# This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tests for SubsMat module.""" try: import numpy del numpy except ImportError: from Bio import MissingExternalDependencyError raise MissingExternalDependencyError( "Install NumPy if you want to use Bio.SubsMat." ) import os import pickle import unittest from Bio import SubsMat from Bio.SubsMat import FreqTable, MatrixInfo class TestGeo(unittest.TestCase): @classmethod def setUpClass(cls): ftab_file = os.path.join("SubsMat", "protein_count.txt") with open(ftab_file) as handle: cls.ftab_prot = FreqTable.read_count(handle) pickle_file = os.path.join("SubsMat", "acc_rep_mat.pik") # Don't want to use text mode on Python 3, with open(pickle_file, "rb") as handle: dictionary = pickle.load(handle) cls.acc_rep_mat = SubsMat.SeqMat(dictionary) cls.obs_freq_mat = SubsMat._build_obs_freq_mat(cls.acc_rep_mat) def checkMatrix(self, mat, expected): text = mat.format() self.assertEqual(text, expected) def test_protein_freq(self): letters = "ACDEFGHIKLMNPQRSTVWY" ctab_file = os.path.join("SubsMat", "protein_freq.txt") with open(ctab_file) as handle: ctab_prot = FreqTable.read_freq(handle) self.assertEqual(self.ftab_prot.alphabet, letters) for letter in letters: difference = self.ftab_prot[letter] - ctab_prot[letter] self.assertAlmostEqual(abs(difference), 0, places=3) def test_freqtable(self): ftab_prot2 = SubsMat._exp_freq_table_from_obs_freq(self.obs_freq_mat) self.assertEqual(len(ftab_prot2), 20) for letter in "ACDEFGHIKLMNPQRSTVWY": difference = self.ftab_prot[letter] - ftab_prot2[letter] self.assertAlmostEqual(abs(difference), 0, places=1) def test_obs_freq_mat(self): self.assertEqual(len(self.obs_freq_mat), 210) self.assertAlmostEqual(self.obs_freq_mat[("A", "A")], 0.010561, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "C")], 0.002452, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "C")], 0.002102, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "D")], 0.008559, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "D")], 0.000751, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "D")], 0.007558, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "E")], 0.010360, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "E")], 0.001301, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "E")], 0.008158, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "E")], 0.005956, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "F")], 0.006106, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "F")], 0.001602, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "F")], 0.003153, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "F")], 0.002503, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "F")], 0.003954, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "G")], 0.011461, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "G")], 0.001952, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "G")], 0.007157, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "G")], 0.007307, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "G")], 0.005105, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "G")], 0.016066, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "H")], 0.003303, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "H")], 0.000501, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "H")], 0.002603, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "H")], 0.001902, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "H")], 0.001952, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "H")], 0.002653, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "H")], 0.002803, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "I")], 0.010110, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "I")], 0.002102, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "I")], 0.003303, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "I")], 0.003153, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "I")], 0.007558, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "I")], 0.004605, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "I")], 0.001552, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "I")], 0.007257, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "K")], 0.009560, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "K")], 0.001201, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "K")], 0.008458, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "K")], 0.008208, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "K")], 0.003353, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "K")], 0.007407, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "K")], 0.003153, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "K")], 0.004004, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "K")], 0.006056, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "L")], 0.015365, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "L")], 0.003103, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "L")], 0.006006, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "L")], 0.006657, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "L")], 0.011812, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "L")], 0.007708, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "L")], 0.003504, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "L")], 0.017417, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "L")], 0.005606, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "L")], 0.016016, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "M")], 0.003954, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "M")], 0.000701, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "M")], 0.001001, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "M")], 0.001652, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "M")], 0.003353, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "M")], 0.002452, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "M")], 0.000801, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "M")], 0.004404, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "M")], 0.001602, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "M")], 0.007658, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "M")], 0.001101, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "N")], 0.006957, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "N")], 0.001201, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "N")], 0.008158, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "N")], 0.005756, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "N")], 0.002753, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "N")], 0.007357, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "N")], 0.002853, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "N")], 0.003253, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "N")], 0.006957, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "N")], 0.005055, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "N")], 0.001702, places=6) self.assertAlmostEqual(self.obs_freq_mat[("N", "N")], 0.003303, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "P")], 0.005956, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "P")], 