# 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 Array in the Bio.Align.substitution_matrices module.""" try: import numpy del numpy except ImportError: from Bio import MissingExternalDependencyError raise MissingExternalDependencyError( "Install NumPy if you want to use Bio.Align.substitution_matrices." ) from None import os from collections import Counter import unittest import numpy from Bio import SeqIO from Bio.Data import IUPACData nucleotide_alphabet = IUPACData.unambiguous_dna_letters protein_alphabet = IUPACData.protein_letters class Test_basics(unittest.TestCase): def test_basics_vector(self): from Bio.Align import substitution_matrices counts = substitution_matrices.Array("XYZ") self.assertEqual( str(counts), """\ X 0.0 Y 0.0 Z 0.0 """, ) self.assertEqual(counts.alphabet, "XYZ") counts["X"] = -9 counts[2] = 5.5 self.assertEqual( str(counts), """\ X -9.0 Y 0.0 Z 5.5 """, ) self.assertAlmostEqual(counts[0], -9) with self.assertRaises(IndexError): counts["U"] with self.assertRaises(IndexError): counts["V"] = 3.0 with self.assertRaises(IndexError): counts[8] def test_basics_matrix(self): from Bio.Align import substitution_matrices counts = substitution_matrices.Array("XYZ", dims=2) self.assertEqual( str(counts), """\ X Y Z X 0.0 0.0 0.0 Y 0.0 0.0 0.0 Z 0.0 0.0 0.0 """, ) counts["X", "Z"] = 12.0 counts[2, 1] = 3.0 counts["Y", 0] = -2.0 counts[0, "Y"] = 5.0 self.assertEqual( str(counts), """\ X Y Z X 0.0 5.0 12.0 Y -2.0 0.0 0.0 Z 0.0 3.0 0.0 """, ) with self.assertRaises(IndexError): counts["U", 1] with self.assertRaises(IndexError): counts["X", 5] self.assertEqual( str(counts["Y"]), """\ X -2.0 Y 0.0 Z 0.0 """, ) self.assertEqual( str(counts[:, "Z"]), """\ X 12.0 Y 0.0 Z 0.0 """, ) def test_read_write(self): from Bio.Align import substitution_matrices path = os.path.join("Align", "hg38.chrom.sizes") sizes = substitution_matrices.read(path, numpy.int64) # Note that sum(sizes) below is larger than 2147483647, and won't # fit in an int on a 32-bits machine. self.assertEqual(len(sizes), 455) self.assertEqual(sizes["chr1"], 248956422) self.assertEqual(sizes["chr2"], 242193529) self.assertEqual(sizes["chr3"], 198295559) self.assertEqual(sizes["chr4"], 190214555) self.assertEqual(sizes["chr5"], 181538259) self.assertEqual(sum(sizes), 3209286105) text = format(sizes) lines = text.split("\n") self.assertEqual(lines[0], "chr1 248956422") self.assertEqual(lines[1], "chr2 242193529") self.assertEqual(lines[2], "chr3 198295559") self.assertEqual(lines[3], "chr4 190214555") self.assertEqual(lines[4], "chr5 181538259") def test_nucleotide_freq(self): from Bio.Align import substitution_matrices counts = Counter() path = os.path.join("Align", "ecoli.fa") records = SeqIO.parse(path, "fasta") for record in records: for nucleotide in record.seq: counts[nucleotide] += 1 letters = sorted(counts.keys()) self.assertEqual(letters, sorted(nucleotide_alphabet)) path = os.path.join("Align", "ecoli.txt") frequencies = substitution_matrices.read(path) self.assertEqual(frequencies.alphabet, nucleotide_alphabet) self.assertEqual(frequencies.shape, (len(nucleotide_alphabet),)) for letter in letters: self.assertAlmostEqual(frequencies[letter], counts[letter]) with open(path) as handle: text = handle.read() self.assertEqual(format(frequencies, "%d"), text) total = sum(frequencies) self.assertAlmostEqual(total, sum(counts.values())) frequencies /= total self.assertEqual(frequencies.alphabet, nucleotide_alphabet) self.assertAlmostEqual(frequencies["A"], 0.251621271076524) self.assertAlmostEqual(frequencies["C"], 0.228274967574578) self.assertAlmostEqual(frequencies["G"], 0.315175097276264) self.assertAlmostEqual(frequencies["T"], 0.204928664072632) counts = Counter() path = os.path.join("Align", "bsubtilis.fa") records = SeqIO.parse(path, "fasta") for record in records: for nucleotide in record.seq: counts[nucleotide] += 1 letters = sorted(counts.keys()) self.assertEqual(letters, sorted(nucleotide_alphabet)) path = os.path.join("Align", "bsubtilis.txt") frequencies = substitution_matrices.read(path) self.assertEqual(frequencies.alphabet, nucleotide_alphabet) self.assertEqual(frequencies.shape, (len(nucleotide_alphabet),)) for letter in letters: self.assertAlmostEqual(frequencies[letter], counts[letter]) with open(path) as handle: text = handle.read() self.assertEqual(format(frequencies, "%d"), text) total = sum(frequencies) self.assertAlmostEqual(total, sum(counts.values())) frequencies /= total self.assertEqual(frequencies.alphabet, nucleotide_alphabet) self.assertAlmostEqual(frequencies["A"], 0.2469453376205788) self.assertAlmostEqual(frequencies["C"], 0.2347266881028939) self.assertAlmostEqual(frequencies["G"], 0.3157556270096463) self.assertAlmostEqual(frequencies["T"], 0.2025723472668810) def test_protein_freq(self): from Bio.Align import substitution_matrices counts = Counter() path = os.path.join("Align", "cow.fa") records = SeqIO.parse(path, "fasta") for record in records: for aminoacid in record.seq: counts[aminoacid] += 1 letters = sorted(counts.keys()) self.assertEqual(letters, list(protein_alphabet)) path = os.path.join("Align", "cow.txt") frequencies = substitution_matrices.read(path) self.assertEqual(frequencies.alphabet, protein_alphabet) self.assertEqual(frequencies.shape, (len(protein_alphabet),)) for letter in letters: self.assertAlmostEqual(frequencies[letter], counts[letter]) with open(path) as handle: text = handle.read() self.assertEqual(format(frequencies, "%d"), text) total = sum(frequencies) self.assertAlmostEqual(total, sum(counts.values())) frequencies /= total self.assertEqual(frequencies.alphabet, protein_alphabet) self.assertAlmostEqual(frequencies["A"], 