def test_recode_freq_vector_ignores(self):
"""recode_freq_vector: ignored chars are ignored
"""
freqs = {
"A": 0.21,
"B": 0.29,
"C": 0.05,
"D": 0.45,
"X": 0.22,
"Z": 0.5
}
a_def = [("A", "A"), ("B", "B"), ("C", "C"), ("D", "D"), ("X", "X"),
("Z", "Z")]
expected = {"A": 0.21, "C": 0.05, "D": 0.45}
self.assertFloatEqual(recode_freq_vector(a_def, freqs), expected)
freqs = {
"D": 0.21,
"E": 0.29,
"N": 0.05,
"Q": 0.45,
"B": 0.26,
"Z": 0.74,
"X": 1.0,
}
a_def = [("D", "DEN"), ("Q", "Q")]
expected = {"D": 0.55, "Q": 0.45}
self.assertFloatEqual(recode_freq_vector(a_def, freqs), expected)
def test_recode_counts_and_freqs(self):
"""recode_counts_and_freqs: functions as expected
"""
alphabet = alphabets["charge_his_3"]
aa_order = "ACDEFGHIKLMNPQRSTVWY"
actual = recode_counts_and_freqs(alphabet)
expected_matrix = recode_count_matrix(alphabet,
count_matrix=DSO78_matrix,
aa_order=aa_order)
expected_freqs = {}.fromkeys(aa_order, 0.0)
expected_freqs.update(recode_freq_vector(alphabet, DSO78_freqs))
expected = (expected_matrix, expected_freqs)
self.assertEqual(actual, expected)
def test_recode_freq_vector(self):
"""recode_freq_vector: bg freqs updated to reflect recoded alphabet"""
freqs = {"A": 0.21, "E": 0.29, "C": 0.05, "D": 0.45}
a_def = [("A", "AEC"), ("E", "D")]
expected = {"A": 0.55, "E": 0.45}
self.assertEqual(recode_freq_vector(a_def, freqs), expected)
# reversal of alphabet
freqs = {"A": 0.21, "E": 0.29, "C": 0.05, "D": 0.45}
a_def = [("A", "D"), ("E", "C"), ("C", "E"), ("D", "A")]
expected = {"A": 0.45, "E": 0.05, "C": 0.29, "D": 0.21}
self.assertEqual(recode_freq_vector(a_def, freqs), expected)
# no change in freqs (old alphabet = new alphabet)
freqs = {"A": 0.21, "E": 0.29, "C": 0.05, "D": 0.45}
a_def = [("A", "A"), ("E", "E"), ("C", "C"), ("D", "D")]
self.assertEqual(recode_freq_vector(a_def, freqs), freqs)
freqs = {"A": 0.21, "E": 0.29, "C": 0.05, "D": 0.45}
a_def = [("X", "AEC"), ("Y", "D")]
expected = {"X": 0.55, "Y": 0.45}
self.assertEqual(recode_freq_vector(a_def, freqs), expected)
