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_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_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_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)