0.069711538) self.assertAlmostEqual(frequencies["C"], 0.025320513) self.assertAlmostEqual(frequencies["D"], 0.040785256) self.assertAlmostEqual(frequencies["E"], 0.058974359) self.assertAlmostEqual(frequencies["F"], 0.044951923) self.assertAlmostEqual(frequencies["G"], 0.058012821) self.assertAlmostEqual(frequencies["H"], 0.024278846) self.assertAlmostEqual(frequencies["I"], 0.056009615) self.assertAlmostEqual(frequencies["K"], 0.055448718) self.assertAlmostEqual(frequencies["L"], 0.117788462) self.assertAlmostEqual(frequencies["M"], 0.026442308) self.assertAlmostEqual(frequencies["N"], 0.035336538) self.assertAlmostEqual(frequencies["P"], 0.052003205) self.assertAlmostEqual(frequencies["Q"], 0.038621795) self.assertAlmostEqual(frequencies["R"], 0.050961538) self.assertAlmostEqual(frequencies["S"], 0.080368590) self.assertAlmostEqual(frequencies["T"], 0.054887821) self.assertAlmostEqual(frequencies["V"], 0.062500000) self.assertAlmostEqual(frequencies["W"], 0.015625000) self.assertAlmostEqual(frequencies["Y"], 0.031971154) counts = Counter() path = os.path.join("Align", "pig.fa") records = SeqIO.parse(path, "fasta") for record in records: for aminoacid in record.seq: counts[aminoacid] += 1 letters = sorted(counts.keys()) self.assertEqual(letters, list(protein_alphabet)) path = os.path.join("Align", "pig.txt") frequencies = substitution_matrices.read(path) self.assertEqual(frequencies.alphabet, protein_alphabet) self.assertEqual(frequencies.shape, (len(protein_alphabet),)) for letter in letters: self.assertAlmostEqual(frequencies[letter], counts[letter]) with open(path) as handle: text = handle.read() self.assertEqual(format(frequencies, "%d"), text) total = sum(frequencies) self.assertAlmostEqual(total, sum(counts.values())) frequencies /= total self.assertEqual(frequencies.alphabet, protein_alphabet) self.assertAlmostEqual(frequencies["A"], 0.070987178) self.assertAlmostEqual(frequencies["C"], 0.025490499) self.assertAlmostEqual(frequencies["D"], 0.041325506) self.assertAlmostEqual(frequencies["E"], 0.058550904) self.assertAlmostEqual(frequencies["F"], 0.046037386) self.assertAlmostEqual(frequencies["G"], 0.058164684) self.assertAlmostEqual(frequencies["H"], 0.022941449) self.assertAlmostEqual(frequencies["I"], 0.054534219) self.assertAlmostEqual(frequencies["K"], 0.054843195) self.assertAlmostEqual(frequencies["L"], 0.116020392) self.assertAlmostEqual(frequencies["M"], 0.026880890) self.assertAlmostEqual(frequencies["N"], 0.036613626) self.assertAlmostEqual(frequencies["P"], 0.051058242) self.assertAlmostEqual(frequencies["Q"], 0.040553067) self.assertAlmostEqual(frequencies["R"], 0.051135486) self.assertAlmostEqual(frequencies["S"], 0.079252279) self.assertAlmostEqual(frequencies["T"], 0.054070755) self.assertAlmostEqual(frequencies["V"], 0.064807663) self.assertAlmostEqual(frequencies["W"], 0.015217055) self.assertAlmostEqual(frequencies["Y"], 0.031515526) class TestScoringMatrices(unittest.TestCase): @classmethod def setUpClass(cls): from Bio import SeqIO from Bio.Align import PairwiseAligner from Bio.Align import substitution_matrices observed = substitution_matrices.Array(alphabet=protein_alphabet, dims=2) aligner = PairwiseAligner() aligner.mode = "local" # By default, the affine gap penalties used by blastp are 11 for # existence of a gap and 1 for extending a gap. Using to Durbin"s # parametrization of affine gap scores, this is equivalent to an # gap score of -12 to open a gap, and -1 to extend an existing gap: aligner.open_gap_score = -12 aligner.extend_gap_score = -1 # Use +6/-1 match and mismatch scores as an approximation of the # BLOSUM62 matrix. aligner.match = 6 aligner.mismatch = -1 cow_path = "Align/cow.fa" pig_path = "Align/pig.fa" cow_records = SeqIO.parse(cow_path, "fasta") pig_records = SeqIO.parse(pig_path, "fasta") for cow_record, pig_record in zip(cow_records, pig_records): cow_sequence = str(cow_record.seq) pig_sequence = str(pig_record.seq) alignments = aligner.align(cow_sequence, pig_sequence) assert len(alignments) == 1 alignment = alignments[0] cow_aligned, pig_aligned = alignment.aligned for cow_segment, pig_segment in zip(cow_aligned, pig_aligned): cow_start, cow_end = cow_segment pig_start, pig_end = pig_segment cow_subsequence = cow_sequence[cow_start:cow_end] pig_subsequence = pig_sequence[pig_start:pig_end] for c1, c2 in zip(cow_subsequence, pig_subsequence): observed[c1, c2] += 1 cls.observed = observed def test1_observed_frequencies(self): observed = self.observed self.assertEqual(observed.alphabet, protein_alphabet) self.assertEqual(observed.shape, (20, 20)) self.assertAlmostEqual(observed["A", "A"], 706) self.assertAlmostEqual(observed["A", "C"], 1) self.assertAlmostEqual(observed["A", "D"], 3) self.assertAlmostEqual(observed["A", "E"], 11) self.assertAlmostEqual(observed["A", "F"], 1) self.assertAlmostEqual(observed["A", "G"], 14) self.assertAlmostEqual(observed["A", "H"], 1) self.assertAlmostEqual(observed["A", "I"], 4) self.assertAlmostEqual(observed["A", "K"], 1) self.assertAlmostEqual(observed["A", "L"], 5) self.assertAlmostEqual(observed["A", "M"], 5) self.assertAlmostEqual(observed["A", "N"], 1) self.assertAlmostEqual(observed["A", "P"], 5) self.assertAlmostEqual(observed["A", "Q"], 0) self.assertAlmostEqual(observed["A", "R"], 1) self.assertAlmostEqual(observed["A", "S"], 22) self.assertAlmostEqual(observed["A", "T"], 37) self.assertAlmostEqual(observed["A", "V"], 35) self.assertAlmostEqual(observed["A", "W"], 0) self.assertAlmostEqual(observed["A", "Y"], 1) self.assertAlmostEqual(observed["C", "A"], 0) self.assertAlmostEqual(observed["C", "C"], 