0.001051, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "P")], 0.005255, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "P")], 0.004555, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "P")], 0.002503, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "P")], 0.005405, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "P")], 0.001151, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "P")], 0.003353, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "P")], 0.004705, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "P")], 0.003954, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "P")], 0.001001, places=6) self.assertAlmostEqual(self.obs_freq_mat[("N", "P")], 0.004705, places=6) self.assertAlmostEqual(self.obs_freq_mat[("P", "P")], 0.006006, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "Q")], 0.006456, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "Q")], 0.000801, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "Q")], 0.005806, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "Q")], 0.005255, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "Q")], 0.001952, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "Q")], 0.004454, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "Q")], 0.002202, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "Q")], 0.003103, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "Q")], 0.005405, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "Q")], 0.003954, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "Q")], 0.001351, places=6) self.assertAlmostEqual(self.obs_freq_mat[("N", "Q")], 0.003854, places=6) self.assertAlmostEqual(self.obs_freq_mat[("P", "Q")], 0.003403, places=6) self.assertAlmostEqual(self.obs_freq_mat[("Q", "Q")], 0.002102, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "R")], 0.007608, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "R")], 0.000751, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "R")], 0.005756, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "R")], 0.005906, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "R")], 0.002853, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "R")], 0.004054, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "R")], 0.002202, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "R")], 0.002903, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "R")], 0.007558, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "R")], 0.005455, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "R")], 0.002002, places=6) self.assertAlmostEqual(self.obs_freq_mat[("N", "R")], 0.004505, places=6) self.assertAlmostEqual(self.obs_freq_mat[("P", "R")], 0.003604, places=6) self.assertAlmostEqual(self.obs_freq_mat[("Q", "R")], 0.003654, places=6) self.assertAlmostEqual(self.obs_freq_mat[("R", "R")], 0.004805, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "S")], 0.009960, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "S")], 0.001151, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "S")], 0.008358, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "S")], 0.007157, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "S")], 0.004605, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "S")], 0.008058, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "S")], 0.002953, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "S")], 0.004204, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "S")], 0.007207, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "S")], 0.007958, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "S")], 0.002052, places=6) self.assertAlmostEqual(self.obs_freq_mat[("N", "S")], 0.005756, places=6) self.assertAlmostEqual(self.obs_freq_mat[("P", "S")], 0.005155, places=6) self.assertAlmostEqual(self.obs_freq_mat[("Q", "S")], 0.005055, places=6) self.assertAlmostEqual(self.obs_freq_mat[("R", "S")], 0.004705, places=6) self.assertAlmostEqual(self.obs_freq_mat[("S", "S")], 0.005806, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "T")], 0.009760, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "T")], 0.001502, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "T")], 0.006256, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "T")], 0.007508, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "T")], 0.003453, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "T")], 0.007658, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "T")], 0.003453, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "T")], 0.004404, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "T")], 0.007007, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "T")], 0.009159, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "T")], 0.001752, places=6) self.assertAlmostEqual(self.obs_freq_mat[("N", "T")], 0.005255, places=6) self.assertAlmostEqual(self.obs_freq_mat[("P", "T")], 0.004605, places=6) self.assertAlmostEqual(self.obs_freq_mat[("Q", "T")], 0.004855, places=6) self.assertAlmostEqual(self.obs_freq_mat[("R", "T")], 0.005706, places=6) self.assertAlmostEqual(self.obs_freq_mat[("S", "T")], 0.008609, places=6) self.assertAlmostEqual(self.obs_freq_mat[("T", "T")], 0.004204, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "V")], 0.012613, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "V")], 0.002953, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "V")], 0.004755, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "V")], 0.005506, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "V")], 0.008008, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "V")], 0.006557, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "V")], 0.002703, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "V")], 0.015516, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "V")], 0.006557, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "V")], 0.022372, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "V")], 0.004755, places=6) self.assertAlmostEqual(self.obs_freq_mat[("N", "V")], 0.004655, places=6) self.assertAlmostEqual(self.obs_freq_mat[("P", "V")], 0.005455, places=6) self.assertAlmostEqual(self.obs_freq_mat[("Q", "V")], 0.003453, places=6) self.assertAlmostEqual(self.obs_freq_mat[("R", "V")], 0.004404, places=6) self.assertAlmostEqual(self.obs_freq_mat[("S", "V")], 0.005706, places=6) self.assertAlmostEqual(self.obs_freq_mat[("T", "V")], 0.007257, places=6) self.assertAlmostEqual(self.obs_freq_mat[("V", "V")], 0.011962, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "W")], 0.002352, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "W")], 0.000400, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "W")], 0.001101, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "W")], 0.001051, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "W")], 0.002152, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "W")], 0.001752, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "W")], 0.000651, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "W")], 0.001902, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "W")], 0.001051, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "W")], 0.003704, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "W")], 