def test_traceback(self):
score_m = [[0, -5, -7, -9], [-5, 2, -3, -5], [-7, -3, 4, -1],
[-9, -5, -1, 6], [-11, -7, -3, 1]]
score_m = np.array(score_m)
tback_m = [[0, 3, 3, 3], [2, 1, 3, 3], [2, 2, 1, 3], [2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
# start at bottom-right
expected = ([DNA("ACG-")], [DNA("ACGT")], 1, 0, 0)
actual = _traceback(tback_m, score_m,
TabularMSA([DNA('ACG', metadata={'id': ''})]),
TabularMSA([DNA('ACGT', metadata={'id': ''})]), 4,
3)
self.assertEqual(actual, expected)
# four sequences in two alignments
score_m = [[0, -5, -7, -9], [-5, 2, -3, -5], [-7, -3, 4, -1],
[-9, -5, -1, 6], [-11, -7, -3, 1]]
score_m = np.array(score_m)
tback_m = [[0, 3, 3, 3], [2, 1, 3, 3], [2, 2, 1, 3], [2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
# start at bottom-right
expected = ([DNA("ACG-"), DNA("ACG-")], [DNA("ACGT"),
DNA("ACGT")], 1, 0, 0)
actual = _traceback(
tback_m, score_m,
TabularMSA([
DNA('ACG', metadata={'id': 's1'}),
DNA('ACG', metadata={'id': 's2'})
]),
TabularMSA([
DNA('ACGT', metadata={'id': 's3'}),
DNA('ACGT', metadata={'id': 's4'})
]), 4, 3)
self.assertEqual(actual, expected)
# start at highest-score
expected = ([DNA("ACG")], [DNA("ACG")], 6, 0, 0)
actual = _traceback(tback_m, score_m,
TabularMSA([DNA('ACG', metadata={'id': ''})]),
TabularMSA([DNA('ACGT', metadata={'id': ''})]), 3,
3)
self.assertEqual(actual, expected)
# terminate traceback before top-right
tback_m = [[0, 3, 3, 3], [2, 1, 3, 3], [2, 2, 0, 3], [2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
expected = ([DNA("G")], [DNA("G")], 6, 2, 2)
actual = _traceback(tback_m, score_m,
TabularMSA([DNA('ACG', metadata={'id': ''})]),
TabularMSA([DNA('ACGT', metadata={'id': ''})]), 3,
3)
self.assertEqual(actual, expected)
def test_traceback(self):
score_m = [[0, -5, -7, -9], [-5, 2, -3, -5], [-7, -3, 4, -1],
[-9, -5, -1, 6], [-11, -7, -3, 1]]
score_m = np.array(score_m)
tback_m = [[0, 3, 3, 3], [2, 1, 3, 3], [2, 2, 1, 3], [2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
# start at bottom-right
expected = ([BiologicalSequence("ACG-")], [BiologicalSequence("ACGT")],
1, 0, 0)
actual = _traceback(tback_m, score_m, Alignment([DNA('ACG')]),
Alignment([DNA('ACGT')]), 4, 3)
self.assertEqual(actual, expected)
# four sequences in two alignments
score_m = [[0, -5, -7, -9], [-5, 2, -3, -5], [-7, -3, 4, -1],
[-9, -5, -1, 6], [-11, -7, -3, 1]]
score_m = np.array(score_m)
tback_m = [[0, 3, 3, 3], [2, 1, 3, 3], [2, 2, 1, 3], [2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
# start at bottom-right
expected = ([BiologicalSequence("ACG-"),
BiologicalSequence("ACG-")],
[BiologicalSequence("ACGT"),
BiologicalSequence("ACGT")], 1, 0, 0)
actual = _traceback(tback_m, score_m,
Alignment([DNA('ACG', 's1'),
DNA('ACG', 's2')]),
Alignment([DNA('ACGT', 's3'),
DNA('ACGT', 's4')]), 4, 3)
self.assertEqual(actual, expected)
# start at highest-score
expected = ([BiologicalSequence("ACG")], [BiologicalSequence("ACG")],
6, 0, 0)
actual = _traceback(tback_m, score_m, Alignment([DNA('ACG')]),
Alignment([DNA('ACGT')]), 3, 3)
self.assertEqual(actual, expected)
# terminate traceback before top-right
tback_m = [[0, 3, 3, 3], [2, 1, 3, 3], [2, 2, 0, 3], [2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
expected = ("G", "G", 6, 2, 2)
expected = ([BiologicalSequence("G")], [BiologicalSequence("G")], 6, 2,
2)
actual = _traceback(tback_m, score_m, Alignment([DNA('ACG')]),
Alignment([DNA('ACGT')]), 3, 3)
self.assertEqual(actual, expected)
def test_traceback(self):
score_m = [[0, -5, -7, -9],
[-5, 2, -3, -5],
[-7, -3, 4, -1],
[-9, -5, -1, 6],