279) self.assertAlmostEqual(observed["C", "D"], 0) self.assertAlmostEqual(observed["C", "E"], 1) self.assertAlmostEqual(observed["C", "F"], 3) self.assertAlmostEqual(observed["C", "G"], 2) self.assertAlmostEqual(observed["C", "H"], 0) self.assertAlmostEqual(observed["C", "I"], 1) self.assertAlmostEqual(observed["C", "K"], 0) self.assertAlmostEqual(observed["C", "L"], 1) self.assertAlmostEqual(observed["C", "M"], 0) self.assertAlmostEqual(observed["C", "N"], 1) self.assertAlmostEqual(observed["C", "P"], 2) self.assertAlmostEqual(observed["C", "Q"], 0) self.assertAlmostEqual(observed["C", "R"], 6) self.assertAlmostEqual(observed["C", "S"], 6) self.assertAlmostEqual(observed["C", "T"], 0) self.assertAlmostEqual(observed["C", "V"], 1) self.assertAlmostEqual(observed["C", "W"], 1) self.assertAlmostEqual(observed["C", "Y"], 6) self.assertAlmostEqual(observed["D", "A"], 7) self.assertAlmostEqual(observed["D", "C"], 1) self.assertAlmostEqual(observed["D", "D"], 427) self.assertAlmostEqual(observed["D", "E"], 25) self.assertAlmostEqual(observed["D", "F"], 0) self.assertAlmostEqual(observed["D", "G"], 8) self.assertAlmostEqual(observed["D", "H"], 0) self.assertAlmostEqual(observed["D", "I"], 0) self.assertAlmostEqual(observed["D", "K"], 1) self.assertAlmostEqual(observed["D", "L"], 2) self.assertAlmostEqual(observed["D", "M"], 0) self.assertAlmostEqual(observed["D", "N"], 19) self.assertAlmostEqual(observed["D", "P"], 0) self.assertAlmostEqual(observed["D", "Q"], 0) self.assertAlmostEqual(observed["D", "R"], 3) self.assertAlmostEqual(observed["D", "S"], 3) self.assertAlmostEqual(observed["D", "T"], 1) self.assertAlmostEqual(observed["D", "V"], 1) self.assertAlmostEqual(observed["D", "W"], 1) self.assertAlmostEqual(observed["D", "Y"], 1) self.assertAlmostEqual(observed["E", "A"], 9) self.assertAlmostEqual(observed["E", "C"], 0) self.assertAlmostEqual(observed["E", "D"], 30) self.assertAlmostEqual(observed["E", "E"], 629) self.assertAlmostEqual(observed["E", "F"], 1) self.assertAlmostEqual(observed["E", "G"], 19) self.assertAlmostEqual(observed["E", "H"], 3) self.assertAlmostEqual(observed["E", "I"], 1) self.assertAlmostEqual(observed["E", "K"], 12) self.assertAlmostEqual(observed["E", "L"], 1) self.assertAlmostEqual(observed["E", "M"], 1) self.assertAlmostEqual(observed["E", "N"], 1) self.assertAlmostEqual(observed["E", "P"], 1) self.assertAlmostEqual(observed["E", "Q"], 12) self.assertAlmostEqual(observed["E", "R"], 5) self.assertAlmostEqual(observed["E", "S"], 3) self.assertAlmostEqual(observed["E", "T"], 1) self.assertAlmostEqual(observed["E", "V"], 1) self.assertAlmostEqual(observed["E", "W"], 0) self.assertAlmostEqual(observed["E", "Y"], 0) self.assertAlmostEqual(observed["F", "A"], 0) self.assertAlmostEqual(observed["F", "C"], 2) self.assertAlmostEqual(observed["F", "D"], 1) self.assertAlmostEqual(observed["F", "E"], 0) self.assertAlmostEqual(observed["F", "F"], 497) self.assertAlmostEqual(observed["F", "G"], 1) self.assertAlmostEqual(observed["F", "H"], 1) self.assertAlmostEqual(observed["F", "I"], 1) self.assertAlmostEqual(observed["F", "K"], 1) self.assertAlmostEqual(observed["F", "L"], 26) self.assertAlmostEqual(observed["F", "M"], 1) self.assertAlmostEqual(observed["F", "N"], 0) self.assertAlmostEqual(observed["F", "P"], 0) self.assertAlmostEqual(observed["F", "Q"], 0) self.assertAlmostEqual(observed["F", "R"], 0) self.assertAlmostEqual(observed["F", "S"], 6) self.assertAlmostEqual(observed["F", "T"], 3) self.assertAlmostEqual(observed["F", "V"], 4) self.assertAlmostEqual(observed["F", "W"], 1) self.assertAlmostEqual(observed["F", "Y"], 12) self.assertAlmostEqual(observed["G", "A"], 12) self.assertAlmostEqual(observed["G", "C"], 2) self.assertAlmostEqual(observed["G", "D"], 10) self.assertAlmostEqual(observed["G", "E"], 14) self.assertAlmostEqual(observed["G", "F"], 0) self.assertAlmostEqual(observed["G", "G"], 612) self.assertAlmostEqual(observed["G", "H"], 0) self.assertAlmostEqual(observed["G", "I"], 1) self.assertAlmostEqual(observed["G", "K"], 1) self.assertAlmostEqual(observed["G", "L"], 1) self.assertAlmostEqual(observed["G", "M"], 1) self.assertAlmostEqual(observed["G", "N"], 2) self.assertAlmostEqual(observed["G", "P"], 1) self.assertAlmostEqual(observed["G", "Q"], 1) self.assertAlmostEqual(observed["G", "R"], 13) self.assertAlmostEqual(observed["G", "S"], 22) self.assertAlmostEqual(observed["G", "T"], 1) self.assertAlmostEqual(observed["G", "V"], 8) self.assertAlmostEqual(observed["G", "W"], 2) self.assertAlmostEqual(observed["G", "Y"], 1) self.assertAlmostEqual(observed["H", "A"], 1) self.assertAlmostEqual(observed["H", "C"], 1) self.assertAlmostEqual(observed["H", "D"], 4) self.assertAlmostEqual(observed["H", "E"], 1) self.assertAlmostEqual(observed["H", "F"], 1) self.assertAlmostEqual(observed["H", "G"], 2) self.assertAlmostEqual(observed["H", "H"], 227) self.assertAlmostEqual(observed["H", "I"], 0) self.assertAlmostEqual(observed["H", "K"], 1) self.assertAlmostEqual(observed["H", "L"], 1) self.assertAlmostEqual(observed["H", "M"], 0) self.assertAlmostEqual(observed["H", "N"], 7) self.assertAlmostEqual(observed["H", "P"], 2) self.assertAlmostEqual(observed["H", "Q"], 14) self.assertAlmostEqual(observed["H", "R"], 20) self.assertAlmostEqual(observed["H", "S"], 3) self.assertAlmostEqual(observed["H", "T"], 0) self.assertAlmostEqual(observed["H", "V"], 1) self.assertAlmostEqual(observed["H", "W"], 0) self.assertAlmostEqual(observed["H", "Y"], 7) self.assertAlmostEqual(observed["I", "A"], 5) self.assertAlmostEqual(observed["I", "C"], 0) self.assertAlmostEqual(observed["I", "D"], 1) self.assertAlmostEqual(observed["I", "E"], 