def test_basic(self):
frequencies = [{
'A': 1 / 3,
'-': 2 / 3
}, {
'G': 1.0
}, {
'A': 2 / 3,
'C': 1 / 3
}]
actual = _most_conserved(frequencies, skbio.DNA)
expected = [1.0, 1.0, 2. / 3.]
self.assertEqual(actual, expected)
frequencies = [{
'A': 1 / 4,
'-': 3 / 4
}, {
'G': 1.0
}, {
'A': 1 / 2,
'C': 1 / 2
}, {
'A': 1 / 4,
'C': 1 / 4,
'G': 1 / 4,
'T': 1 / 4
}]
actual = _most_conserved(frequencies, skbio.DNA)
expected = [1.0, 1.0, 0.5, 0.25]
self.assertEqual(actual, expected)
def test_basic(self):
frequencies = [{'A': 1/3, '-': 2/3}, {'G': 1.0}, {'A': 2/3, 'C': 1/3}]
actual = _most_conserved(frequencies, skbio.DNA)
expected = [1.0, 1.0, 2./3.]
self.assertEqual(actual, expected)
frequencies = [{'A': 1/4, '-': 3/4}, {'G': 1.0}, {'A': 1/2, 'C': 1/2},
{'A': 1/4, 'C': 1/4, 'G': 1/4, 'T': 1/4}]
actual = _most_conserved(frequencies, skbio.DNA)
expected = [1.0, 1.0, 0.5, 0.25]
self.assertEqual(actual, expected)
def test_unknown_gap_mode(self):
frequencies = [{
'A': 1 / 3,
'-': 2 / 3
}, {
'G': 1.0
}, {
'A': 2 / 3,
'C': 1 / 3
}]
with self.assertRaises(ValueError):
_most_conserved(frequencies, skbio.DNA, gap_mode='not-real')
def test_N(self):
frequencies = [{
'A': 1 / 3,
'-': 2 / 3
}, {
'G': 1.0
}, {
'A': 2 / 3,
'N': 1 / 3
}]
actual = _most_conserved(frequencies, skbio.DNA)
expected = [1.0, 1.0, 2. / 3.]
self.assertEqual(actual, expected)
def test_empty(self):
frequencies = []
actual = _most_conserved(frequencies, skbio.DNA)
expected = []
self.assertEqual(actual, expected)
def test_all_gap(self):
frequencies = [{'-': 1.0}]
actual = _most_conserved(frequencies, skbio.DNA)
expected = [0.0]
self.assertEqual(actual, expected)
def test_unknown_gap_mode(self):
frequencies = [{'A': 1/3, '-': 2/3}, {'G': 1.0}, {'A': 2/3, 'C': 1/3}]
with self.assertRaises(ValueError):
_most_conserved(frequencies, skbio.DNA, gap_mode='not-real')
def test_N(self):
frequencies = [{'A': 1/3, '-': 2/3}, {'G': 1.0}, {'A': 2/3, 'N': 1/3}]
actual = _most_conserved(frequencies, skbio.DNA)
expected = [1.0, 1.0, 2./3.]
self.assertEqual(actual, expected)
def test_empty(self):
frequencies = []
actual = _most_conserved(frequencies, skbio.DNA)
expected = []
self.assertEqual(actual, expected)
def test_all_gap(self):
frequencies = [{'-': 1.0}]
actual = _most_conserved(frequencies, skbio.DNA)
expected = [0.0]
self.assertEqual(actual, expected)
