def test_recode_count_matrix_no_change(self):
"""recode_count_matrix: no changes applied when they shouldn't be"""
# recoding recoded matrices
actual = recode_count_matrix(self.alphabet1, self.recoded_m1, self.aa_order1)
expected = self.recoded_m1
assert_allclose(actual, expected)
actual = recode_count_matrix(self.alphabet2, self.recoded_m2, self.aa_order2)
expected = self.recoded_m2
assert_allclose(actual, expected)
def test_recode_count_matrix_3_states_ambig_ignored(self):
"""recode_count_matrix: correct result w 3-state alphabet w ambig chars
"""
actual = recode_count_matrix(self.alphabet2_w_ambig, self.m2,
self.aa_order2)
expected = self.recoded_m2
self.assertEqual(actual, 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_count_matrix_3_states(self):
"""recode_count_matrix: returns correct result with 3-state alphabet
"""
actual = recode_count_matrix(self.alphabet2, self.m2, self.aa_order2)
expected = self.recoded_m2
self.assertEqual(actual, expected)
def test_recode_count_matrix_2_states(self):
"""recode_count_matrix: returns correct result with 2-state alphabet
"""
actual = recode_count_matrix(self.alphabet1, self.m1, self.aa_order1)
expected = self.recoded_m1
self.assertEqual(actual, expected)