2) self.assertAlmostEqual(observed["I", "F"], 5) self.assertAlmostEqual(observed["I", "G"], 0) self.assertAlmostEqual(observed["I", "H"], 1) self.assertAlmostEqual(observed["I", "I"], 558) self.assertAlmostEqual(observed["I", "K"], 1) self.assertAlmostEqual(observed["I", "L"], 22) self.assertAlmostEqual(observed["I", "M"], 11) self.assertAlmostEqual(observed["I", "N"], 3) self.assertAlmostEqual(observed["I", "P"], 1) self.assertAlmostEqual(observed["I", "Q"], 0) self.assertAlmostEqual(observed["I", "R"], 1) self.assertAlmostEqual(observed["I", "S"], 2) self.assertAlmostEqual(observed["I", "T"], 18) self.assertAlmostEqual(observed["I", "V"], 61) self.assertAlmostEqual(observed["I", "W"], 0) self.assertAlmostEqual(observed["I", "Y"], 1) self.assertAlmostEqual(observed["K", "A"], 3) self.assertAlmostEqual(observed["K", "C"], 1) self.assertAlmostEqual(observed["K", "D"], 1) self.assertAlmostEqual(observed["K", "E"], 17) self.assertAlmostEqual(observed["K", "F"], 0) self.assertAlmostEqual(observed["K", "G"], 2) self.assertAlmostEqual(observed["K", "H"], 2) self.assertAlmostEqual(observed["K", "I"], 2) self.assertAlmostEqual(observed["K", "K"], 573) self.assertAlmostEqual(observed["K", "L"], 0) self.assertAlmostEqual(observed["K", "M"], 2) self.assertAlmostEqual(observed["K", "N"], 11) self.assertAlmostEqual(observed["K", "P"], 1) self.assertAlmostEqual(observed["K", "Q"], 13) self.assertAlmostEqual(observed["K", "R"], 46) self.assertAlmostEqual(observed["K", "S"], 0) self.assertAlmostEqual(observed["K", "T"], 9) self.assertAlmostEqual(observed["K", "V"], 1) self.assertAlmostEqual(observed["K", "W"], 0) self.assertAlmostEqual(observed["K", "Y"], 1) self.assertAlmostEqual(observed["L", "A"], 7) self.assertAlmostEqual(observed["L", "C"], 1) self.assertAlmostEqual(observed["L", "D"], 0) self.assertAlmostEqual(observed["L", "E"], 1) self.assertAlmostEqual(observed["L", "F"], 26) self.assertAlmostEqual(observed["L", "G"], 2) self.assertAlmostEqual(observed["L", "H"], 1) self.assertAlmostEqual(observed["L", "I"], 21) self.assertAlmostEqual(observed["L", "K"], 1) self.assertAlmostEqual(observed["L", "L"], 1300) self.assertAlmostEqual(observed["L", "M"], 19) self.assertAlmostEqual(observed["L", "N"], 1) self.assertAlmostEqual(observed["L", "P"], 17) self.assertAlmostEqual(observed["L", "Q"], 4) self.assertAlmostEqual(observed["L", "R"], 3) self.assertAlmostEqual(observed["L", "S"], 9) self.assertAlmostEqual(observed["L", "T"], 4) self.assertAlmostEqual(observed["L", "V"], 37) self.assertAlmostEqual(observed["L", "W"], 2) self.assertAlmostEqual(observed["L", "Y"], 0) self.assertAlmostEqual(observed["M", "A"], 0) self.assertAlmostEqual(observed["M", "C"], 1) self.assertAlmostEqual(observed["M", "D"], 1) self.assertAlmostEqual(observed["M", "E"], 0) self.assertAlmostEqual(observed["M", "F"], 1) self.assertAlmostEqual(observed["M", "G"], 2) self.assertAlmostEqual(observed["M", "H"], 1) self.assertAlmostEqual(observed["M", "I"], 14) self.assertAlmostEqual(observed["M", "K"], 3) self.assertAlmostEqual(observed["M", "L"], 18) self.assertAlmostEqual(observed["M", "M"], 263) self.assertAlmostEqual(observed["M", "N"], 0) self.assertAlmostEqual(observed["M", "P"], 1) self.assertAlmostEqual(observed["M", "Q"], 0) self.assertAlmostEqual(observed["M", "R"], 1) self.assertAlmostEqual(observed["M", "S"], 2) self.assertAlmostEqual(observed["M", "T"], 7) self.assertAlmostEqual(observed["M", "V"], 6) self.assertAlmostEqual(observed["M", "W"], 0) self.assertAlmostEqual(observed["M", "Y"], 1) self.assertAlmostEqual(observed["N", "A"], 2) self.assertAlmostEqual(observed["N", "C"], 0) self.assertAlmostEqual(observed["N", "D"], 21) self.assertAlmostEqual(observed["N", "E"], 1) self.assertAlmostEqual(observed["N", "F"], 2) self.assertAlmostEqual(observed["N", "G"], 5) self.assertAlmostEqual(observed["N", "H"], 4) self.assertAlmostEqual(observed["N", "I"], 2) self.assertAlmostEqual(observed["N", "K"], 8) self.assertAlmostEqual(observed["N", "L"], 2) self.assertAlmostEqual(observed["N", "M"], 1) self.assertAlmostEqual(observed["N", "N"], 360) self.assertAlmostEqual(observed["N", "P"], 0) self.assertAlmostEqual(observed["N", "Q"], 3) self.assertAlmostEqual(observed["N", "R"], 1) self.assertAlmostEqual(observed["N", "S"], 15) self.assertAlmostEqual(observed["N", "T"], 8) self.assertAlmostEqual(observed["N", "V"], 0) self.assertAlmostEqual(observed["N", "W"], 0) self.assertAlmostEqual(observed["N", "Y"], 2) self.assertAlmostEqual(observed["P", "A"], 14) self.assertAlmostEqual(observed["P", "C"], 0) self.assertAlmostEqual(observed["P", "D"], 1) self.assertAlmostEqual(observed["P", "E"], 0) self.assertAlmostEqual(observed["P", "F"], 1) self.assertAlmostEqual(observed["P", "G"], 0) self.assertAlmostEqual(observed["P", "H"], 5) self.assertAlmostEqual(observed["P", "I"], 0) self.assertAlmostEqual(observed["P", "K"], 0) self.assertAlmostEqual(observed["P", "L"], 16) self.assertAlmostEqual(observed["P", "M"], 0) self.assertAlmostEqual(observed["P", "N"], 1) self.assertAlmostEqual(observed["P", "P"], 551) self.assertAlmostEqual(observed["P", "Q"], 3) self.assertAlmostEqual(observed["P", "R"], 2) self.assertAlmostEqual(observed["P", "S"], 24) self.assertAlmostEqual(observed["P", "T"], 7) self.assertAlmostEqual(observed["P", "V"], 2) self.assertAlmostEqual(observed["P", "W"], 1) self.assertAlmostEqual(observed["P", "Y"], 0) self.assertAlmostEqual(observed["Q", "A"], 1) self.assertAlmostEqual(observed["Q", "C"], 1) self.assertAlmostEqual(observed["Q", "D"], 1) self.assertAlmostEqual(observed["Q", "E"], 10) self.assertAlmostEqual(observed["Q", "F"], 1) self.assertAlmostEqual(observed["Q", "G"], 