + 0
self.ss_sp_helper(11.0, blosum_62)
def test_sum_aligned_char_scores_3(self):
seq_1 = 'ZWBB'
seq_2 = 'ZWWB'
seq_3 = 'ZWBW'
self._alignment.add_sequence(seq_1)
self._alignment.add_sequence(seq_2)
self._alignment.add_sequence(seq_3)
# -(0 + 0 + -(2/3 * log(2/3,2) + 1/3 * log(1/3,2)) + -(2/3 * log(2/3,2) + 1/3 * log(1/3,2))
self.ss_entropy_helper(1.8)
# 4 + 4 + 4 + 11 + 11 + 11 + -4 + 4 + -4 + 4 + -4 + -4
self.ss_sp_helper(37.0, blosum_62)
def test_sum_aligned_char_scores_4(self):
seq_1 = 'ZWBB'
seq_2 = 'ZW--'
seq_3 = 'ZW--'
self._alignment.add_sequence(seq_1)
self._alignment.add_sequence(seq_2)
self._alignment.add_sequence(seq_3)
# -(0 + 0 + 0 + 0)
self.ss_entropy_helper(0.0)
# 4 + 4 + 4 + 11 + 11 + 11 + 0 + 0 + 0 + 0 + 0 + 0
self.ss_sp_helper(45.0, blosum_62)
def test_SOURCE_STABALIZER_sum_aligned_char_scores_1(self):
seq_1 = 'ZWBB'
seq_2 = 'ZWWB'
seq_3 = 'ZWBW'
seq_4 = 'ZWBB'
seq_5 = 'ZWWB'
seq_6 = 'ZWBW'
self._alignment.add_sequence(seq_1)
self._alignment.add_sequence(seq_2)
self._alignment.add_sequence(seq_3)
self._alignment.add_sequence(seq_4)
self._alignment.add_sequence(seq_5)
self._alignment.add_sequence(seq_6)
self.ss_entropy_helper(1.8)
self.ss_sp_helper(231.0, blosum_62)
def test_SOURCE_STABALIZER_sum_aligned_char_scores_2(self):
seq_1 = 'ZWBB'
seq_2 = 'ZW--'
seq_3 = 'ZW--'
seq_4 = 'ZWBB'
seq_5 = 'ZW--'
seq_6 = 'ZW--'
self._alignment.add_sequence(seq_1)
self._alignment.add_sequence(seq_2)
self._alignment.add_sequence(seq_3)
self._alignment.add_sequence(seq_4)
self._alignment.add_sequence(seq_5)
self._alignment.add_sequence(seq_6)
self.ss_entropy_helper(0.0)
self.ss_sp_helper(225.0, blosum_62)
