def testOutput(self):
sequence = 'CCAAAGGGGAAACC'
self.nussinov = Nussinov(sequence)
self.nussinov.initiate()
self.nussinov.calculate()
expected = [
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, ''],
['C', 'C', 'A', 'A', 'A', 'G', 'G', 'G', 'G', 'A', 'A', 'A', 'C', 'C', '', ''],
[0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 3, 4, 'C', 1],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 2, 3, 'C', 2],
['', 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 'A', 3],
['', '', 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 'A', 4],
['', '', '', 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 'A', 5],
['', '', '', '', 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 'G', 6],
['', '', '', '', '', 0, 0, 0, 0, 0, 0, 0, 1, 2, 'G', 7],
['', '', '', '', '', '', 0, 0, 0, 0, 0, 0, 1, 2, 'G', 8],
['', '', '', '', '', '', '', 0, 0, 0, 0, 0, 1, 1, 'G', 9],
['', '', '', '', '', '', '', '', 0, 0, 0, 0, 0, 0, 'A', 10],
['', '', '', '', '', '', '', '', '', 0, 0, 0, 0, 0, 'A', 11],
['', '', '', '', '', '', '', '', '', '', 0, 0, 0, 0, 'A', 12],
['', '', '', '', '', '', '', '', '', '', '', 0, 0, 0, 'C', 13],
['', '', '', '', '', '', '', '', '', '', '', '', 0, 0, 'C', 14]
]
result = self.nussinov.output()
self.assertEqual(expected, result)
def testGetBasePairedValue(self):
self.nussinov = Nussinov('AGUC')
expected = 1
self.assertEqual(expected, self.nussinov._getBasePairedValue(0, 2))
expected = 0
self.assertEqual(expected, self.nussinov._getBasePairedValue(2, 3))
def testGetK(self):
self.nussinov = Nussinov('AGUC')
expected = []
self.assertEqual(expected, self.nussinov._getK(1, 1))
expected = [2, 3, 4]
self.assertEqual(expected, self.nussinov._getK(1, 4))
def testBacktracking(self):
sequence = 'CCAAAGGGGAAACC'
self.nussinov = Nussinov(sequence)
self.nussinov.initiate()
self.nussinov.calculate()
expected = ['(', '(', '.', '.', '.', ')', ')', '(', '(', '.', '.', '.', ')', ')']
result = self.nussinov.backtracking()
self.assertEqual(expected, result)
def testInit(self):
sequence = 'AGUC'
self.nussinov = Nussinov(sequence)
self.assertEqual(sequence, self.nussinov._sequence)
self.assertEqual(len(sequence), self.nussinov._sequence_len)
expected_result_sequence_init = [''] * len(sequence)
self.assertEqual(expected_result_sequence_init,
self.nussinov._result_sequence)
matrix = [[''] * len(sequence) for i in range(len(sequence))]
self.assertEqual(matrix, self.nussinov._matrix)
def testInitiate(self):
sequence = 'AGUCGAUC'
self.nussinov = Nussinov(sequence)
self.nussinov.initiate()
expected = [
[0, 0, 0, 0, '', '', '', ''],
[0, 0, 0, 0, 0, '', '', ''],
['', 0, 0, 0, 0, 0, '', ''],
['', '', 0, 0, 0, 0, 0, ''],
['', '', '', 0, 0, 0, 0, 0],
['', '', '', '', 0, 0, 0, 0],
['', '', '', '', '', 0, 0, 0],
['', '', '', '', '', '', 0, 0]
]
self.assertEqual(expected, self.nussinov._matrix)
def testCalculate(self):
sequence = 'GGCAGACUAU'
self.nussinov = Nussinov(sequence)
self.nussinov.initiate()
self.nussinov.calculate()
expected = [
[0, 0, 0, 0, 0, 0, 1, 2, 2, 2],
[0, 0, 0, 0, 0, 0, 1, 1, 1, 2],
['', 0, 0, 0, 0, 0, 0, 1, 1, 1],
['', '', 0, 0, 0, 0, 0, 1, 1, 1],
['', '', '', 0, 0, 0, 0, 0, 0, 1],
['', '', '', '', 0, 0, 0, 0, 0, 1],
['', '', '', '', '', 0, 0, 0, 0, 0],
['', '', '', '', '', '', 0, 0, 0, 0],
['', '', '', '', '', '', '', 0, 0, 0],
['', '', '', '', '', '', '', '', 0, 0]
]
self.assertEqual(expected, self.nussinov._matrix)