0) self.assertAlmostEqual(observed["Q", "H"], 6) self.assertAlmostEqual(observed["Q", "I"], 1) self.assertAlmostEqual(observed["Q", "K"], 13) self.assertAlmostEqual(observed["Q", "L"], 5) self.assertAlmostEqual(observed["Q", "M"], 1) self.assertAlmostEqual(observed["Q", "N"], 2) self.assertAlmostEqual(observed["Q", "P"], 1) self.assertAlmostEqual(observed["Q", "Q"], 409) self.assertAlmostEqual(observed["Q", "R"], 18) self.assertAlmostEqual(observed["Q", "S"], 1) self.assertAlmostEqual(observed["Q", "T"], 0) self.assertAlmostEqual(observed["Q", "V"], 1) self.assertAlmostEqual(observed["Q", "W"], 0) self.assertAlmostEqual(observed["Q", "Y"], 0) self.assertAlmostEqual(observed["R", "A"], 3) self.assertAlmostEqual(observed["R", "C"], 3) self.assertAlmostEqual(observed["R", "D"], 0) self.assertAlmostEqual(observed["R", "E"], 2) self.assertAlmostEqual(observed["R", "F"], 1) self.assertAlmostEqual(observed["R", "G"], 13) self.assertAlmostEqual(observed["R", "H"], 6) self.assertAlmostEqual(observed["R", "I"], 0) self.assertAlmostEqual(observed["R", "K"], 40) self.assertAlmostEqual(observed["R", "L"], 5) self.assertAlmostEqual(observed["R", "M"], 2) self.assertAlmostEqual(observed["R", "N"], 4) self.assertAlmostEqual(observed["R", "P"], 5) self.assertAlmostEqual(observed["R", "Q"], 29) self.assertAlmostEqual(observed["R", "R"], 492) self.assertAlmostEqual(observed["R", "S"], 9) self.assertAlmostEqual(observed["R", "T"], 3) self.assertAlmostEqual(observed["R", "V"], 2) self.assertAlmostEqual(observed["R", "W"], 1) self.assertAlmostEqual(observed["R", "Y"], 0) self.assertAlmostEqual(observed["S", "A"], 34) self.assertAlmostEqual(observed["S", "C"], 3) self.assertAlmostEqual(observed["S", "D"], 3) self.assertAlmostEqual(observed["S", "E"], 3) self.assertAlmostEqual(observed["S", "F"], 9) self.assertAlmostEqual(observed["S", "G"], 18) self.assertAlmostEqual(observed["S", "H"], 2) self.assertAlmostEqual(observed["S", "I"], 4) self.assertAlmostEqual(observed["S", "K"], 4) self.assertAlmostEqual(observed["S", "L"], 3) self.assertAlmostEqual(observed["S", "M"], 0) self.assertAlmostEqual(observed["S", "N"], 25) self.assertAlmostEqual(observed["S", "P"], 19) self.assertAlmostEqual(observed["S", "Q"], 2) self.assertAlmostEqual(observed["S", "R"], 11) self.assertAlmostEqual(observed["S", "S"], 803) self.assertAlmostEqual(observed["S", "T"], 26) self.assertAlmostEqual(observed["S", "V"], 3) self.assertAlmostEqual(observed["S", "W"], 2) self.assertAlmostEqual(observed["S", "Y"], 6) self.assertAlmostEqual(observed["T", "A"], 43) self.assertAlmostEqual(observed["T", "C"], 1) self.assertAlmostEqual(observed["T", "D"], 4) self.assertAlmostEqual(observed["T", "E"], 1) self.assertAlmostEqual(observed["T", "F"], 0) self.assertAlmostEqual(observed["T", "G"], 2) self.assertAlmostEqual(observed["T", "H"], 1) self.assertAlmostEqual(observed["T", "I"], 18) self.assertAlmostEqual(observed["T", "K"], 4) self.assertAlmostEqual(observed["T", "L"], 4) self.assertAlmostEqual(observed["T", "M"], 16) self.assertAlmostEqual(observed["T", "N"], 8) self.assertAlmostEqual(observed["T", "P"], 9) self.assertAlmostEqual(observed["T", "Q"], 2) self.assertAlmostEqual(observed["T", "R"], 2) self.assertAlmostEqual(observed["T", "S"], 27) self.assertAlmostEqual(observed["T", "T"], 526) self.assertAlmostEqual(observed["T", "V"], 6) self.assertAlmostEqual(observed["T", "W"], 1) self.assertAlmostEqual(observed["T", "Y"], 1) self.assertAlmostEqual(observed["V", "A"], 25) self.assertAlmostEqual(observed["V", "C"], 1) self.assertAlmostEqual(observed["V", "D"], 3) self.assertAlmostEqual(observed["V", "E"], 2) self.assertAlmostEqual(observed["V", "F"], 6) self.assertAlmostEqual(observed["V", "G"], 9) self.assertAlmostEqual(observed["V", "H"], 0) self.assertAlmostEqual(observed["V", "I"], 48) self.assertAlmostEqual(observed["V", "K"], 1) self.assertAlmostEqual(observed["V", "L"], 21) self.assertAlmostEqual(observed["V", "M"], 8) self.assertAlmostEqual(observed["V", "N"], 1) self.assertAlmostEqual(observed["V", "P"], 2) self.assertAlmostEqual(observed["V", "Q"], 1) self.assertAlmostEqual(observed["V", "R"], 3) self.assertAlmostEqual(observed["V", "S"], 3) self.assertAlmostEqual(observed["V", "T"], 13) self.assertAlmostEqual(observed["V", "V"], 623) self.assertAlmostEqual(observed["V", "W"], 1) self.assertAlmostEqual(observed["V", "Y"], 0) self.assertAlmostEqual(observed["W", "A"], 2) self.assertAlmostEqual(observed["W", "C"], 1) self.assertAlmostEqual(observed["W", "D"], 0) self.assertAlmostEqual(observed["W", "E"], 1) self.assertAlmostEqual(observed["W", "F"], 0) self.assertAlmostEqual(observed["W", "G"], 4) self.assertAlmostEqual(observed["W", "H"], 1) self.assertAlmostEqual(observed["W", "I"], 1) self.assertAlmostEqual(observed["W", "K"], 1) self.assertAlmostEqual(observed["W", "L"], 2) self.assertAlmostEqual(observed["W", "M"], 1) self.assertAlmostEqual(observed["W", "N"], 1) self.assertAlmostEqual(observed["W", "P"], 0) self.assertAlmostEqual(observed["W", "Q"], 1) self.assertAlmostEqual(observed["W", "R"], 7) self.assertAlmostEqual(observed["W", "S"], 0) self.assertAlmostEqual(observed["W", "T"], 1) self.assertAlmostEqual(observed["W", "V"], 0) self.assertAlmostEqual(observed["W", "W"], 170) self.assertAlmostEqual(observed["W", "Y"], 0) self.assertAlmostEqual(observed["Y", "A"], 0) self.assertAlmostEqual(observed["Y", "C"], 4) self.assertAlmostEqual(observed["Y", "D"], 1) self.assertAlmostEqual(observed["Y", "E"], 1) self.assertAlmostEqual(observed["Y", "F"], 13) self.assertAlmostEqual(observed["Y", "G"], 0) self.assertAlmostEqual(observed["Y", "H"], 15) self.assertAlmostEqual(observed["Y", "I"], 