def test_multiple_sequences(self):
pssm = Pssm()
nucs = [('TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAG'
'AGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT'),
('TGTACAAGTCCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAG'
'AGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT')]
expected_aa = None # Not returned when submitting more than one seq.
expected_scores = [0.06775, 0.06486]
scores, aligned_aa = pssm.run_g2p(nucs)
rounded_scores = [round(score, 5) for score in scores]
self.assertEqual(expected_aa, aligned_aa)
self.assertEqual(expected_scores, rounded_scores)
def test_multiple_sequences(self):
pssm = Pssm()
nucs = [('TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAG'
'AGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT'),
('TGTACAAGTCCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAG'
'AGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT')]
expected_aa = None # Not returned when submitting more than one seq.
expected_scores = [0.06775, 0.06486]
scores, aligned_aa = pssm.run_g2p(nucs)
rounded_scores = [round(score, 5) for score in scores]
self.assertEqual(expected_aa, aligned_aa)
self.assertEqual(expected_scores, rounded_scores)
def test_single_sequence(self):
pssm = Pssm()
nucs = ('TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAG'
'AGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT')
expected_aa = [['C'], ['T'], ['R'], ['P'], ['N'], ['-'], ['N'], ['N'],
['T'], ['-'], ['-'], ['R'], ['K'], ['S'], ['I'], ['H'],
['I'], ['-'], ['-'], ['-'], ['G'], ['P'], ['G'], ['R'],
['-'], ['-'], ['-'], ['A'], ['F'], ['Y'], ['A'], ['T'],
['-'], ['-'], ['-'], ['-'], ['G'], ['E'], ['I'], ['I'],
['G'], ['D'], ['I'], ['-'], ['-'], ['R'], ['Q'], ['A'],
['H'], ['C']]
expected_score = 0.067753
score, aligned_aa = pssm.run_g2p(nucs)
self.assertEqual(expected_aa, aligned_aa)
self.assertAlmostEqual(expected_score, score, places=5)
def test_single_sequence(self):
pssm = Pssm()
nucs = ('TGTACAAGACCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAG'
'AGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT')
expected_aa = [['C'], ['T'], ['R'], ['P'], ['N'], ['-'], ['N'], ['N'],
['T'], ['-'], ['-'], ['R'], ['K'], ['S'], ['I'], ['H'],
['I'], ['-'], ['-'], ['-'], ['G'], ['P'], ['G'], ['R'],
['-'], ['-'], ['-'], ['A'], ['F'], ['Y'], ['A'], ['T'],
['-'], ['-'], ['-'], ['-'], ['G'], ['E'], ['I'], ['I'],
['G'], ['D'], ['I'], ['-'], ['-'], ['R'], ['Q'], ['A'],
['H'], ['C']]
expected_score = 0.067753
score, aligned_aa = pssm.run_g2p(nucs)
self.assertEqual(expected_aa, aligned_aa)
self.assertAlmostEqual(expected_score, score, places=5)
def test_ambiguous_sequence(self):
pssm = Pssm()
nucs = ('TGTACAAGWCCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAG'
'AGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT')
expected_aa = [['C'], ['T'], ['R', 'S'], ['P'], ['N'], ['-'], ['N'], ['N'],
['T'], ['-'], ['-'], ['R'], ['K'], ['S'], ['I'], ['H'],
['I'], ['-'], ['-'], ['-'], ['G'], ['P'], ['G'], ['R'],
['-'], ['-'], ['-'], ['A'], ['F'], ['Y'], ['A'], ['T'],
['-'], ['-'], ['-'], ['-'], ['G'], ['E'], ['I'], ['I'],
['G'], ['D'], ['I'], ['-'], ['-'], ['R'], ['Q'], ['A'],
['H'], ['C']]
# Average of two possible scores (see test_multiple_sequences).
expected_score = (0.06775 + 0.06486) / 2
score, aligned_aa = pssm.run_g2p(nucs)
self.assertEqual(expected_aa, aligned_aa)
self.assertAlmostEqual(expected_score, score, places=5)
def test_ambiguous_sequence(self):
pssm = Pssm()
nucs = ('TGTACAAGWCCCAACAACAATACAAGAAAAAGTATACATATAGGACCAGGGAG'
'AGCATTTTATGCAACAGGAGAAATAATAGGAGATATAAGACAAGCACATTGT')
expected_aa = [['C'], ['T'], ['R', 'S'], ['P'], ['N'], ['-'], ['N'],
['N'], ['T'], ['-'], ['-'], ['R'], ['K'], ['S'], ['I'],
['H'], ['I'], ['-'], ['-'], ['-'], ['G'], ['P'], ['G'],
['R'], ['-'], ['-'], ['-'], ['A'], ['F'], ['Y'], ['A'],
['T'], ['-'], ['-'], ['-'], ['-'], ['G'], ['E'], ['I'],
['I'], ['G'], ['D'], ['I'], ['-'], ['-'], ['R'], ['Q'],
['A'], ['H'], ['C']]
# Average of two possible scores (see test_multiple_sequences).
expected_score = (0.06775 + 0.06486) / 2
score, aligned_aa = pssm.run_g2p(nucs)
self.assertEqual(expected_aa, aligned_aa)
self.assertAlmostEqual(expected_score, score, places=5)
