def test_count_column_freqs(self):
columns = aligned_columns_to_rows(self.aln, 1)
obs = count_column_freqs(columns)
expect = {'A C G' : 4, 'C G T' : 3, 'G T A' : 3, 'T A C' : 3}
assert obs == expect, (obs, expect)
columns = aligned_columns_to_rows(self.aln[:-1], 2)
obs = count_column_freqs(columns)
expect = {'AA CC GG': 1, 'AC CG GT': 1, 'CC GG TT':1, 'GG TT AA':1,
'GT TA AC':1, 'TT AA CC':1}
self.assertEqual(obs, expect)
def test_count_column_freqs(self):
columns = aligned_columns_to_rows(self.aln, 1)
obs = count_column_freqs(columns)
expect = {'A C G' : 4, 'C G T' : 3, 'G T A' : 3, 'T A C' : 3}
self.assertEqual(obs, expect)
columns = aligned_columns_to_rows(self.aln[:-1], 2)
obs = count_column_freqs(columns)
expect = {'AA CC GG': 1, 'AC CG GT': 1, 'CC GG TT':1, 'GG TT AA':1,
'GT TA AC':1, 'TT AA CC':1}
self.assertEqual(obs, expect)
def test_get_ML_probs(self):
columns = aligned_columns_to_rows(self.aln, 1)
obs = get_ML_probs(columns, with_patterns=True)
expect = {'A C G' : 4/13.0, 'C G T' : 3/13.0, 'G T A' : 3/13.0, 'T A C' : 3/13.0}
sum = 0
for pattern, lnL, freq in obs:
self.assertFloatEqual(lnL, expect[pattern])
sum += lnL
assert lnL >= 0
self.assertFloatEqual(sum, 1)
def test_get_ML_probs(self):
columns = aligned_columns_to_rows(self.aln, 1)
obs = get_ML_probs(columns, with_patterns=True)
expect = {'A C G' : 4/13.0, 'C G T' : 3/13.0, 'G T A' : 3/13.0, 'T A C' : 3/13.0}
sum = 0
for pattern, lnL, freq in obs:
self.assertFloatEqual(lnL, expect[pattern])
sum += lnL
self.assertTrue(lnL >= 0)
self.assertFloatEqual(sum, 1)
def test_aligned_columns_to_rows(self):
obs = aligned_columns_to_rows(self.aln[:-1], 3)
expect = [['AAA','CCC','GGG'],['CCC','GGG','TTT'],
['GGG','TTT','AAA'], ['TTT','AAA','CCC']]
assert obs == expect, (obs, expect)
obs = aligned_columns_to_rows(self.aln, 1)
expect = [['A','C','G'],['A','C','G'],['A','C','G'],
['C','G','T'],['C','G','T'],['C','G','T'],
['G','T','A'],['G','T','A'],['G','T','A'],
['T','A','C'],['T','A','C'],['T','A','C'],
['A','C','G']]
assert obs == expect, (obs, expect)
obs = aligned_columns_to_rows(self.gapped_aln[:-1], 3)
expect = [['TTT','TAT','TTT']]
assert obs == expect, (obs, expect)
obs = aligned_columns_to_rows(self.ambig_aln, 2, IUPAC_DNA_ambiguities)
expect = [['AA','CC','CA'],['CC','CC','CC'],['TT','TT','TG']]
assert obs == expect, (obs, expect)
def test_aligned_columns_to_rows(self):
obs = aligned_columns_to_rows(self.aln[:-1], 3)
expect = [['AAA','CCC','GGG'],['CCC','GGG','TTT'],
['GGG','TTT','AAA'], ['TTT','AAA','CCC']]
assert obs == expect, (obs, expect)
obs = aligned_columns_to_rows(self.aln, 1)
expect = [['A','C','G'],['A','C','G'],['A','C','G'],
['C','G','T'],['C','G','T'],['C','G','T'],
['G','T','A'],['G','T','A'],['G','T','A'],
['T','A','C'],['T','A','C'],['T','A','C'],
['A','C','G']]
self.assertEqual(obs, expect)
obs = aligned_columns_to_rows(self.gapped_aln[:-1], 3, allowed_chars='ACGT')
expect = [['TTT','TAT','TTT']]
self.assertEqual(obs, expect)
obs = aligned_columns_to_rows(self.ambig_aln, 2, exclude_chars=IUPAC_DNA_ambiguities)
expect = [['AA','CC','CA'],['CC','CC','CC'],['TT','TT','TG']]
self.assertEqual(obs, expect)
def test_aligned_columns_to_rows(self):
obs = aligned_columns_to_rows(self.aln[:-1], 3)
expect = [['AAA', 'CCC', 'GGG'], ['CCC', 'GGG', 'TTT'],
['GGG', 'TTT', 'AAA'], ['TTT', 'AAA', 'CCC']]
assert obs == expect, (obs, expect)
obs = aligned_columns_to_rows(self.aln, 1)
expect = [['A', 'C', 'G'], ['A', 'C', 'G'], ['A', 'C', 'G'],
['C', 'G', 'T'], ['C', 'G', 'T'], ['C', 'G', 'T'],
['G', 'T', 'A'], ['G', 'T', 'A'], ['G', 'T', 'A'],
['T', 'A', 'C'], ['T', 'A', 'C'], ['T', 'A', 'C'],
['A', 'C', 'G']]
assert obs == expect, (obs, expect)
obs = aligned_columns_to_rows(self.gapped_aln[:-1], 3)
expect = [['TTT', 'TAT', 'TTT']]
assert obs == expect, (obs, expect)
obs = aligned_columns_to_rows(self.ambig_aln, 2, IUPAC_DNA_ambiguities)
expect = [['AA', 'CC', 'CA'], ['CC', 'CC', 'CC'], ['TT', 'TT', 'TG']]
assert obs == expect, (obs, expect)
def test_aligned_columns_to_rows(self):
obs = aligned_columns_to_rows(self.aln[:-1], 3)
expect = [['AAA','CCC','GGG'],['CCC','GGG','TTT'],
['GGG','TTT','AAA'], ['TTT','AAA','CCC']]
assert obs == expect, (obs, expect)
obs = aligned_columns_to_rows(self.aln, 1)
expect = [['A','C','G'],['A','C','G'],['A','C','G'],
['C','G','T'],['C','G','T'],['C','G','T'],
['G','T','A'],['G','T','A'],['G','T','A'],
['T','A','C'],['T','A','C'],['T','A','C'],
['A','C','G']]
self.assertEqual(obs, expect)
obs = aligned_columns_to_rows(self.gapped_aln[:-1], 3, allowed_chars='ACGT')
expect = [['TTT','TAT','TTT']]
self.assertEqual(obs, expect)
obs = aligned_columns_to_rows(self.ambig_aln, 2, exclude_chars=IUPAC_DNA_ambiguities)
expect = [['AA','CC','CA'],['CC','CC','CC'],['TT','TT','TG']]
self.assertEqual(obs, expect)
def test_get_G93_lnL_from_array(self):
columns = aligned_columns_to_rows(self.aln, 1)
obs = get_G93_lnL_from_array(columns)
expect = math.log(math.pow(4/13.0, 4)) + 3*math.log(math.pow(3/13.0, 3))
self.assertFloatEqual(obs, expect)
def test_get_G93_lnL_from_array(self):
columns = aligned_columns_to_rows(self.aln, 1)
obs = get_G93_lnL_from_array(columns)
expect = math.log(math.pow(4 / 13.0,
4)) + 3 * math.log(math.pow(3 / 13.0, 3))
self.assertFloatEqual(obs, expect)