0) self.assertAlmostEqual(observed["Y", "K"], 1) self.assertAlmostEqual(observed["Y", "L"], 2) self.assertAlmostEqual(observed["Y", "M"], 0) self.assertAlmostEqual(observed["Y", "N"], 0) self.assertAlmostEqual(observed["Y", "P"], 1) self.assertAlmostEqual(observed["Y", "Q"], 2) self.assertAlmostEqual(observed["Y", "R"], 1) self.assertAlmostEqual(observed["Y", "S"], 2) self.assertAlmostEqual(observed["Y", "T"], 0) self.assertAlmostEqual(observed["Y", "V"], 1) self.assertAlmostEqual(observed["Y", "W"], 1) self.assertAlmostEqual(observed["Y", "Y"], 352) def test2_observed_probabilities(self): observed = self.observed # convert observed frequencies to probabilities total = observed.sum() observed[:, :] /= total self.assertEqual(observed.alphabet, protein_alphabet) self.assertEqual(observed.shape, (20, 20)) self.assertAlmostEqual(observed["A", "A"], 0.057491857) self.assertAlmostEqual(observed["A", "C"], 0.000081433) self.assertAlmostEqual(observed["A", "D"], 0.000244300) self.assertAlmostEqual(observed["A", "E"], 0.000895765) self.assertAlmostEqual(observed["A", "F"], 0.000081433) self.assertAlmostEqual(observed["A", "G"], 0.001140065) self.assertAlmostEqual(observed["A", "H"], 0.000081433) self.assertAlmostEqual(observed["A", "I"], 0.000325733) self.assertAlmostEqual(observed["A", "K"], 0.000081433) self.assertAlmostEqual(observed["A", "L"], 0.000407166) self.assertAlmostEqual(observed["A", "M"], 0.000407166) self.assertAlmostEqual(observed["A", "N"], 0.000081433) self.assertAlmostEqual(observed["A", "P"], 0.000407166) self.assertAlmostEqual(observed["A", "Q"], 0.000000000) self.assertAlmostEqual(observed["A", "R"], 0.000081433) self.assertAlmostEqual(observed["A", "S"], 0.001791531) self.assertAlmostEqual(observed["A", "T"], 0.003013029) self.assertAlmostEqual(observed["A", "V"], 0.002850163) self.assertAlmostEqual(observed["A", "W"], 0.000000000) self.assertAlmostEqual(observed["A", "Y"], 0.000081433) self.assertAlmostEqual(observed["C", "A"], 0.000000000) self.assertAlmostEqual(observed["C", "C"], 0.022719870) self.assertAlmostEqual(observed["C", "D"], 0.000000000) self.assertAlmostEqual(observed["C", "E"], 0.000081433) self.assertAlmostEqual(observed["C", "F"], 0.000244300) self.assertAlmostEqual(observed["C", "G"], 0.000162866) self.assertAlmostEqual(observed["C", "H"], 0.000000000) self.assertAlmostEqual(observed["C", "I"], 0.000081433) self.assertAlmostEqual(observed["C", "K"], 0.000000000) self.assertAlmostEqual(observed["C", "L"], 0.000081433) self.assertAlmostEqual(observed["C", "M"], 0.000000000) self.assertAlmostEqual(observed["C", "N"], 0.000081433) self.assertAlmostEqual(observed["C", "P"], 0.000162866) self.assertAlmostEqual(observed["C", "Q"], 0.000000000) self.assertAlmostEqual(observed["C", "R"], 0.000488599) self.assertAlmostEqual(observed["C", "S"], 0.000488599) self.assertAlmostEqual(observed["C", "T"], 0.000000000) self.assertAlmostEqual(observed["C", "V"], 0.000081433) self.assertAlmostEqual(observed["C", "W"], 0.000081433) self.assertAlmostEqual(observed["C", "Y"], 0.000488599) self.assertAlmostEqual(observed["D", "A"], 0.000570033) self.assertAlmostEqual(observed["D", "C"], 0.000081433) self.assertAlmostEqual(observed["D", "D"], 0.034771987) self.assertAlmostEqual(observed["D", "E"], 0.002035831) self.assertAlmostEqual(observed["D", "F"], 0.000000000) self.assertAlmostEqual(observed["D", "G"], 0.000651466) self.assertAlmostEqual(observed["D", "H"], 0.000000000) self.assertAlmostEqual(observed["D", "I"], 0.000000000) self.assertAlmostEqual(observed["D", "K"], 0.000081433) self.assertAlmostEqual(observed["D", "L"], 0.000162866) self.assertAlmostEqual(observed["D", "M"], 0.000000000) self.assertAlmostEqual(observed["D", "N"], 0.001547231) self.assertAlmostEqual(observed["D", "P"], 0.000000000) self.assertAlmostEqual(observed["D", "Q"], 0.000000000) self.assertAlmostEqual(observed["D", "R"], 0.000244300) self.assertAlmostEqual(observed["D", "S"], 0.000244300) self.assertAlmostEqual(observed["D", "T"], 0.000081433) self.assertAlmostEqual(observed["D", "V"], 0.000081433) self.assertAlmostEqual(observed["D", "W"], 0.000081433) self.assertAlmostEqual(observed["D", "Y"], 0.000081433) self.assertAlmostEqual(observed["E", "A"], 0.000732899) self.assertAlmostEqual(observed["E", "C"], 0.000000000) self.assertAlmostEqual(observed["E", "D"], 0.002442997) self.assertAlmostEqual(observed["E", "E"], 0.051221498) self.assertAlmostEqual(observed["E", "F"], 0.000081433) self.assertAlmostEqual(observed["E", "G"], 0.001547231) self.assertAlmostEqual(observed["E", "H"], 0.000244300) self.assertAlmostEqual(observed["E", "I"], 0.000081433) self.assertAlmostEqual(observed["E", "K"], 0.000977199) self.assertAlmostEqual(observed["E", "L"], 0.000081433) self.assertAlmostEqual(observed["E", "M"], 0.000081433) self.assertAlmostEqual(observed["E", "N"], 0.000081433) self.assertAlmostEqual(observed["E", "P"], 0.000081433) self.assertAlmostEqual(observed["E", "Q"], 0.000977199) self.assertAlmostEqual(observed["E", "R"], 0.000407166) self.assertAlmostEqual(observed["E", "S"], 0.000244300) self.assertAlmostEqual(observed["E", "T"], 0.000081433) self.assertAlmostEqual(observed["E", "V"], 0.000081433) self.assertAlmostEqual(observed["E", "W"], 0.000000000) self.assertAlmostEqual(observed["E", "Y"], 0.000000000) self.assertAlmostEqual(observed["F", "A"], 0.000000000) self.assertAlmostEqual(observed["F", "C"], 0.000162866) self.assertAlmostEqual(observed["F", "D"], 0.000081433) self.assertAlmostEqual(observed["F", "E"], 0.000000000) self.assertAlmostEqual(observed["F", "F"], 0.040472313) self.assertAlmostEqual(observed["F", "G"], 