class TestNussinov(unittest.TestCase):
def testInit(self):
sequence = 'AGUC'
self.nussinov = Nussinov(sequence)
self.assertEqual(sequence, self.nussinov._sequence)
self.assertEqual(len(sequence), self.nussinov._sequence_len)
expected_result_sequence_init = [''] * len(sequence)
self.assertEqual(expected_result_sequence_init,
self.nussinov._result_sequence)
matrix = [[''] * len(sequence) for i in range(len(sequence))]
self.assertEqual(matrix, self.nussinov._matrix)
def testInitiate(self):
sequence = 'AGUCGAUC'
self.nussinov = Nussinov(sequence)
self.nussinov.initiate()
expected = [
[0, 0, 0, 0, '', '', '', ''],
[0, 0, 0, 0, 0, '', '', ''],
['', 0, 0, 0, 0, 0, '', ''],
['', '', 0, 0, 0, 0, 0, ''],
['', '', '', 0, 0, 0, 0, 0],
['', '', '', '', 0, 0, 0, 0],
['', '', '', '', '', 0, 0, 0],
['', '', '', '', '', '', 0, 0]
]
self.assertEqual(expected, self.nussinov._matrix)
def testGetK(self):
self.nussinov = Nussinov('AGUC')
expected = []
self.assertEqual(expected, self.nussinov._getK(1, 1))
expected = [2, 3, 4]
self.assertEqual(expected, self.nussinov._getK(1, 4))
def testGetBasePairedValue(self):
self.nussinov = Nussinov('AGUC')
expected = 1
self.assertEqual(expected, self.nussinov._getBasePairedValue(0, 2))
expected = 0
self.assertEqual(expected, self.nussinov._getBasePairedValue(2, 3))
def testCalculate(self):
sequence = 'GGCAGACUAU'
self.nussinov = Nussinov(sequence)
self.nussinov.initiate()
self.nussinov.calculate()
expected = [
[0, 0, 0, 0, 0, 0, 1, 2, 2, 2],
[0, 0, 0, 0, 0, 0, 1, 1, 1, 2],
['', 0, 0, 0, 0, 0, 0, 1, 1, 1],
['', '', 0, 0, 0, 0, 0, 1, 1, 1],
['', '', '', 0, 0, 0, 0, 0, 0, 1],
['', '', '', '', 0, 0, 0, 0, 0, 1],
['', '', '', '', '', 0, 0, 0, 0, 0],
['', '', '', '', '', '', 0, 0, 0, 0],
['', '', '', '', '', '', '', 0, 0, 0],
['', '', '', '', '', '', '', '', 0, 0]
]
self.assertEqual(expected, self.nussinov._matrix)
def testOutput(self):
sequence = 'CCAAAGGGGAAACC'
self.nussinov = Nussinov(sequence)
self.nussinov.initiate()
self.nussinov.calculate()
expected = [
[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, ''],
['C', 'C', 'A', 'A', 'A', 'G', 'G', 'G', 'G', 'A', 'A', 'A', 'C', 'C', '', ''],
[0, 0, 0, 0, 0, 1, 2, 2, 2, 2, 2, 2, 3, 4, 'C', 1],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 2, 3, 'C', 2],
['', 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 'A', 3],
['', '', 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 'A', 4],
['', '', '', 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 'A', 5],
['', '', '', '', 0, 0, 0, 0, 0, 0, 0, 0, 1, 2, 'G', 6],
['', '', '', '', '', 0, 0, 0, 0, 0, 0, 0, 1, 2, 'G', 7],
['', '', '', '', '', '', 0, 0, 0, 0, 0, 0, 1, 2, 'G', 8],
['', '', '', '', '', '', '', 0, 0, 0, 0, 0, 1, 1, 'G', 9],
['', '', '', '', '', '', '', '', 0, 0, 0, 0, 0, 0, 'A', 10],
['', '', '', '', '', '', '', '', '', 0, 0, 0, 0, 0, 'A', 11],
['', '', '', '', '', '', '', '', '', '', 0, 0, 0, 0, 'A', 12],
['', '', '', '', '', '', '', '', '', '', '', 0, 0, 0, 'C', 13],
['', '', '', '', '', '', '', '', '', '', '', '', 0, 0, 'C', 14]
]
result = self.nussinov.output()
self.assertEqual(expected, result)
def testBacktracking(self):
sequence = 'CCAAAGGGGAAACC'
self.nussinov = Nussinov(sequence)
self.nussinov.initiate()
self.nussinov.calculate()
expected = ['(', '(', '.', '.', '.', ')', ')', '(', '(', '.', '.', '.', ')', ')']
result = self.nussinov.backtracking()
self.assertEqual(expected, result)