0.001251, places=6) self.assertAlmostEqual(self.obs_freq_mat[("N", "W")], 0.001451, places=6) self.assertAlmostEqual(self.obs_freq_mat[("P", "W")], 0.000901, places=6) self.assertAlmostEqual(self.obs_freq_mat[("Q", "W")], 0.000751, places=6) self.assertAlmostEqual(self.obs_freq_mat[("R", "W")], 0.001151, places=6) self.assertAlmostEqual(self.obs_freq_mat[("S", "W")], 0.001101, places=6) self.assertAlmostEqual(self.obs_freq_mat[("T", "W")], 0.001752, places=6) self.assertAlmostEqual(self.obs_freq_mat[("V", "W")], 0.002202, places=6) self.assertAlmostEqual(self.obs_freq_mat[("W", "W")], 0.001602, places=6) self.assertAlmostEqual(self.obs_freq_mat[("A", "Y")], 0.006206, places=6) self.assertAlmostEqual(self.obs_freq_mat[("C", "Y")], 0.000951, places=6) self.assertAlmostEqual(self.obs_freq_mat[("D", "Y")], 0.003203, places=6) self.assertAlmostEqual(self.obs_freq_mat[("E", "Y")], 0.003003, places=6) self.assertAlmostEqual(self.obs_freq_mat[("F", "Y")], 0.007107, places=6) self.assertAlmostEqual(self.obs_freq_mat[("G", "Y")], 0.005055, places=6) self.assertAlmostEqual(self.obs_freq_mat[("H", "Y")], 0.002152, places=6) self.assertAlmostEqual(self.obs_freq_mat[("I", "Y")], 0.004705, places=6) self.assertAlmostEqual(self.obs_freq_mat[("K", "Y")], 0.003303, places=6) self.assertAlmostEqual(self.obs_freq_mat[("L", "Y")], 0.008659, places=6) self.assertAlmostEqual(self.obs_freq_mat[("M", "Y")], 0.002052, places=6) self.assertAlmostEqual(self.obs_freq_mat[("N", "Y")], 0.003754, places=6) self.assertAlmostEqual(self.obs_freq_mat[("P", "Y")], 0.003003, places=6) self.assertAlmostEqual(self.obs_freq_mat[("Q", "Y")], 0.002052, places=6) self.assertAlmostEqual(self.obs_freq_mat[("R", "Y")], 0.003103, places=6) self.assertAlmostEqual(self.obs_freq_mat[("S", "Y")], 0.003654, places=6) self.assertAlmostEqual(self.obs_freq_mat[("T", "Y")], 0.004555, places=6) self.assertAlmostEqual(self.obs_freq_mat[("V", "Y")], 0.006707, places=6) self.assertAlmostEqual(self.obs_freq_mat[("W", "Y")], 0.002553, places=6) self.assertAlmostEqual(self.obs_freq_mat[("Y", "Y")], 0.004104, places=6) def test_observed_frequency_to_substitution_matrix(self): of_to_sm = SubsMat.observed_frequency_to_substitution_matrix(self.obs_freq_mat) self.assertEqual( str(of_to_sm), """\ A 1 C 0 8 D 0 0 2 E 1 0 1 2 F 0 1 0 0 1 G 0 0 0 0 0 3 H 0 0 0 0 0 0 4 I 1 1 0 0 1 0 0 2 K 0 0 1 1 0 0 1 0 1 L 0 1 0 0 1 0 0 1 0 1 M 0 0 0 0 1 0 0 1 0 1 1 N 0 0 1 1 0 1 1 0 1 0 0 1 P 0 0 1 1 0 0 0 0 1 0 0 1 3 Q 1 0 1 1 0 0 1 0 1 0 0 1 1 1 R 1 0 1 1 0 0 1 0 1 0 0 1 1 1 2 S 1 0 1 1 0 0 1 0 1 0 0 1 1 1 0 1 T 1 0 0 1 0 0 1 0 1 0 0 1 0 1 1 1 1 V 0 1 0 0 1 0 0 1 0 1 1 0 0 0 0 0 0 1 W 0 0 0 0 1 0 0 1 0 1 1 0 0 0 0 0 0 0 6 Y 0 0 0 0 1 0 1 0 0 1 1 0 0 0 0 0 0 1 1 2 A C D E F G H I K L M N P Q R S T V W Y""", ) def test_obs_freq_mat_sum(self): counts = self.obs_freq_mat.sum() self.assertEqual(len(counts), 20) self.assertAlmostEqual(counts["A"], 0.0851, places=3) self.assertAlmostEqual(counts["C"], 0.0153, places=3) self.assertAlmostEqual(counts["D"], 0.0565, places=3) self.assertAlmostEqual(counts["E"], 0.0544, places=3) self.assertAlmostEqual(counts["F"], 0.0449, places=3) self.assertAlmostEqual(counts["G"], 0.0701, places=3) self.assertAlmostEqual(counts["H"], 0.0239, places=3) self.assertAlmostEqual(counts["I"], 0.0580, places=3) self.assertAlmostEqual(counts["K"], 0.0572, places=3) self.assertAlmostEqual(counts["L"], 0.0936, places=3) self.assertAlmostEqual(counts["M"], 0.0238, places=3) self.assertAlmostEqual(counts["N"], 0.0463, places=3) self.assertAlmostEqual(counts["P"], 0.0409, places=3) self.assertAlmostEqual(counts["Q"], 0.0360, places=3) self.assertAlmostEqual(counts["R"], 0.0437, places=3) self.assertAlmostEqual(counts["S"], 0.0575, places=3) self.assertAlmostEqual(counts["T"], 0.0565, places=3) self.assertAlmostEqual(counts["V"], 0.0780, places=3) self.assertAlmostEqual(counts["W"], 0.0162, places=3) self.assertAlmostEqual(counts["Y"], 0.0420, places=3) def test_log_odds_matris(self): lo_mat_prot = SubsMat.make_log_odds_matrix( acc_rep_mat=self.acc_rep_mat, round_digit=1 ) text = lo_mat_prot.format(fmt=" %d", alphabet="AVILMCFWYHSTNQKRDEGP") self.assertEqual( text, """\ A 0 V 0 1 I 0 0 1 L 0 0 0 0 M 0 0 0 0 1 C 0 0 0 0 0 3 F 0 0 0 0 0 0 1 W 0 0 0 0 0 0 0 2 Y 0 0 0 0 0 0 0 0 1 H 0 0 0 0 0 0 0 0 0 2 S 0 0 0 0 0 0 0 0 0 0 0 T 0 0 0 0 0 0 0 0 0 0 0 0 N 0 0 0 0 0 0 0 0 0 0 0 0 0 Q 0 0 0 0 0 0 0 0 0 0 0 0 0 0 K 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 D 0 0 -1 0 -1 -1 0 0 0 0 0 0 0 0 0 0 1 E 0 0 -1 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 1 G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 P 0 0 0 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 A V I L M C F W Y H S T N Q K R D E G P""", ) text = lo_mat_prot.format(fmt=" %d", alphabet="AVILMCFWYHSTNQKRDEGP", full=True) self.assertEqual( text, """\ A V I L M C F W Y H S T N Q K R D E G P A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 V 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 I 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 -1 0 0 L 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 M 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 -1 0 0 -1 C 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 0 -1 0 0 0 F 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 -1 0 0 W 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 Y 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 H 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 S 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 T 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 N 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Q 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 K 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 D 0 0 -1 0 -1 -1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 E 0 0 -1 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 1 0 0 G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 P 0 0 0 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1""", ) relative_entropy = lo_mat_prot.calculate_relative_entropy(self.obs_freq_mat) self.assertAlmostEqual(relative_entropy, 0.162, places=3) def test_matrices(self): self.assertEqual(len(MatrixInfo.available_matrices), 40) mat = SubsMat.SeqMat(MatrixInfo.benner6) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 2 C -1 12 D 0 -3 5 E 0 -4 4 5 F -3 0 -5 -6 8 G 0 -1 0 0 -5 5 H -2 -1 0 0 0 -2 6 I 0 -3 -4 -4 0 -3 -3 4 K -1 -2 0 0 -6 -1 0 -3 5 L -1 -3 -5 -5 2 -4 -2 2 -4 4 M 0 -3 -4 -4 0 -3 -3 4 -2 -2 4 N 0 -1 2 1 -3 0 1 -2 1 -3 -2 3 P 1 -2 -2 -2 -3 -1 0 -2 -2 0 -1 -1 6 Q -1 -3 0 2 -4 -1 3 -3 2 -2 -3 0 0 5 R -1 0 -1 0 -4 0 1 -3 4 -3 -3 0 -1 2 5 S 1 0 0 -1 -1 0 0 -1 -1 -1 -1 1 1 -1 0 2 T 1 -1 -1 -1 -2 0 -1 0 -1 0 0 0 0 -1 -1 1 2 V 0 -3 -3 -3 0 -2 -3 3 -3 1 3 -2 -1 -3 -3 0 0 4 W -4 1 -6 -5 -1 -1 -2 -5 -1 -3 -4 -4 -4 -2 2 -2 -2 -4 14 Y -4 2 -2 -4 5 -4 4 -3 -4 -1 -3 0 -3 -1 -2 -1 -3 -3 0 9 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.benner22) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 2 C -1 12 D 0 -3 4 E 0 -4 3 4 F -3 0 -5 -5 7 G 0 -1 0 0 -5 6 H -1 -1 0 0 0 -2 6 I 0 -2 -4 -3 0 -3 -3 4 K -1 -3 0 1 -5 -1 0 -3 4 L -1 -2 -4 -4 2 -4 -2 2 -3 4 