0.000081433) self.assertAlmostEqual(observed["F", "H"], 0.000081433) self.assertAlmostEqual(observed["F", "I"], 0.000081433) self.assertAlmostEqual(observed["F", "K"], 0.000081433) self.assertAlmostEqual(observed["F", "L"], 0.002117264) self.assertAlmostEqual(observed["F", "M"], 0.000081433) self.assertAlmostEqual(observed["F", "N"], 0.000000000) self.assertAlmostEqual(observed["F", "P"], 0.000000000) self.assertAlmostEqual(observed["F", "Q"], 0.000000000) self.assertAlmostEqual(observed["F", "R"], 0.000000000) self.assertAlmostEqual(observed["F", "S"], 0.000488599) self.assertAlmostEqual(observed["F", "T"], 0.000244300) self.assertAlmostEqual(observed["F", "V"], 0.000325733) self.assertAlmostEqual(observed["F", "W"], 0.000081433) self.assertAlmostEqual(observed["F", "Y"], 0.000977199) self.assertAlmostEqual(observed["G", "A"], 0.000977199) self.assertAlmostEqual(observed["G", "C"], 0.000162866) self.assertAlmostEqual(observed["G", "D"], 0.000814332) self.assertAlmostEqual(observed["G", "E"], 0.001140065) self.assertAlmostEqual(observed["G", "F"], 0.000000000) self.assertAlmostEqual(observed["G", "G"], 0.049837134) self.assertAlmostEqual(observed["G", "H"], 0.000000000) self.assertAlmostEqual(observed["G", "I"], 0.000081433) self.assertAlmostEqual(observed["G", "K"], 0.000081433) self.assertAlmostEqual(observed["G", "L"], 0.000081433) self.assertAlmostEqual(observed["G", "M"], 0.000081433) self.assertAlmostEqual(observed["G", "N"], 0.000162866) self.assertAlmostEqual(observed["G", "P"], 0.000081433) self.assertAlmostEqual(observed["G", "Q"], 0.000081433) self.assertAlmostEqual(observed["G", "R"], 0.001058632) self.assertAlmostEqual(observed["G", "S"], 0.001791531) self.assertAlmostEqual(observed["G", "T"], 0.000081433) self.assertAlmostEqual(observed["G", "V"], 0.000651466) self.assertAlmostEqual(observed["G", "W"], 0.000162866) self.assertAlmostEqual(observed["G", "Y"], 0.000081433) self.assertAlmostEqual(observed["H", "A"], 0.000081433) self.assertAlmostEqual(observed["H", "C"], 0.000081433) self.assertAlmostEqual(observed["H", "D"], 0.000325733) self.assertAlmostEqual(observed["H", "E"], 0.000081433) self.assertAlmostEqual(observed["H", "F"], 0.000081433) self.assertAlmostEqual(observed["H", "G"], 0.000162866) self.assertAlmostEqual(observed["H", "H"], 0.018485342) self.assertAlmostEqual(observed["H", "I"], 0.000000000) self.assertAlmostEqual(observed["H", "K"], 0.000081433) self.assertAlmostEqual(observed["H", "L"], 0.000081433) self.assertAlmostEqual(observed["H", "M"], 0.000000000) self.assertAlmostEqual(observed["H", "N"], 0.000570033) self.assertAlmostEqual(observed["H", "P"], 0.000162866) self.assertAlmostEqual(observed["H", "Q"], 0.001140065) self.assertAlmostEqual(observed["H", "R"], 0.001628664) self.assertAlmostEqual(observed["H", "S"], 0.000244300) self.assertAlmostEqual(observed["H", "T"], 0.000000000) self.assertAlmostEqual(observed["H", "V"], 0.000081433) self.assertAlmostEqual(observed["H", "W"], 0.000000000) self.assertAlmostEqual(observed["H", "Y"], 0.000570033) self.assertAlmostEqual(observed["I", "A"], 0.000407166) self.assertAlmostEqual(observed["I", "C"], 0.000000000) self.assertAlmostEqual(observed["I", "D"], 0.000081433) self.assertAlmostEqual(observed["I", "E"], 0.000162866) self.assertAlmostEqual(observed["I", "F"], 0.000407166) self.assertAlmostEqual(observed["I", "G"], 0.000000000) self.assertAlmostEqual(observed["I", "H"], 0.000081433) self.assertAlmostEqual(observed["I", "I"], 0.045439739) self.assertAlmostEqual(observed["I", "K"], 0.000081433) self.assertAlmostEqual(observed["I", "L"], 0.001791531) self.assertAlmostEqual(observed["I", "M"], 0.000895765) self.assertAlmostEqual(observed["I", "N"], 0.000244300) self.assertAlmostEqual(observed["I", "P"], 0.000081433) self.assertAlmostEqual(observed["I", "Q"], 0.000000000) self.assertAlmostEqual(observed["I", "R"], 0.000081433) self.assertAlmostEqual(observed["I", "S"], 0.000162866) self.assertAlmostEqual(observed["I", "T"], 0.001465798) self.assertAlmostEqual(observed["I", "V"], 0.004967427) self.assertAlmostEqual(observed["I", "W"], 0.000000000) self.assertAlmostEqual(observed["I", "Y"], 0.000081433) self.assertAlmostEqual(observed["K", "A"], 0.000244300) self.assertAlmostEqual(observed["K", "C"], 0.000081433) self.assertAlmostEqual(observed["K", "D"], 0.000081433) self.assertAlmostEqual(observed["K", "E"], 0.001384365) self.assertAlmostEqual(observed["K", "F"], 0.000000000) self.assertAlmostEqual(observed["K", "G"], 0.000162866) self.assertAlmostEqual(observed["K", "H"], 0.000162866) self.assertAlmostEqual(observed["K", "I"], 0.000162866) self.assertAlmostEqual(observed["K", "K"], 0.046661238) self.assertAlmostEqual(observed["K", "L"], 0.000000000) self.assertAlmostEqual(observed["K", "M"], 0.000162866) self.assertAlmostEqual(observed["K", "N"], 0.000895765) self.assertAlmostEqual(observed["K", "P"], 0.000081433) self.assertAlmostEqual(observed["K", "Q"], 0.001058632) self.assertAlmostEqual(observed["K", "R"], 0.003745928) self.assertAlmostEqual(observed["K", "S"], 0.000000000) self.assertAlmostEqual(observed["K", "T"], 0.000732899) self.assertAlmostEqual(observed["K", "V"], 0.000081433) self.assertAlmostEqual(observed["K", "W"], 0.000000000) self.assertAlmostEqual(observed["K", "Y"], 0.000081433) self.assertAlmostEqual(observed["L", "A"], 0.000570033) self.assertAlmostEqual(observed["L", "C"], 0.000081433) self.assertAlmostEqual(observed["L", "D"], 0.000000000) self.assertAlmostEqual(observed["L", "E"], 0.000081433) self.assertAlmostEqual(observed["L", "F"], 0.002117264) self.assertAlmostEqual(observed["L", "G"], 0.000162866) self.assertAlmostEqual(observed["L", "H"], 