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)