M 0 -2 -3 -3 0 -3 -2 3 -2 3 4 N 0 -1 2 1 -3 0 1 -2 1 -3 -2 3 P 0 -3 -1 -1 -3 -1 0 -2 -1 -1 -2 -1 7 Q 0 -3 0 1 -3 -1 2 -2 2 -2 -1 0 0 4 R -1 -1 -1 0 -4 0 1 -3 3 -2 -2 0 -1 2 5 S 1 0 0 0 -2 0 0 -1 0 -2 -1 1 1 0 0 2 T 1 -1 0 0 -2 0 -1 0 0 -1 0 0 0 0 0 1 2 V 0 -1 -3 -2 0 -2 -3 3 -2 2 2 -2 -1 -2 -2 0 0 3 W -5 0 -6 -6 0 -4 -2 -4 -3 -1 -2 -5 -5 -3 -1 -3 -4 -4 15 Y -3 0 -3 -4 5 -4 3 -2 -3 0 -1 -1 -3 -1 -2 -1 -3 -2 1 9 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.benner74) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 2 C 0 11 D 0 -3 4 E 0 -3 2 3 F -2 0 -4 -4 7 G 0 -2 0 0 -5 6 H -1 -1 0 0 0 -1 6 I 0 -1 -3 -2 0 -4 -2 4 K 0 -2 0 1 -3 -1 0 -2 3 L -1 -1 -4 -3 2 -4 -1 2 -2 4 M 0 -1 -3 -2 1 -3 -1 2 -1 2 4 N 0 -1 2 1 -3 0 1 -2 0 -3 -2 3 P 0 -3 -1 0 -3 -1 -1 -2 0 -2 -2 -1 7 Q 0 -2 0 1 -2 -1 1 -2 1 -1 -1 0 0 3 R 0 -2 0 0 -3 -1 1 -2 2 -2 -1 0 0 1 4 S 1 0 0 0 -2 0 0 -1 0 -2 -1 0 0 0 0 2 T 0 0 0 0 -2 -1 0 0 0 -1 0 0 0 0 0 1 2 V 0 0 -2 -2 0 -3 -2 3 -1 1 1 -2 -1 -1 -2 -1 0 3 W -4 0 -5 -4 3 -4 -1 -2 -3 0 -1 -4 -5 -2 -1 -3 -3 -2 14 Y -2 0 -2 -3 5 -4 2 -1 -2 0 0 -1 -3 -1 -2 -1 -2 -1 3 8 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum100) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -3 4 C -1 -5 9 D -3 4 -5 7 E -2 0 -6 1 6 F -4 -5 -3 -5 -5 7 G -1 -2 -5 -3 -4 -5 6 H -3 -1 -5 -2 -1 -2 -4 9 I -3 -5 -2 -6 -5 -1 -6 -5 5 K -2 -1 -5 -2 0 -4 -3 -2 -4 6 L -3 -5 -3 -6 -5 0 -5 -4 1 -4 5 M -2 -4 -3 -5 -4 -1 -5 -3 1 -2 2 8 N -2 4 -4 1 -1 -5 -2 0 -5 -1 -5 -4 7 P -1 -3 -5 -3 -3 -5 -4 -3 -4 -2 -4 -4 -4 8 Q -1 -1 -5 -2 1 -4 -3 0 -4 1 -3 -1 -1 -2 7 R -2 -2 -5 -3 -2 -4 -4 -1 -4 2 -4 -2 -1 -3 0 7 S 1 -1 -2 -1 -1 -3 -1 -2 -4 -1 -4 -3 0 -2 -1 -2 6 T -1 -2 -2 -2 -2 -3 -3 -3 -2 -2 -3 -2 -1 -3 -2 -2 1 6 V -1 -5 -2 -5 -3 -2 -5 -5 2 -4 0 0 -4 -4 -3 -4 -3 -1 5 W -4 -6 -5 -7 -5 0 -5 -3 -4 -5 -4 -3 -6 -6 -3 -4 -4 -5 -4 11 X -1 -2 -3 -3 -2 -3 -3 -2 -2 -2 -2 -2 -2 -3 -2 -2 -1 -1 -2 -4 -2 Y -4 -4 -4 -5 -4 3 -6 1 -3 -4 -3 -3 -3 -5 -3 -3 -3 -3 -3 1 -3 8 Z -2 1 -6 0 5 -5 -4 -1 -4 0 -4 -3 -1 -3 3 -1 -1 -2 -3 -4 -2 -4 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum30) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 4 B 0 5 C -3 -2 17 D 0 5 -3 9 E 0 0 1 1 6 F -2 -3 -3 -5 -4 10 G 0 0 -4 -1 -2 -3 8 H -2 -2 -5 -2 0 -3 -3 14 I 0 -2 -2 -4 -3 0 -1 -2 6 K 0 0 -3 0 2 -1 -1 -2 -2 4 L -1 -1 0 -1 -1 2 -2 -1 2 -2 4 M 1 -2 -2 -3 -1 -2 -2 2 1 2 2 6 N 0 4 -1 1 -1 -1 0 -1 0 0 -2 0 8 P -1 -2 -3 -1 1 -4 -1 1 -3 1 -3 -4 -3 11 Q 1 -1 -2 -1 2 -3 -2 0 -2 0 -2 -1 -1 0 8 R -1 -2 -2 -1 -1 -1 -2 -1 -3 1 -2 0 -2 -1 3 8 S 1 0 -2 0 0 -1 0 -1 -1 0 -2 -2 0 -1 -1 -1 4 T 1 0 -2 -1 -2 -2 -2 -2 0 -1 0 0 1 0 0 -3 2 5 V 1 -2 -2 -2 -3 1 -3 -3 4 -2 1 0 -2 -4 -3 -1 -1 1 5 W -5 -5 -2 -4 -1 1 1 -5 -3 -2 -2 -3 -7 -3 -1 0 -3 -5 -3 20 X 0 -1 -2 -1 -1 -1 -1 -1 0 0 0 0 0 -1 0 -1 0 0 0 -2 -1 Y -4 -3 -6 -1 -2 3 -3 0 -1 -1 3 -1 -4 -2 -1 0 -2 -1 1 5 -1 9 Z 0 0 0 0 5 -4 -2 0 -3 1 -1 -1 -1 0 4 0 -1 -1 -3 -1 0 -2 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum35) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -1 5 C -2 -2 15 D -1 5 -3 8 E -1 0 -1 2 6 F -2 -2 -4 -3 -3 8 G 0 0 -3 -2 -2 -3 7 H -2 0 -4 0 -1 -3 -2 12 I -1 -2 -4 -3 -3 1 -3 -3 5 K 0 0 -2 -1 1 -1 -1 -2 -2 5 L -2 -2 -2 -2 -1 2 -3 -2 2 -2 5 M 0 -2 -4 -3 -2 0 -1 1 1 0 3 6 N -1 4 -1 1 -1 -1 1 1 -1 0 -2 -1 7 P -2 -1 -4 -1 0 -4 -2 -1 -1 0 -3 -3 -2 10 Q 0 0 -3 -1 2 -4 -2 -1 -2 0 -2 -1 1 0 7 R -1 -1 -3 -1 -1 -1 -2 -1 -3 2 -2 0 -1 -2 2 8 S 1 0 -3 -1 0 -1 1 -1 -2 0 -2 -1 0 -2 0 -1 4 T 0 -1 -1 -1 -1 -1 -2 -2 -1 0 0 0 0 0 0 -2 2 5 V 0 -2 -2 -2 -2 1 -3 -4 4 -2 2 1 -2 -3 -3 -1 -1 1 5 W -2 -3 -5 -3 -1 1 -1 -4 -1 0 0 1 -2 -4 -1 0 -2 -2 -2 16 X 0 -1 -2 -1 -1 -1 -1 -1 0 0 0 0 0 -1 -1 -1 0 0 0 -1 -1 Y -1 -2 -5 -2 -1 3 -2 0 0 -1 0 0 -2 -3 0 0 -1 -2 0 3 -1 8 Z -1 0 -2 1 5 -3 -2 -1 -3 1 -2 -2 0 0 4 0 0 -1 -2 -1 0 -1 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum40) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -1 5 C -2 -2 16 D -1 6 -2 9 E -1 1 -2 2 7 F -3 -3 -2 -4 -3 9 G 1 -1 -3 -2 -3 -3 8 H -2 0 -4 0 0 -2 -2 13 I -1 -3 -4 -4 -4 1 -4 -3 6 K -1 0 -3 0 1 -3 -2 -1 -3 6 L -2 -3 -2 -3 -2 2 -4 -2 2 -2 6 M -1 -3 -3 -3 -2 0 -2 1 1 -1 3 7 N -1 4 -2 2 -1 -3 0 1 -2 0 -3 -2 8 P -2 -2 -5 -2 0 -4 -1 -2 -2 -1 -4 -2 -2 11 Q 0 0 -4 -1 2 -4 -2 0 -3 1 -2 -1 1 -2 8 R -2 -1 -3 -1 -1 -2 -3 0 -3 3 -2 -1 0 -3 2 9 S 1 0 -1 0 0 -2 0 -1 -2 0 -3 -2 1 -1 1 -1 5 T 0 0 -1 -1 -1 -1 -2 -2 -1 0 -1 -1 0 0 -1 -2 2 6 V 0 -3 -2 -3 -3 0 -4 -4 4 -2 2 1 -3 -3 -3 -2 -1 1 5 W -3 -4 -6 -5 -2 1 -2 -5 -3 -2 -1 -2 -4 -4 -1 -2 -5 -4 -3 19 X 0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 -1 -1 0 0 -1 -2 -1 Y -2 -3 -4 -3 -2 4 -3 2 0 -1 0 1 -2 -3 -1 -1 -2 -1 -1 3 -1 9 Z -1 2 -3 1 5 -4 -2 0 -4 1 -2 -2 0 -1 4 0 0 -1 -3 -2 -1 -2 5 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum45) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -1 4 C -1 -2 12 D -2 5 -3 7 E -1 1 -3 2 6 F -2 -3 -2 -4 -3 8 G 0 -1 -3 -1 -2 -3 7 H -2 0 -3 0 0 -2 -2 10 I -1 -3 -3 -4 -3 0 -4 -3 5 K -1 0 -3 0 1 -3 -2 -1 -3 5 L -1 -3 -2 -3 -2 1 -3 -2 2 -3 5 M -1 -2 -2 -3 -2 0 -2 0 2 -1 2 6 N -1 4 -2 2 0 -2 0 1 -2 0 -3 -2 6 P -1 -2 -4 -1 0 -3 -2 -2 -2 -1 -3 -2 -2 9 Q -1 0 -3 0 2 -4 -2 1 -2 1 -2 0 0 -1 6 R -2 -1 -3 -1 0 -2 -2 0 -3 3 -2 -1 0 -2 1 7 S 1 0 -1 0 0 -2 0 -1 -2 -1 -3 -2 1 -1 0 -1 4 T 0 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 0 -1 -1 -1 2 5 V 0 -3 -1 -3 -3 0 -3 -3 3 -2 1 1 -3 -3 -3 -2 -1 0 5 W -2 -4 -5 -4 -3 1 -2 -3 -2 -2 -2 -2 -4 -3 -2 -2 -4 -3 -3 15 X 0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -1 -2 -1 Y -2 -2 -3 -2 -2 3 -3 2 0 -1 0 0 -2 -3 -1 -1 -2 -1 -1 3 -1 8 Z -1 2 -3 1 4 -3 -2 0 -3 1 -2 -1 0 -1 4 0 0 -1 -3 -2 -1 -2 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum50) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -2 5 C -1 -3 13 D -2 5 -4 8 E -1 1 -3 2 6 F -3 -4 -2 -5 -3 8 G 0 -1 -3 -1 -3 -4 8 H -2 0 -3 -1 0 -1 -2 10 I -1 -4 -2 -4 -4 0 -4 -4 5 K -1 0 -3 -1 1 -4 -2 0 -3 6 L -2 -4 -2 -4 -3 1 -4 -3 2 -3 5 M -1 -3 -2 -4 -2 0 -3 -1 2 -2 3 7 N -1 4 -2 2 0 -4 0 1 -3 0 -4 -2 7 P -1 -2 -4 -1 -1 -4 -2 -2 -3 -1 -4 -3 -2 10 Q -1 0 -3 0 2 -4 -2 1 -3 2 -2 0 0 -1 7 R -2 -1 -4 -2 0 -3 -3 0 -4 3 -3 -2 -1 -3 1 7 S 1 0 -1 0 -1 -3 0 -1 -3 0 -3 -2 1 -1 0 -1 5 T 0 0 -1 -1 -1 -2 -2 -2 -1 -1 -1 -1 0 -1 -1 -1 2 5 V 0 -4 -1 -4 -3 -1 -4 -4 4 -3 1 1 -3 -3 -3 -3 -2 0 5 W -3 -5 -5 -5 -3 1 -3 -3 -3 -3 -2 -1 -4 -4 -1 -3 -4 -3 -3 15 X -1 -1 -2 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 0 -1 -3 -1 Y -2 -3 -3 -3 -2 4 -3 2 -1 -2 -1 0 -2 -3 -1 -1 -2 -2 -1 2 -1 8 Z -1 2 -3 1 5 -4 -2 0 -3 1 -3 -1 0 -1 4 0 0 -1 -3 -2 -1 -2 5 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum55) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -2 5 C -1 -3 13 D -2 5 -4 8 E -1 1 -3 2 6 F -3 -4 -2 -5 -3 8 G 0 -1 -3 -1 -3 -4 8 H -2 0 -3 -1 0 -1 -2 10 I -1 -4 -2 -4 -4 0 -4 -4 5 K -1 0 -3 -1 1 -4 -2 0 -3 6 L -2 -4 -2 -4 -3 1 -4 -3 2 -3 5 M -1 -3 -2 -4 -2 0 -3 -1 2 -2 3 7 N -1 4 -2 2 0 -4 0 1 -3 0 -4 -2 7 P -1 -2 -4 -1 -1 -4 -2 -2 -3 -1 -4 -3 -2 10 Q -1 0 -3 0 2 -4 -2 1 -3 2 -2 0 0 -1 7 R -2 -1 -4 -2 0 -3 -3 0 -4 3 -3 -2 -1 -3 1 7 S 1 0 -1 0 -1 -3 0 -1 -3 0 -3 -2 1 -1 0 -1 5 T 0 0 -1 -1 -1 -2 -2 -2 -1 -1 -1 -1 0 -1 -1 -1 2 5 V 0 -4 -1 -4 -3 -1 -4 -4 4 -3 1 1 -3 -3 -3 -3 -2 0 5 W -3 -5 -5 -5 -3 1 -3 -3 -3 -3 -2 -1 -4 -4 -1 -3 -4 -3 -3 15 X -1 -1 -2 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 0 -1 -3 -1 Y -2 -3 -3 -3 -2 4 -3 2 -1 -2 -1 0 -2 -3 -1 -1 -2 -2 -1 2 -1 8 Z -1 2 -3 1 5 -4 -2 0 -3 1 -3 -1 0 -1 4 0 0 -1 -3 -2 -1 -2 5 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum60) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 4 B -2 4 C 0 -3 9 D -2 4 -3 6 E -1 1 -3 2 5 F -2 -3 -2 -3 -3 6 G 0 -1 -2 -1 -2 -3 6 H -2 0 -3 -1 0 -1 -2 7 I -1 -3 -1 -3 -3 0 -3 -3 4 K -1 0 -3 -1 1 -3 -1 -1 -3 4 L -1 -3 -1 -3 -3 0 -4 -3 2 -2 4 M -1 -3 -1 -3 -2 0 -2 -1 1 -1 2 5 N -1 3 -2 1 0 -3 0 1 -3 0 -3 -2 6 P -1 -2 -3 -1 -1 -4 -2 -2 -3 -1 -3 -2 -2 7 Q -1 0 -3 0 2 -3 -2 1 -3 1 -2 0 0 -1 5 R -1 -1 -3 -1 0 -3 -2 0 -3 2 -2 -1 0 -2 1 5 S 1 0 -1 0 0 -2 0 -1 -2 0 -2 -1 1 -1 0 -1 4 T 0 0 -1 -1 -1 -2 -2 -2 -1 -1 -1 -1 0 -1 -1 -1 1 4 V 0 -3 -1 -3 -2 -1 -3 -3 3 -2 1 1 -3 -2 -2 -2 -2 0 4 W -3 -4 -2 -4 -3 1 -2 -2 -2 -3 -2 -1 -4 -4 -2 -3 -3 -2 -3 10 X 0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 -1 0 0 -1 -2 -1 Y -2 -2 -2 -3 -2 3 -3 2 -1 -2 -1 -1 -2 -3 -1 -2 -2 -2 -1 2 -1 6 Z -1 1 -3 1 4 -3 -2 0 -3 1 -2 -1 0 -1 3 0 0 -1 -2 -2 -1 -2 3 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum62) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 4 B -2 4 C 0 -3 9 D -2 4 -3 6 E -1 1 -4 2 5 F -2 -3 -2 -3 -3 6 G 0 -1 -3 -1 -2 -3 6 H -2 0 -3 -1 0 -1 -2 8 I -1 -3 -1 -3 -3 0 -4 -3 4 K -1 0 -3 -1 1 -3 -2 -1 -3 5 L -1 -4 -1 -4 -3 0 -4 -3 2 -2 4 M -1 -3 -1 -3 -2 0 -3 -2 1 -1 2 5 N -2 3 -3 1 0 -3 0 1 -3 0 -3 -2 6 P -1 -2 -3 -1 -1 -4 -2 -2 -3 -1 -3 -2 -2 7 Q -1 0 -3 0 2 -3 -2 0 -3 1 -2 0 0 -1 5 R -1 -1 -3 -2 0 -3 -2 0 -3 2 -2 -1 0 -2 1 5 S 1 0 -1 0 0 -2 0 -1 -2 0 -2 -1 1 -1 0 -1 4 T 0 -1 -1 -1 -1 -2 -2 -2 -1 -1 -1 -1 0 -1 -1 -1 1 5 V 0 -3 -1 -3 -2 -1 -3 -3 3 -2 1 1 -3 -2 -2 -3 -2 0 4 W -3 -4 -2 -4 -3 1 -2 -2 -3 -3 -2 -1 -4 -4 -2 -3 -3 -2 -3 11 X 0 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 -1 0 0 -1 -2 -1 Y -2 -3 -2 -3 -2 3 -3 2 -1 -2 -1 -1 -2 -3 -1 -2 -2 -2 -1 2 -1 7 Z -1 1 -3 1 4 -3 -2 0 -3 1 -3 -1 0 -1 3 0 0 -1 -2 -3 -1 -2 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum65) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 4 B -2 4 C 0 -3 9 D -2 4 -4 6 E -1 1 -4 2 5 F -2 -3 -2 -4 -3 6 G 0 -1 -3 -1 -2 -3 6 H -2 0 -3 -1 0 -1 -2 8 I -1 -3 -1 -3 -3 0 -4 -3 4 K -1 0 -3 -1 1 -3 -2 -1 -3 5 L -2 -4 -1 -4 -3 0 -4 -3 2 -3 4 M -1 -3 -2 -3 -2 0 -3 -2 1 -2 2 6 N -2 3 -3 1 0 -3 -1 1 -3 0 -4 -2 6 P -1 -2 -3 -2 -1 -4 -2 -2 -3 -1 -3 -3 -2 8 Q -1 0 -3 0 2 -3 -2 1 -3 1 -2 0 0 -1 6 R -1 -1 -4 -2 0 -3 -2 0 -3 2 -2 -2 0 -2 1 6 S 1 0 -1 0 0 -2 0 -1 -2 0 -3 -2 1 -1 0 -1 4 T 0 -1 -1 -1 -1 -2 -2 -2 -1 -1 -1 -1 0 -1 -1 -1 1 5 V 0 -3 -1 -3 -3 -1 -3 -3 3 -2 1 1 -3 -2 -2 -3 -2 0 4 W -3 -4 -2 -5 -3 1 -3 -2 -2 -3 -2 -2 -4 -4 -2 -3 -3 -3 -3 10 X -1 -1 -2 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1 -2 -1 Y -2 -3 -2 -3 -2 3 -3 2 -1 -2 -1 -1 -2 -3 -2 -2 -2 -2 -1 2 -1 7 Z -1 1 -4 1 4 -3 -2 0 -3 1 -3 -2 0 -1 3 0 0 -1 -2 -3 -1 -2 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum70) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 4 B -2 4 C -1 -4 9 D -2 4 -4 6 E -1 1 -4 1 5 F -2 -4 -2 -4 -4 6 G 0 -1 -3 -2 -2 -4 6 H -2 -1 -4 -1 0 -1 -2 8 I -2 -4 -1 -4 -4 0 -4 -4 4 K -1 -1 -4 -1 1 -3 -2 -1 -3 5 L -2 -4 -2 -4 -3 0 -4 -3 2 -3 4 M -1 -3 -2 -3 -2 0 -3 -2 1 -2 2 6 N -2 3 -3 1 0 -3 -1 0 -4 0 -4 -2 6 P -1 -2 -3 -2 -1 -4 -3 -2 -3 -1 -3 -3 -2 8 Q -1 0 -3 -1 2 -3 -2 1 -3 1 -2 0 0 -2 6 R -2 -1 -4 -2 0 -3 -3 0 -3 2 -3 -2 -1 -2 1 6 S 1 0 -1 0 0 -3 -1 -1 -3 0 -3 -2 0 -1 0 -1 4 T 0 -1 -1 -1 -1 -2 -2 -2 -1 -1 -2 -1 0 -1 -1 -1 1 5 V 0 -3 -1 -4 -3 -1 -4 -3 3 -3 1 1 -3 -3 -2 -3 -2 0 4 W -3 -4 -3 -5 -4 1 -3 -2 -3 -3 -2 -2 -4 -4 -2 -3 -3 -3 -3 11 X -1 -1 -2 -2 -1 -2 -2 -1 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1 -3 -1 Y -2 -3 -3 -4 -3 3 -4 2 -1 -2 -1 -1 -2 -3 -2 -2 -2 -2 -2 2 -2 7 Z -1 0 -4 1 4 -4 -2 0 -3 1 -3 -2 0 -1 3 0 0 -1 -3 -3 -1 -2 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum75) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 4 B -2 4 C -1 -4 9 D -2 4 -4 6 E -1 1 -5 1 5 F -3 -4 -2 -4 -4 6 G 0 -1 -3 -2 -3 -4 6 H -2 -1 -4 -1 0 -2 -2 8 I -2 -4 -1 -4 -4 0 -5 -4 4 K -1 -1 -4 -1 1 -4 -2 -1 -3 5 L -2 -4 -2 -4 -4 0 -4 -3 1 -3 4 M -1 -3 -2 -4 -2 0 -3 -2 1 -2 2 6 N -2 3 -3 1 -1 -4 -1 0 -4 0 -4 -3 6 P -1 -2 -4 -2 -1 -4 -3 -2 -3 -1 -3 -3 -3 8 Q -1 0 -3 -1 2 -4 -2 1 -3 1 -3 0 0 -2 6 R -2 -1 -4 -2 0 -3 -3 0 -3 2 -3 -2 -1 -2 1 6 S 1 0 -1 -1 0 -3 -1 -1 -3 0 -3 -2 0 -1 0 -1 5 T 0 -1 -1 -1 -1 -2 -2 -2 -1 -1 -2 -1 0 -1 -1 -1 1 5 V 0 -4 -1 -4 -3 -1 -4 -4 3 -3 1 1 -3 -3 -2 -3 -2 0 4 W -3 -5 -3 -5 -4 1 -3 -2 -3 -4 -2 -2 -4 -5 -2 -3 -3 -3 -3 11 X -1 -2 -2 -2 -1 -2 -2 -1 -2 -1 -1 -1 -1 -2 -1 -1 -1 -1 -1 -3 -1 Y -2 -3 -3 -4 -3 3 -4 2 -2 -2 -1 -2 -3 -4 -2 -2 -2 -2 -2 2 -2 7 Z -1 0 -4 1 4 -4 -2 0 -4 1 -3 -2 0 -2 3 0 0 -1 -3 -3 -1 -3 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum80) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -2 4 C -1 -4 9 D -2 4 -4 6 E -1 1 -5 1 6 F -3 -4 -3 -4 -4 6 G 0 -1 -4 -2 -3 -4 6 H -2 -1 -4 -2 0 -2 -3 8 I -2 -4 -2 -4 -4 -1 -5 -4 5 K -1 -1 -4 -1 1 -4 -2 -1 -3 5 L -2 -4 -2 -5 -4 0 -4 -3 1 -3 4 M -1 -3 -2 -4 -2 0 -4 -2 1 -2 2 6 N -2 4 -3 1 -1 -4 -1 0 -4 0 -4 -3 6 P -1 -2 -4 -2 -2 -4 -3 -3 -4 -1 -3 -3 -3 8 Q -1 0 -4 -1 2 -4 -2 1 -3 1 -3 0 0 -2 6 R -2 -2 -4 -2 -1 -4 -3 0 -3 2 -3 -2 -1 -2 1 6 S 1 0 -2 -1 0 -3 -1 -1 -3 -1 -3 -2 0 -1 0 -1 5 T 0 -1 -1 -1 -1 -2 -2 -2 -1 -1 -2 -1 0 -2 -1 -1 1 5 V 0 -4 -1 -4 -3 -1 -4 -4 3 -3 1 1 -4 -3 -3 -3 -2 0 4 W -3 -5 -3 -6 -4 0 -4 -3 -3 -4 -2 -2 -4 -5 -3 -4 -4 -4 -3 11 X -1 -2 -3 -2 -1 -2 -2 -2 -2 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -3 -1 Y -2 -3 -3 -4 -3 3 -4 2 -2 -3 -2 -2 -3 -4 -2 -3 -2 -2 -2 2 -2 7 Z -1 0 -4 1 4 -4 -3 0 -4 1 -3 -2 0 -2 3 0 0 -1 -3 -4 -1 -3 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum85) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -2 4 C -1 -4 9 D -2 4 -5 7 E -1 0 -5 1 6 F -3 -4 -3 -4 -4 7 G 0 -1 -4 -2 -3 -4 6 H -2 -1 -5 -2 -1 -2 -3 8 I -2 -5 -2 -5 -4 -1 -5 -4 5 K -1 -1 -4 -1 0 -4 -2 -1 -3 6 L -2 -5 -2 -5 -4 0 -5 -3 1 -3 4 M -2 -4 -2 -4 -3 -1 -4 -3 1 -2 2 7 N -2 4 -4 1 -1 -4 -1 0 -4 0 -4 -3 7 P -1 -3 -4 -2 -2 -4 -3 -3 -4 -2 -4 -3 -3 8 Q -1 -1 -4 -1 2 -4 -3 1 -4 1 -3 0 0 -2 6 R -2 -2 -4 -2 -1 -4 -3 0 -4 2 -3 -2 -1 -2 1 6 S 1 0 -2 -1 -1 -3 -1 -1 -3 -1 -3 -2 0 -1 -1 -1 5 T 0 -1 -2 -2 -1 -3 -2 -2 -1 -1 -2 -1 0 -2 -1 -2 1 5 V -1 -4 -1 -4 -3 -1 -4 -4 3 -3 0 0 -4 -3 -3 -3 -2 0 5 W -3 -5 -4 -6 -4 0 -4 -3 -3 -5 -3 -2 -5 -5 -3 -4 -4 -4 -3 11 X -1 -2 -3 -2 -1 -2 -2 -2 -2 -1 -2 -1 -2 -2 -1 -2 -1 -1 -1 -3 -2 Y -3 -4 -3 -4 -4 3 -5 2 -2 -3 -2 -2 -3 -4 -2 -3 -2 -2 -2 2 -2 7 Z -1 0 -5 1 4 -4 -3 0 -4 1 -4 -2 -1 -2 4 0 -1 -1 -3 -4 -1 -3 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum90) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -2 4 C -1 -4 9 D -3 4 -5 7 E -1 0 -6 1 6 F -3 -4 -3 -5 -5 7 G 0 -2 -4 -2 -3 -5 6 H -2 -1 -5 -2 -1 -2 -3 8 I -2 -5 -2 -5 -4 -1 -5 -4 5 K -1 -1 -4 -1 0 -4 -2 -1 -4 6 L -2 -5 -2 -5 -4 0 -5 -4 1 -3 5 M -2 -4 -2 -4 -3 -1 -4 -3 1 -2 2 7 N -2 4 -4 1 -1 -4 -1 0 -4 0 -4 -3 7 P -1 -3 -4 -3 -2 -4 -3 -3 -4 -2 -4 -3 -3 8 Q -1 -1 -4 -1 2 -4 -3 1 -4 1 -3 0 0 -2 7 R -2 -2 -5 -3 -1 -4 -3 0 -4 2 -3 -2 -1 -3 1 6 S 1 0 -2 -1 -1 -3 -1 -2 -3 -1 -3 -2 0 -2 -1 -1 5 T 0 -1 -2 -2 -1 -3 -3 -2 -1 -1 -2 -1 0 -2 -1 -2 1 6 V -1 -4 -2 -5 -3 -2 -5 -4 3 -3 0 0 -4 -3 -3 -3 -2 -1 5 W -4 -6 -4 -6 -5 0 -4 -3 -4 -5 -3 -2 -5 -5 -3 -4 -4 -4 -3 11 X -1 -2 -3 -2 -2 -2 -2 -2 -2 -1 -2 -1 -2 -2 -1 -2 -1 -1 -2 -3 -2 Y -3 -4 -4 -4 -4 3 -5 1 -2 -3 -2 -2 -3 -4 -3 -3 -3 -2 -3 2 -2 8 Z -1 0 -5 0 4 -4 -3 0 -4 1 -4 -2 -1 -2 4 0 -1 -1 -3 -4 -1 -3 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.blosum95) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -3 4 C -1 -4 9 D -3 4 -5 7 E -1 0 -6 1 6 F -3 -5 -3 -5 -5 7 G -1 -2 -5 -2 -3 -5 6 H -3 -1 -5 -2 -1 -2 -3 9 I -2 -5 -2 -5 -4 -1 -6 -4 5 K -1 -1 -5 -2 0 -4 -3 -1 -4 6 L -2 -5 -3 -5 -4 0 -5 -4 1 -3 5 M -2 -4 -3 -5 -3 -1 -4 -3 1 -2 2 7 N -2 4 -4 1 -1 -4 -1 0 -4 0 -5 -3 7 P -1 -3 -5 -3 -2 -5 -4 -3 -4 -2 -4 -3 -3 8 Q -1 -1 -4 -1 2 -4 -3 1 -4 1 -3 -1 0 -2 7 R -2 -2 -5 -3 -1 -4 -4 -1 -4 2 -3 -2 -1 -3 0 7 S 1 -1 -2 -1 -1 -3 -1 -2 -3 -1 -3 -3 0 -2 -1 -2 5 T 0 -1 -2 -2 -2 -3 -3 -2 -2 -1 -2 -1 -1 -2 -1 -2 1 6 V -1 -5 -2 -5 -3 -2 -5 -4 3 -3 0 0 -4 -4 -3 -4 -3 -1 5 W -4 -6 -4 -6 -5 0 -5 -3 -4 -5 -3 -2 -5 -5 -3 -4 -4 -4 -3 11 X -1 -2 -3 -2 -2 -2 -3 -2 -2 -1 -2 -2 -2 -3 -1 -2 -1 -1 -2 -4 -2 Y -3 -4 -4 -5 -4 3 -5 1 -2 -3 -2 -3 -3 -5 -3 -3 -3 -3 -3 2 -2 8 Z -1 0 -5 0 4 -4 -3 0 -4 0 -4 -2 -1 -2 4 -1 -1 -2 -3 -4 -1 -4 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.feng) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 6 C 2 6 D 4 1 6 E 4 0 5 6 F 2 3 1 0 6 G 5 3 4 4 1 6 H 2 2 3 2 2 1 6 I 2 2 1 1 4 2 1 6 K 3 0 3 4 0 2 3 2 6 L 2 2 1 1 4 2 3 5 2 6 M 2 2 0 1 2 1 1 4 2 5 6 N 3 2 5 3 1 3 4 2 4 1 1 6 P 5 2 2 3 2 3 3 2 2 3 2 2 6 Q 3 1 4 4 1 2 4 1 4 2 2 3 3 6 R 2 2 2 2 1 3 4 2 5 2 2 2 3 3 6 S 5 4 3 3 3 5 3 2 3 2 1 5 4 3 3 6 T 5 2 2 3 1 2 2 3 4 2 3 4 4 3 3 5 6 V 5 2 3 4 4 4 1 5 3 5 4 2 3 2 2 2 3 6 W 2 3 0 1 3 3 1 2 1 4 3 0 2 1 2 2 1 3 6 Y 2 3 2 1 5 2 3 3 1 3 2 3 2 2 1 3 2 3 3 6 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.fitch) self.assertEqual(len(mat), 171) self.checkMatrix( mat, """\ A 3 C 1 3 E 1 1 3 F 1 2 1 3 H 2 1 1 1 3 I 1 0 2 0 1 3 L 2 1 2 1 1 1 3 M 0 0 2 1 0 2 1 3 N 2 1 2 1 2 2 1 1 3 O 2 2 1 2 2 1 1 0 2 3 Q 1 1 1 1 2 2 1 1 1 2 3 R 1 2 2 1 2 2 1 2 1 1 2 3 S 1 2 2 2 1 1 2 1 2 2 2 2 3 T 0 2 1 1 0 1 1 1 0 1 2 2 2 3 U 1 1 1 2 2 1 1 2 1 1 2 2 2 2 3 V 2 2 1 2 1 1 2 2 1 1 1 1 1 1 2 3 W 1 1 2 2 1 1 1 2 2 1 0 1 2 0 2 2 3 Y 2 2 1 1 1 1 2 1 1 1 1 2 2 2 2 2 1 3 A C E F H I L M N O Q R S T U V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.genetic) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 4 C -1 5 D 1 -1 4 E 1 -3 3 5 F -2 1 -1 -2 4 G 1 1 1 1 -1 4 H -2 -1 1 0 -1 -2 4 I -1 -1 -2 -2 1 -2 -1 4 K -1 -3 0 2 -2 -2 0 0 5 L -2 -1 -2 -2 2 -2 0 1 -2 3 M -2 -2 -2 -1 0 -2 -1 3 1 1 5 N -1 -1 1 0 -1 -2 1 0 3 -2 0 4 P 0 -1 -2 -2 -1 -1 0 -1 -1 0 -1 -1 3 Q -2 -3 0 2 -2 -2 3 -1 2 0 -1 0 1 5 R -1 0 -2 -2 -1 0 3 -1 0 0 0 -1 0 0 2 S 0 1 -2 -2 0 0 -1 0 -1 -1 -1 0 0 -2 0 2 T 0 -1 -2 -2 -2 -2 -1 0 1 -1 0 0 1 -1 0 1 4 V 1 -2 1 1 1 1 -2 1 -2 1 1 -2 -2 -2 -2 -2 -2 4 W -2 4 -2 -3 0 1 -2 -2 -3 0 -2 -3 -1 -2 1 0 -2 -2 7 Y -2 2 2 0 2 -1 2 -1 0 -1 -2 2 -2 0 -1 0 -2 -2 0 6 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.gonnet) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 2 C 0 11 D 0 -3 4 E 0 -3 2 3 F -2 0 -4 -3 7 G 0 -2 0 0 -5 6 H 0 -1 0 0 0 -1 6 I 0 -1 -3 -2 1 -4 -2 4 K 0 -2 0 1 -3 -1 0 -2 3 L -1 -1 -4 -2 2 -4 -1 2 -2 4 M 0 0 -3 -2 1 -3 -1 2 -1 2 4 N 0 -1 2 0 -3 0 1 -2 0 -3 -2 3 P 0 -3 0 0 -3 -1 -1 -2 0 -2 -2 0 7 Q 0 -2 0 1 -2 -1 1 -1 1 -1 -1 0 0 2 R 0 -2 0 0 -3 -1 0 -2 2 -2 -1 0 0 1 4 S 1 0 0 0 -2 0 0 -1 0 -2 -1 0 0 0 0 2 T 0 0 0 0 -2 -1 0 0 0 -1 0 0 0 0 0 1 2 V 0 0 -2 -1 0 -3 -2 3 -1 1 1 -2 -1 -1 -2 -1 0 3 W -3 -1 -5 -4 3 -4 0 -1 -3 0 -1 -3 -5 -2 -1 -3 -3 -2 14 Y -2 0 -2 -2 5 -4 2 0 -2 0 0 -1 -3 -1 -1 -1 -1 -1 4 7 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.grant) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 215 C 20 215 D 89 61 215 E 108 45 170 215 F 102 10 38 75 215 G 155 56 121 117 62 215 H 129 41 134 175 115 117 215 I 121 17 47 81 194 80 121 215 K 109 13 114 159 113 88 183 113 215 L 119 17 43 77 193 77 116 210 108 215 M 131 19 55 89 187 88 128 205 120 200 215 N 104 76 192 173 57 135 147 66 121 62 73 215 P 188 46 107 122 101 173 138 120 112 117 128 124 215 Q 124 61 154 186 99 128 191 106 162 102 114 169 139 215 R 103 35 119 161 118 90 186 118 189 113 124 129 112 172 215 S 116 103 150 135 60 159 126 73 94 70 80 169 141 147 105 215 T 157 66 130 150 112 156 168 126 137 123 134 150 177 173 144 157 215 V 151 23 63 94 165 106 131 186 118 183 194 82 147 119 119 91 146 215 W 67 0 34 63 175 31 100 154 105 154 148 41 68 85 114 38 87 127 215 Y 103 21 55 93 193 68 132 182 130 179 179 72 105 116 138 71 123 160 178 215 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.ident) self.checkMatrix( mat, """\ A 6 C -1 6 D -1 -1 6 E -1 -1 -1 6 F -1 -1 -1 -1 6 G -1 -1 -1 -1 -1 6 H -1 -1 -1 -1 -1 -1 6 I -1 -1 -1 -1 -1 -1 -1 6 K -1 -1 -1 -1 -1 -1 -1 -1 6 L -1 -1 -1 -1 -1 -1 -1 -1 -1 6 M -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 N -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 P -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 Q -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 R -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 S -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 T -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 V -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 W -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 Y -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.johnson) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 6 C -3 16 D -1 -9 8 E 0 -6 2 8 F -3 -4 -7 -6 10 G 0 -8 -2 -2 -8 8 H -3 -8 0 -2 -1 -3 12 I -2 -7 -4 -4 0 -5 -5 8 K 0 -8 -1 1 -5 -3 0 -4 7 L -3 -8 -8 -5 1 -7 -4 2 -3 7 M -1 -4 -5 -2 0 -5 -2 2 -1 4 11 N -1 -7 2 0 -3 -1 1 -4 0 -4 -3 8 P -1 -8 -1 -1 -5 -2 -4 -5 0 -2 -9 -2 10 Q 0 -6 -1 2 -6 -2 1 -7 1 -4 0 0 -3 9 R -1 -5 -3 0 -6 -2 0 -5 3 -3 -4 -1 -3 2 10 S 0 -7 0 -2 -4 -1 -2 -4 -1 -5 -4 1 -1 -1 0 5 T 0 -6 -1 0 -5 -3 -3 -3 0 -4 -3 0 -2 0 -1 2 6 V 0 -4 -5 -4 -1 -5 -3 3 -3 1 0 -5 -5 -3 -4 -4 -1 7 W -5 -9 -6 -7 3 -6 -4 -3 -5 -1 0 -6 -7 -8 -3 -6 -9 -4 15 Y -4 -7 -3 -3 3 -5 0 -2 -3 -2 -1 -1 -7 -5 -2 -3 -2 -1 2 10 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.levin) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 2 C 0 2 D 0 0 2 E 1 0 1 2 F -1 -1 -1 -1 2 G 0 0 0 0 -1 2 H 0 0 0 0 -1 0 2 I 0 0 -1 -1 1 -1 -1 2 K 0 0 0 0 -1 0 0 -1 2 L 0 0 -1 -1 0 -1 -1 0 -1 2 M 0 0 -1 -1 0 -1 -1 0 -1 2 2 N 0 0 1 0 -1 0 0 -1 1 -1 -1 3 P -1 0 0 -1 -1 0 0 -1 0 -1 -1 0 3 Q 0 0 0 1 -1 0 0 -1 0 -1 -1 1 0 2 R 0 0 0 0 -1 0 0 -1 1 -1 -1 0 0 0 2 S 1 0 0 0 -1 0 0 -1 0 -1 -1 0 0 0 0 2 T 0 0 0 0 -1 0 0 0 0 0 0 0 0 0 0 0 2 V 0 0 -1 -1 0 -1 -1 1 -1 1 0 -1 -1 -1 -1 -1 0 2 W -1 -1 -1 -1 0 -1 -1 0 -1 0 0 -1 -1 -1 0 -1 -1 0 2 Y -1 -1 -1 -1 1 -1 0 0 -1 0 0 -1 -1 -1 -1 -1 -1 0 0 2 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.mclach) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 8 C 1 9 D 3 1 8 E 4 0 5 8 F 1 0 1 0 9 G 3 1 3 3 0 8 H 3 3 4 2 4 2 8 I 2 1 1 1 3 1 2 8 K 3 0 3 4 0 3 4 1 8 L 2 0 1 1 5 1 2 5 2 8 M 3 3 2 1 5 1 3 5 1 6 8 N 3 1 5 4 0 3 4 1 4 1 2 8 P 4 0 3 4 1 3 3 1 3 1 1 1 8 Q 3 0 4 5 0 2 4 0 4 3 3 4 3 8 R 2 1 1 3 1 3 5 1 5 2 1 3 3 