[-11, -7, -3, 1]]
score_m = np.array(score_m)
tback_m = [[0, 3, 3, 3],
[2, 1, 3, 3],
[2, 2, 1, 3],
[2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
# start at bottom-right
expected = ([DNA("ACG-", metadata={'id': 'foo'})],
[DNA("ACGT", metadata={'id': 'bar'})], 1, 0, 0)
actual = _traceback(tback_m, score_m,
TabularMSA([DNA('ACG', metadata={'id': 'foo'})]),
TabularMSA([DNA('ACGT', metadata={'id': 'bar'})]),
4, 3)
self.assertEqual(actual, expected)
# four sequences in two alignments
score_m = [[0, -5, -7, -9],
[-5, 2, -3, -5],
[-7, -3, 4, -1],
[-9, -5, -1, 6],
[-11, -7, -3, 1]]
score_m = np.array(score_m)
tback_m = [[0, 3, 3, 3],
[2, 1, 3, 3],
[2, 2, 1, 3],
[2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
# start at bottom-right
expected = ([DNA("ACG-", metadata={'id': 's1'}),
DNA("ACG-", metadata={'id': 's2'})],
[DNA("ACGT", metadata={'id': 's3'}),
DNA("ACGT", metadata={'id': 's4'})],
1, 0, 0)
actual = _traceback(tback_m, score_m,
TabularMSA([DNA('ACG', metadata={'id': 's1'}),
DNA('ACG', metadata={'id': 's2'})]),
TabularMSA([DNA('ACGT', metadata={'id': 's3'}),
DNA('ACGT', metadata={'id': 's4'})]),
4, 3)
self.assertEqual(actual, expected)
# start at highest-score
expected = ([DNA("ACG", metadata={'id': 'foo'})],
[DNA("ACG", metadata={'id': 'bar'})], 6, 0, 0)
actual = _traceback(tback_m, score_m,
TabularMSA([DNA('ACG', metadata={'id': 'foo'})]),
TabularMSA([DNA('ACGT', metadata={'id': 'bar'})]),
3, 3)
self.assertEqual(actual, expected)
# terminate traceback before top-right
tback_m = [[0, 3, 3, 3],
[2, 1, 3, 3],
[2, 2, 0, 3],
[2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
expected = ([DNA("G", metadata={'id': 'a'})],
[DNA("G", metadata={'id': 'a'})], 6, 2, 2)
actual = _traceback(tback_m, score_m,
TabularMSA([DNA('ACG', metadata={'id': 'a'})]),
TabularMSA([DNA('ACGT', metadata={'id': 'a'})]),
3, 3)
self.assertEqual(actual, expected)
def test_traceback(self):
score_m = [[0, -5, -7, -9],
[-5, 2, -3, -5],
[-7, -3, 4, -1],
[-9, -5, -1, 6],
[-11, -7, -3, 1]]
score_m = np.array(score_m)
tback_m = [[0, 3, 3, 3],
[2, 1, 3, 3],
[2, 2, 1, 3],
[2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
# start at bottom-right
expected = ([Sequence("ACG-", id='0')],
[Sequence("ACGT", id='1')], 1, 0, 0)
actual = _traceback(tback_m, score_m, Alignment([DNA('ACG')]),
Alignment([DNA('ACGT')]), 4, 3)
self.assertEqual(actual, expected)
# four sequences in two alignments
score_m = [[0, -5, -7, -9],
[-5, 2, -3, -5],
[-7, -3, 4, -1],
[-9, -5, -1, 6],
[-11, -7, -3, 1]]
score_m = np.array(score_m)
tback_m = [[0, 3, 3, 3],
[2, 1, 3, 3],
[2, 2, 1, 3],
[2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
# start at bottom-right
expected = ([Sequence("ACG-", id='s1'), Sequence("ACG-", id='s2')],
[Sequence("ACGT", id='s3'), Sequence("ACGT", id='s4')],
1, 0, 0)
actual = _traceback(tback_m, score_m,
Alignment([DNA('ACG', 's1'), DNA('ACG', 's2')]),
Alignment([DNA('ACGT', 's3'), DNA('ACGT', 's4')]),
4, 3)
self.assertEqual(actual, expected)
# start at highest-score
expected = ([Sequence("ACG", id='0')],
[Sequence("ACG", id='1')], 6, 0, 0)
actual = _traceback(tback_m, score_m, Alignment([DNA('ACG')]),
Alignment([DNA('ACGT')]), 3, 3)
self.assertEqual(actual, expected)
# terminate traceback before top-right
tback_m = [[0, 3, 3, 3],
[2, 1, 3, 3],
[2, 2, 0, 3],
[2, 2, 2, 1],
[2, 2, 2, 2]]
tback_m = np.array(tback_m)
expected = ("G", "G", 6, 2, 2)
expected = ([Sequence("G", id='0')],
[Sequence("G", id='1')], 6, 2, 2)
actual = _traceback(tback_m, score_m, Alignment([DNA('ACG')]),
Alignment([DNA('ACGT')]), 3, 3)
self.assertEqual(actual, expected)