5 8 S 4 2 3 4 2 3 3 2 3 2 2 5 3 4 4 8 T 3 2 3 4 1 2 4 3 3 3 3 3 3 3 3 5 8 V 3 1 1 2 3 2 2 5 2 5 4 1 2 2 2 2 3 8 W 1 2 0 1 6 1 3 3 1 3 1 0 0 2 3 3 2 2 9 Y 1 1 1 2 6 0 4 3 1 3 2 2 0 1 2 3 1 3 6 9 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.miyata) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 1 C 0 1 D -1 -2 1 E -1 -2 0 1 F -1 0 -3 -2 1 G 0 0 -1 -1 -2 1 H 0 -1 0 0 -1 -1 1 I -1 0 -2 -2 0 -2 -1 1 K -1 -2 0 0 -1 -2 0 -1 1 L -1 0 -2 -2 0 -2 -1 1 -1 1 M -1 0 -2 -1 0 -2 0 0 -1 0 1 N 0 -1 0 0 -2 0 0 -2 0 -2 -1 1 P 1 0 -1 -1 -1 0 0 -1 -1 -1 -1 0 1 Q 0 -1 0 0 -1 -1 0 -1 0 -1 -1 0 0 1 R -1 -1 -1 0 -1 -2 0 -1 0 -1 -1 0 -1 0 1 S 0 0 0 0 -2 0 0 -1 -1 -1 -1 0 0 0 -1 1 T 0 0 0 0 -1 0 0 0 0 -1 0 0 0 0 0 0 1 V 0 0 -2 -1 0 -1 0 0 -1 0 0 -1 0 0 -1 0 0 1 W -2 -2 -3 -2 0 -3 -1 0 -1 0 0 -3 -2 -2 -1 -3 -2 -1 1 Y -1 -1 -2 -1 0 -2 -1 0 -1 0 0 -2 -1 -1 0 -2 -1 0 0 1 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.nwsgappep) self.assertEqual(len(mat), 253) self.checkMatrix( mat, """\ A 1 B 0 1 C 0 0 1 D 0 1 0 1 E 0 0 0 1 1 F 0 0 0 -1 0 1 G 0 0 0 0 0 0 1 H 0 0 0 0 0 0 0 1 I 0 0 0 0 0 0 0 0 1 K 0 0 0 0 0 0 0 0 0 1 L 0 0 0 0 0 1 0 0 0 0 1 M 0 0 0 0 0 0 0 0 0 0 1 1 N 0 1 0 0 0 0 0 0 0 0 0 0 1 P 0 0 0 0 0 0 0 0 0 0 0 0 0 1 Q 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 R 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 S 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 T 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 V 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 W 0 0 -1 -1 -1 1 -1 0 0 0 0 0 0 0 0 1 0 0 0 1 Y 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 Z 0 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 1 A B C D E F G H I K L M N P Q R S T V W Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.pam120) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 3 B 0 4 C -3 -6 9 D 0 4 -7 5 E 0 3 -7 3 5 F -4 -5 -6 -7 -7 8 G 1 0 -4 0 -1 -5 5 H -3 1 -4 0 -1 -3 -4 7 I -1 -3 -3 -3 -3 0 -4 -4 6 K -2 0 -7 -1 -1 -7 -3 -2 -3 5 L -3 -4 -7 -5 -4 0 -5 -3 1 -4 5 M -2 -4 -6 -4 -3 -1 -4 -4 1 0 3 8 N -1 3 -5 2 1 -4 0 2 -2 1 -4 -3 4 P 1 -2 -4 -3 -2 -5 -2 -1 -3 -2 -3 -3 -2 6 Q -1 0 -7 1 2 -6 -3 3 -3 0 -2 -1 0 0 6 R -3 -2 -4 -3 -3 -5 -4 1 -2 2 -4 -1 -1 -1 1 6 S 1 0 0 0 -1 -3 1 -2 -2 -1 -4 -2 1 1 -2 -1 3 T 1 0 -3 -1 -2 -4 -1 -3 0 -1 -3 -1 0 -1 -2 -2 2 4 V 0 -3 -3 -3 -3 -3 -2 -3 3 -4 1 1 -3 -2 -3 -3 -2 0 5 W -7 -6 -8 -8 -8 -1 -8 -3 -6 -5 -3 -6 -4 -7 -6 1 -2 -6 -8 12 X -1 -1 -4 -2 -1 -3 -2 -2 -1 -2 -2 -2 -1 -2 -1 -2 -1 -1 -1 -5 -2 Y -4 -3 -1 -5 -5 4 -6 -1 -2 -5 -2 -4 -2 -6 -5 -5 -3 -3 -3 -2 -3 8 Z -1 2 -7 3 4 -6 -2 1 -3 -1 -3 -2 0 -1 4 -1 -1 -2 -3 -7 -1 -5 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.pam180) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 3 B 0 4 C -3 -6 13 D 0 4 -7 5 E 0 3 -7 4 5 F -5 -6 -6 -8 -7 10 G 1 0 -5 0 0 -6 6 H -2 1 -4 0 0 -3 -3 8 I -1 -3 -3 -3 -3 1 -4 -4 6 K -2 0 -7 0 -1 -7 -3 -1 -3 6 L -3 -5 -8 -6 -5 1 -6 -3 2 -4 7 M -2 -3 -7 -4 -3 0 -4 -3 2 1 4 9 N 0 3 -5 3 2 -5 0 2 -3 1 -4 -3 4 P 1 -2 -4 -2 -1 -6 -1 -1 -3 -2 -4 -3 -1 8 Q -1 1 -7 2 3 -6 -2 4 -3 0 -2 -1 0 0 6 R -3 -2 -5 -3 -2 -6 -4 2 -3 4 -4 -1 -1 -1 1 8 S 1 1 0 0 -1 -4 1 -2 -2 -1 -4 -2 1 1 -1 -1 3 T 2 0 -3 -1 -1 -4 -1 -2 0 0 -3 -1 0 0 -2 -2 2 4 V 0 -3 -3 -3 -3 -2 -2 -3 5 -4 2 2 -3 -2 -3 -4 -2 0 6 W -8 -7 -10 -9 -9 0 -9 -4 -7 -5 -3 -6 -5 -7 -6 2 -3 -7 -8 18 X -1 -1 -4 -1 -1 -3 -2 -1 -1 -1 -2 -1 -1 -1 -1 -2 0 -1 -1 -6 -1 Y -5 -4 0 -6 -6 7 -7 0 -2 -6 -2 -4 -2 -7 -6 -6 -4 -4 -4 -1 -3 11 Z 0 3 -7 3 5 -7 -1 2 -3 0 -3 -2 1 -1 5 0 -1 -1 -3 -8 -1 -6 5 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.pam250) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 2 B 0 3 C -2 -4 12 D 0 3 -5 4 E 0 3 -5 3 4 F -3 -4 -4 -6 -5 9 G 1 0 -3 1 0 -5 5 H -1 1 -3 1 1 -2 -2 6 I -1 -2 -2 -2 -2 1 -3 -2 5 K -1 1 -5 0 0 -5 -2 0 -2 5 L -2 -3 -6 -4 -3 2 -4 -2 2 -3 6 M -1 -2 -5 -3 -2 0 -3 -2 2 0 4 6 N 0 2 -4 2 1 -3 0 2 -2 1 -3 -2 2 P 1 -1 -3 -1 -1 -5 0 0 -2 -1 -3 -2 0 6 Q 0 1 -5 2 2 -5 -1 3 -2 1 -2 -1 1 0 4 R -2 -1 -4 -1 -1 -4 -3 2 -2 3 -3 0 0 0 1 6 S 1 0 0 0 0 -3 1 -1 -1 0 -3 -2 1 1 -1 0 2 T 1 0 -2 0 0 -3 0 -1 0 0 -2 -1 0 0 -1 -1 1 3 V 0 -2 -2 -2 -2 -1 -1 -2 4 -2 2 2 -2 -1 -2 -2 -1 0 4 W -6 -5 -8 -7 -7 0 -7 -3 -5 -3 -2 -4 -4 -6 -5 2 -2 -5 -6 17 X 0 -1 -3 -1 -1 -2 -1 -1 -1 -1 -1 -1 0 -1 -1 -1 0 0 -1 -4 -1 Y -3 -3 0 -4 -4 7 -5 0 -1 -4 -1 -2 -2 -5 -4 -4 -3 -3 -2 0 -2 10 Z 0 2 -5 3 3 -5 0 2 -2 0 -3 -2 1 0 3 0 0 -1 -2 -6 -1 -4 3 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.pam30) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 6 B -3 6 C -6 -12 10 D -3 6 -14 8 E -2 1 -14 2 8 F -8 -10 -13 -15 -14 9 G -2 -3 -9 -3 -4 -9 6 H -7 -1 -7 -4 -5 -6 -9 9 I -5 -6 -6 -7 -5 -2 -11 -9 8 K -7 -2 -14 -4 -4 -14 -7 -6 -6 7 L -6 -9 -15 -12 -9 -3 -10 -6 -1 -8 7 M -5 -10 -13 -11 -7 -4 -8 -10 -1 -2 1 11 N -4 6 -11 2 -2 -9 -3 0 -5 -1 -7 -9 8 P -2 -7 -8 -8 -5 -10 -6 -4 -8 -6 -7 -8 -6 8 Q -4 -3 -14 -2 1 -13 -7 1 -8 -3 -5 -4 -3 -3 8 R -7 -7 -8 -10 -9 -9 -9 -2 -5 0 -8 -4 -6 -4 -2 8 S 0 -1 -3 -4 -4 -6 -2 -6 -7 -4 -8 -5 0 -2 -5 -3 6 T -1 -3 -8 -5 -6 -9 -6 -7 -2 -3 -7 -4 -2 -4 -5 -6 0 7 V -2 -8 -6 -8 -6 -8 -5 -6 2 -9 -2 -1 -8 -6 -7 -8 -6 -3 7 W -13 -10 -15 -15 -17 -4 -15 -7 -14 -12 -6 -13 -8 -14 -13 -2 -5 -13 -15 13 X -3 -5 -9 -5 -5 -8 -5 -5 -5 -5 -6 -5 -3 -5 -5 -6 -3 -4 -5 -11 -5 Y -8 -6 -4 -11 -8 2 -14 -3 -6 -9 -7 -11 -4 -13 -12 -10 -7 -6 -7 -5 -7 10 Z -3 0 -14 1 6 -13 -5 -1 -6 -4 -7 -5 -3 -4 6 -4 -5 -6 -6 -14 -5 -9 6 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.pam300) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 2 B 0 3 C -2 -5 15 D 0 3 -6 4 E 0 3 -6 4 4 F -4 -5 -5 -6 -6 11 G 2 1 -4 1 0 -5 5 H -1 1 -4 1 1 -2 -2 7 I 0 -2 -3 -2 -2 1 -3 -2 5 K -1 1 -6 0 0 -6 -2 0 -2 5 L -2 -4 -7 -4 -4 3 -4 -2 3 -3 7 M -1 -2 -6 -3 -2 1 -3 -2 3 0 4 6 N 0 2 -4 2 2 -4 1 2 -2 1 -3 -2 2 P 1 0 -3 -1 0 -5 0 0 -2 -1 -3 -2 0 6 Q 0 2 -6 2 3 -5 -1 3 -2 1 -2 -1 1 0 4 R -1 0 -4 -1 -1 -5 -2 2 -2 4 -3 0 0 0 2 7 S 1 1 0 0 0 -4 1 -1 -1 0 -3 -2 1 1 0 0 1 T 1 0 -2 0 0 -3 0 -1 0 0 -2 -1 0 1 -1 -1 1 2 V 0 -2 -2 -2 -2 -1 -1 -2 4 -2 2 2 -2 -1 -2 -3 -1 0 5 W -6 -6 -9 -7 -8 1 -8 -3 -6 -4 -2 -5 -5 -6 -5 3 -3 -6 -7 22 X 0 0 -3 -1 -1 -2 -1 0 -1 -1 -1 -1 0 -1 0 -1 0 0 0 -4 -1 Y -4 -4 1 -5 -5 9 -6 0 -1 -5 0 -2 -2 -5 -4 -5 -3 -3 -3 0 -2 12 Z 0 2 -6 3 3 -5 0 2 -2 1 -3 -2 1 0 3 0 0 0 -2 -6 -1 -5 3 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.pam60) self.assertEqual(len(mat), 276) self.checkMatrix( mat, """\ A 5 B -2 5 C -5 -9 9 D -2 5 -10 7 E -1 2 -10 3 7 F -6 -8 -9 -11 -10 8 G 0 -2 -7 -2 -2 -7 6 H -5 0 -6 -2 -3 -4 -6 8 I -3 -4 -4 -5 -4 -1 -7 -6 7 K -5 -1 -10 -2 -3 -10 -5 -4 -4 6 L -4 -7 -11 -9 -7 -1 -8 -4 0 -6 6 M -3 -6 -10 -7 -5 -2 -6 -7 1 0 2 10 N -2 5 -7 2 0 -6 -1 1 -4 0 -5 -6 6 P 0 -4 -6 -5 -3 -7 -4 -2 -6 -4 -5 -6 -4 7 Q -3 -1 -10 -1 2 -9 -5 2 -5 -1 -3 -2 -2 -1 7 R -5 -5 -6 -6 -6 -7 -7 0 -4 2 -6 -2 -3 -2 0 8 S 1 0 -1 -2 -2 -5 0 -4 -4 -2 -6 -4 1 0 -3 -2 5 T 1 -2 -5 -3 -4 -6 -3 -5 -1 -2 -5 -2 -1 -2 -4 -4 1 6 V -1 -5 -4 -6 -4 -5 -4 -5 3 -6 -1 0 -5 -4 -5 -5 -4 -1 6 W -10 -8 -12 -11 -12 -3 -11 -5 -10 -8 -4 -9 -6 -10 -9 0 -4 -9 -11 13 X -2 -3 -6 -3 -3 -5 -3 -3 -3 -3 -4 -3 -2 -3 -3 -4 -2 -2 -3 -8 -3 Y -6 -5 -2 -8 -7 3 -10 -2 -4 -7 -5 -7 -3 -10 -8 -8 -5 -5 -5 -3 -5 9 Z -2 1 -10 2 5 -10 -3 0 -4 -2 -5 -4 -1 -2 6 -2 -3 -4 -5 -11 -3 -7 5 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.pam90) self.assertEqual(len(mat), 253) self.checkMatrix( mat, """\ A 4 B -1 4 C -3 -7 9 D -1 5 -8 6 E 0 2 -8 4 6 F -5 -6 -7 -8 -8 8 G 0 -1 -5 -1 -1 -6 5 H -4 1 -5 -1 -1 -3 -5 8 I -2 -3 -3 -4 -3 0 -5 -5 6 K -3 0 -8 -2 -2 -8 -4 -2 -3 5 L -3 -5 -9 -7 -5 0 -6 -3 1 -5 6 M -2 -5 -8 -5 -4 -1 -5 -5 1 0 2 9 N -1 4 -6 3 0 -5 -1 2 -3 1 -4 -4 5 P 0 -3 -5 -4 -2 -6 -3 -2 -4 -3 -4 -4 -2 7 Q -2 0 -8 0 2 -7 -3 2 -4 -1 -3 -2 -1 -1 6 R -4 -3 -5 -5 -4 -6 -5 1 -3 2 -5 -2 -2 -1 0 7 S 1 0 -1 -1 -2 -4 0 -3 -3 -1 -5 -3 1 0 -2 -1 4 T 1 -1 -4 -2 -2 -5 -2 -3 0 -1 -3 -2 0 -1 -3 -3 2 5 V 0 -4 -3 -4 -3 -4 -3 -4 3 -5 0 1 -4 -3 -4 -4 -3 -1 6 W -8 -7 -10 -9 -10 -2 -9 -4 -8 -6 -3 -7 -5 -8 -7 0 -3 -7 -9 13 Y -5 -4 -1 -6 -6 4 -8 -1 -3 -6 -3 -6 -2 -8 -6 -6 -4 -4 -4 -2 9 Z -1 2 -8 3 5 -8 -2 1 -3 -1 -4 -3 0 -2 5 -1 -2 -2 -3 -8 -6 5 A B C D E F G H I K L M N P Q R S T V W Y Z""", ) mat = SubsMat.SeqMat(MatrixInfo.rao) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 16 C 11 16 D 9 8 16 E 10 9 11 16 F 10 10 4 6 16 G 8 8 9 6 7 16 H 11 10 9 11 9 7 16 I 9 8 3 4 12 6 8 16 K 10 9 11 11 6 7 11 4 16 L 11 11 6 7 11 6 10 10 7 16 M 11 10 5 8 10 4 10 9 8 11 16 N 9 9 11 10 6 10 10 5 11 7 6 16 P 6 7 8 5 4 11 5 3 6 4 2 9 16 Q 11 10 11 11 7 8 11 6 12 9 9 11 7 16 R 8 8 10 9 5 7 10 4 11 6 6 10 6 10 16 S 10 10 10 9 8 11 10 8 10 8 7 11 10 10 9 16 T 10 10 9 8 10 10 10 10 9 9 8 10 8 10 9 11 16 V 9 8 3 4 11 6 9 12 5 10 9 5 3 6 5 8 10 16 W 11 11 6 7 11 8 10 11 7 11 10 8 6 9 7 10 11 11 16 Y 9 10 7 6 10 10 9 10 7 9 8 8 8 8 7 11 11 10 11 16 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.risler) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 2 C -1 2 D 0 -1 2 E 1 -1 1 2 F 0 -1 0 0 2 G 0 -1 0 0 0 2 H 0 -1 -1 0 -1 -1 2 I 1 -1 0 1 1 0 0 2 K 1 -1 0 1 0 0 -1 1 2 L 1 -1 0 0 1 0 0 2 0 2 M 1 -1 0 0 0 0 -1 0 0 1 2 N 1 -1 0 1 0 0 0 0 1 0 0 2 P 0 -1 -1 0 -1 -1 -1 0 0 0 -1 -1 2 Q 1 -1 0 2 0 0 0 1 1 1 1 1 0 2 R 1 -1 0 1 0 0 0 1 2 1 1 1 0 2 2 S 2 -1 0 1 0 0 0 1 1 1 0 1 0 1 2 2 T 1 -1 0 1 0 0 0 1 1 1 0 1 0 1 1 2 2 V 2 -1 0 1 0 0 0 2 1 2 0 1 0 1 1 1 1 2 W 0 -1 -1 -1 0 -1 -1 0 -1 0 -1 -1 -1 -1 0 0 -1 0 2 Y 0 -1 0 0 2 0 0 0 0 0 0 0 -1 0 0 0 0 0 0 2 A C D E F G H I K L M N P Q R S T V W Y""", ) mat = SubsMat.SeqMat(MatrixInfo.structure) self.assertEqual(len(mat), 210) self.checkMatrix( mat, """\ A 4 C -2 11 D -1 -7 6 E 0 -3 2 5 F -3 -2 -5 -4 7 G 0 -6 -1 -2 -6 5 H -2 -6 0 -2 -2 -3 8 I -2 -4 -3 -3 1 -5 -5 6 K -1 -4 -1 1 -3 -3 0 -3 5 L -2 -6 -6 -4 2 -5 -3 2 -2 5 M 0 -5 -4 -2 0 -4 -2 1 -1 3 8 N -1 -6 2 0 -3 -1 2 -3 0 -3 -2 5 P -1 -8 -1 -1 -5 -2 -3 -4 -1 -3 -6 -2 7 Q 0 -3 0 2 -4 -2 0 -5 1 -3 1 0 -2 6 R -1 -2 -2 0 -4 -2 0 -3 2 -3 -4 -1 -2 1 7 S 0 -4 0 -1 -3 -1 -2 -3 -1 -4 -4 0 -1 -1 0 4 T -1 -5 -1 0 -3 -3 -2 -2 0 -3 -2 0 -1 0 -1 1 5 V 0 -4 -4 -2 -1 -4 -2 2 -3 1 0 -4 -4 -2 -3 -3 -1 5 W -3 -6 -6 -6 2 -4 -3 -2 -3 -1 -2 -5 -4 -5 -2 -5 -5 -4 10 Y -3 -6 -3 -2 3 -3 0 -1 -2 -2 -1 -1 -6 -3 -1 -2 -2 -1 2 7 A C D E F G H I K L M N P Q R S T V W Y""", ) def test_sequence_matrix_make_entropy(self): blosum30 = SubsMat.SeqMat(MatrixInfo.blosum30) blosum30.make_entropy() self.assertAlmostEqual(blosum30.entropy, -644.0119, places=4) def test_sequence_matrix_str(self): blosum30 = SubsMat.SeqMat(MatrixInfo.blosum30) self.assertEqual( str(blosum30), """\ A 4 B 0 5 C -3 -2 17 D 0 5 -3 9 E 0 0 1 1 6 F -2 -3 -3 -5 -4 10 G 0 0 -4 -1 -2 -3 8 H -2 -2 -5 -2 0 -3 -3 14 I 0 -2 -2 -4 -3 0 -1 -2 6 K 0 0 -3 0 2 -1 -1 -2 -2 4 L -1 -1 0 -1 -1 2 -2 -1 2 -2 4 M 1 -2 -2 -3 -1 -2 -2 2 1 2 2 6 N 0 4 -1 1 -1 -1 0 -1 0 0 -2 0 8 P -1 -2 -3 -1 1 -4 -1 1 -3 1 -3 -4 -3 11 Q 1 -1 -2 -1 2 -3 -2 0 -2 0 -2 -1 -1 0 8 R -1 -2 -2 -1 -1 -1 -2 -1 -3 1 -2 0 -2 -1 3 8 S 1 0 -2 0 0 -1 0 -1 -1 0 -2 -2 0 -1 -1 -1 4 T 1 0 -2 -1 -2 -2 -2 -2 0 -1 0 0 1 0 0 -3 2 5 V 1 -2 -2 -2 -3 1 -3 -3 4 -2 1 0 -2 -4 -3 -1 -1 1 5 W -5 -5 -2 -4 -1 1 1 -5 -3 -2 -2 -3 -7 -3 -1 0 -3 -5 -3 20 X 0 -1 -2 -1 -1 -1 -1 -1 0 0 0 0 0 -1 0 -1 0 0 0 -2 -1 Y -4 -3 -6 -1 -2 3 -3 0 -1 -1 3 -1 -4 -2 -1 0 -2 -1 1 5 -1 9 Z 0 0 0 0 5 -4 -2 0 -3 1 -1 -1 -1 0 4 0 -1 -1 -3 -1 0 -2 4 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) def test_sequence_matrix_operations(self): blosum90 = SubsMat.SeqMat(MatrixInfo.blosum90) blosum30 = SubsMat.SeqMat(MatrixInfo.blosum30) # subtraction seqmatdiff = blosum90 - blosum30 self.assertEqual(seqmatdiff, -321) # multiplication seqmatmul = blosum90 * blosum30 self.assertEqual( str(seqmatmul), """\ A 20 B 0 20 C 3 8 153 D 0 20 15 63 E 0 0 -6 1 36 F 6 12 9 25 20 70 G 0 0 16 2 6 15 48 H 4 2 25 4 0 6 9 112 I 0 10 4 20 12 0 5 8 30 K 0 0 12 0 0 4 2 2 8 24 L 2 5 0 5 4 0 10 4 2 6 20 M -2 8 4 12 3 2 8 -6 1 -4 4 42 N 0 16 4 1 1 4 0 0 0 0 8 0 56 P 1 6 12 3 -2 16 3 -3 12 -2 12 12 9 88 Q -1 1 8 1 4 12 6 0 8 0 6 0 0 0 56 R 2 4 10 3 1 4 6 0 12 2 6 0 2 3 3 48 S 1 0 4 0 0 3 0 2 3 0 6 4 0 2 1 1 20 T 0 0 4 2 2 6 6 4 0 1 0 0 0 0 0 6 2 30 V -1 8 4 10 9 -2 15 12 12 6 0 0 8 12 9 3 2 -1 25 W 20 30 8 24 5 0 -4 15 12 10 6 6 35 15 3 0 12 20 9 220 X 0 2 6 2 2 2 2 2 0 0 0 0 0 2 0 2 0 0 0 6 2 Y 12 12 24 4 8 9 15 0 2 3 -6 2 12 8 3 0 6 2 -3 10 2 72 Z 0 0 0 0 20 16 6 0 12 1 4 2 1 0 16 0 1 1 9 4 0 6 16 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) # Addition seqmatadd = blosum90 + blosum30 self.assertEqual( str(seqmatadd), """\ A 9 B -2 9 C -4 -6 26 D -3 9 -8 16 E -1 0 -5 2 12 F -5 -7 -6 -10 -9 17 G 0 -2 -8 -3 -5 -8 14 H -4 -3 -10 -4 -1 -5 -6 22 I -2 -7 -4 -9 -7 -1 -6 -6 11 K -1 -1 -7 -1 2 -5 -3 -3 -6 10 L -3 -6 -2 -6 -5 2 -7 -5 3 -5 9 M -1 -6 -4 -7 -4 -3 -6 -1 2 0 4 13 N -2 8 -5 2 -2 -5 -1 -1 -4 0 -6 -3 15 P -2 -5 -7 -4 -1 -8 -4 -2 -7 -1 -7 -7 -6 19 Q 0 -2 -6 -2 4 -7 -5 1 -6 1 -5 -1 -1 -2 15 R -3 -4 -7 -4 -2 -5 -5 -1 -7 3 -5 -2 -3 -4 4 14 S 2 0 -4 -1 -1 -4 -1 -3 -4 -1 -5 -4 0 -3 -2 -2 9 T 1 -1 -4 -3 -3 -5 -5 -4 -1 -2 -2 -1 1 -2 -1 -5 3 11 V 0 -6 -4 -7 -6 -1 -8 -7 7 -5 1 0 -6 -7 -6 -4 -3 0 10 W -9 -11 -6 -10 -6 1 -3 -8 -7 -7 -5 -5 -12 -8 -4 -4 -7 -9 -6 31 X -1 -3 -5 -3 -3 -3 -3 -3 -2 -1 -2 -1 -2 -3 -1 -3 -1 -1 -2 -5 -3 Y -7 -7 -10 -5 -6 6 -8 1 -3 -4 1 -3 -7 -6 -4 -3 -5 -3 -2 7 -3 17 Z -1 0 -5 0 9 -8 -5 0 -7 2 -5 -3 -2 -2 8 0 -2 -2 -6 -5 -1 -5 8 A B C D E F G H I K L M N P Q R S T V W X Y Z""", ) def test_two_mat_relative_entropy(self): blosum90 = SubsMat.SeqMat(MatrixInfo.blosum90) blosum30 = SubsMat.SeqMat(MatrixInfo.blosum30) rel_entropy = SubsMat.two_mat_relative_entropy(blosum30, blosum90) self.assertAlmostEqual(rel_entropy, 0.0688, places=4) def test_matrix_correlations(self): try: blosum90 = SubsMat.SeqMat(MatrixInfo.blosum90) blosum30 = SubsMat.SeqMat(MatrixInfo.blosum30) correlation = SubsMat.two_mat_correlation(blosum30, blosum90) self.assertAlmostEqual(correlation, 0.878, places=3) correlation = SubsMat.two_mat_correlation(blosum90, blosum30) self.assertAlmostEqual(correlation, 0.878, places=3) except ValueError as err: if ( "TRAVIS_CPU_ARCH" in os.environ and os.environ["TRAVIS_CPU_ARCH"] == "s390x" ): print("Known failure on the s390x architecture.") else: raise err def test_two_mat_DJS(self): blosum90 = SubsMat.SeqMat(MatrixInfo.blosum90) blosum30 = SubsMat.SeqMat(MatrixInfo.blosum30) djs = SubsMat.two_mat_DJS(blosum30, blosum90) self.assertAlmostEqual(djs, 15.319, places=3) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)