0.000081433) self.assertAlmostEqual(observed["L", "I"], 0.001710098) self.assertAlmostEqual(observed["L", "K"], 0.000081433) self.assertAlmostEqual(observed["L", "L"], 0.105863192) self.assertAlmostEqual(observed["L", "M"], 0.001547231) self.assertAlmostEqual(observed["L", "N"], 0.000081433) self.assertAlmostEqual(observed["L", "P"], 0.001384365) self.assertAlmostEqual(observed["L", "Q"], 0.000325733) self.assertAlmostEqual(observed["L", "R"], 0.000244300) self.assertAlmostEqual(observed["L", "S"], 0.000732899) self.assertAlmostEqual(observed["L", "T"], 0.000325733) self.assertAlmostEqual(observed["L", "V"], 0.003013029) self.assertAlmostEqual(observed["L", "W"], 0.000162866) self.assertAlmostEqual(observed["L", "Y"], 0.000000000) self.assertAlmostEqual(observed["M", "A"], 0.000000000) self.assertAlmostEqual(observed["M", "C"], 0.000081433) self.assertAlmostEqual(observed["M", "D"], 0.000081433) self.assertAlmostEqual(observed["M", "E"], 0.000000000) self.assertAlmostEqual(observed["M", "F"], 0.000081433) self.assertAlmostEqual(observed["M", "G"], 0.000162866) self.assertAlmostEqual(observed["M", "H"], 0.000081433) self.assertAlmostEqual(observed["M", "I"], 0.001140065) self.assertAlmostEqual(observed["M", "K"], 0.000244300) self.assertAlmostEqual(observed["M", "L"], 0.001465798) self.assertAlmostEqual(observed["M", "M"], 0.021416938) self.assertAlmostEqual(observed["M", "N"], 0.000000000) self.assertAlmostEqual(observed["M", "P"], 0.000081433) self.assertAlmostEqual(observed["M", "Q"], 0.000000000) self.assertAlmostEqual(observed["M", "R"], 0.000081433) self.assertAlmostEqual(observed["M", "S"], 0.000162866) self.assertAlmostEqual(observed["M", "T"], 0.000570033) self.assertAlmostEqual(observed["M", "V"], 0.000488599) self.assertAlmostEqual(observed["M", "W"], 0.000000000) self.assertAlmostEqual(observed["M", "Y"], 0.000081433) self.assertAlmostEqual(observed["N", "A"], 0.000162866) self.assertAlmostEqual(observed["N", "C"], 0.000000000) self.assertAlmostEqual(observed["N", "D"], 0.001710098) self.assertAlmostEqual(observed["N", "E"], 0.000081433) self.assertAlmostEqual(observed["N", "F"], 0.000162866) self.assertAlmostEqual(observed["N", "G"], 0.000407166) self.assertAlmostEqual(observed["N", "H"], 0.000325733) self.assertAlmostEqual(observed["N", "I"], 0.000162866) self.assertAlmostEqual(observed["N", "K"], 0.000651466) self.assertAlmostEqual(observed["N", "L"], 0.000162866) self.assertAlmostEqual(observed["N", "M"], 0.000081433) self.assertAlmostEqual(observed["N", "N"], 0.029315961) self.assertAlmostEqual(observed["N", "P"], 0.000000000) self.assertAlmostEqual(observed["N", "Q"], 0.000244300) self.assertAlmostEqual(observed["N", "R"], 0.000081433) self.assertAlmostEqual(observed["N", "S"], 0.001221498) self.assertAlmostEqual(observed["N", "T"], 0.000651466) self.assertAlmostEqual(observed["N", "V"], 0.000000000) self.assertAlmostEqual(observed["N", "W"], 0.000000000) self.assertAlmostEqual(observed["N", "Y"], 0.000162866) self.assertAlmostEqual(observed["P", "A"], 0.001140065) self.assertAlmostEqual(observed["P", "C"], 0.000000000) self.assertAlmostEqual(observed["P", "D"], 0.000081433) self.assertAlmostEqual(observed["P", "E"], 0.000000000) self.assertAlmostEqual(observed["P", "F"], 0.000081433) self.assertAlmostEqual(observed["P", "G"], 0.000000000) self.assertAlmostEqual(observed["P", "H"], 0.000407166) self.assertAlmostEqual(observed["P", "I"], 0.000000000) self.assertAlmostEqual(observed["P", "K"], 0.000000000) self.assertAlmostEqual(observed["P", "L"], 0.001302932) self.assertAlmostEqual(observed["P", "M"], 0.000000000) self.assertAlmostEqual(observed["P", "N"], 0.000081433) self.assertAlmostEqual(observed["P", "P"], 0.044869707) self.assertAlmostEqual(observed["P", "Q"], 0.000244300) self.assertAlmostEqual(observed["P", "R"], 0.000162866) self.assertAlmostEqual(observed["P", "S"], 0.001954397) self.assertAlmostEqual(observed["P", "T"], 0.000570033) self.assertAlmostEqual(observed["P", "V"], 0.000162866) self.assertAlmostEqual(observed["P", "W"], 0.000081433) self.assertAlmostEqual(observed["P", "Y"], 0.000000000) self.assertAlmostEqual(observed["Q", "A"], 0.000081433) self.assertAlmostEqual(observed["Q", "C"], 0.000081433) self.assertAlmostEqual(observed["Q", "D"], 0.000081433) self.assertAlmostEqual(observed["Q", "E"], 0.000814332) self.assertAlmostEqual(observed["Q", "F"], 0.000081433) self.assertAlmostEqual(observed["Q", "G"], 0.000000000) self.assertAlmostEqual(observed["Q", "H"], 0.000488599) self.assertAlmostEqual(observed["Q", "I"], 0.000081433) self.assertAlmostEqual(observed["Q", "K"], 0.001058632) self.assertAlmostEqual(observed["Q", "L"], 0.000407166) self.assertAlmostEqual(observed["Q", "M"], 0.000081433) self.assertAlmostEqual(observed["Q", "N"], 0.000162866) self.assertAlmostEqual(observed["Q", "P"], 0.000081433) self.assertAlmostEqual(observed["Q", "Q"], 0.033306189) self.assertAlmostEqual(observed["Q", "R"], 0.001465798) self.assertAlmostEqual(observed["Q", "S"], 0.000081433) self.assertAlmostEqual(observed["Q", "T"], 0.000000000) self.assertAlmostEqual(observed["Q", "V"], 0.000081433) self.assertAlmostEqual(observed["Q", "W"], 0.000000000) self.assertAlmostEqual(observed["Q", "Y"], 0.000000000) self.assertAlmostEqual(observed["R", "A"], 0.000244300) self.assertAlmostEqual(observed["R", "C"], 0.000244300) self.assertAlmostEqual(observed["R", "D"], 0.000000000) self.assertAlmostEqual(observed["R", "E"], 0.000162866) self.assertAlmostEqual(observed["R", "F"], 0.000081433) self.assertAlmostEqual(observed["R", "G"], 0.001058632) self.assertAlmostEqual(observed["R", "H"], 0.000488599) self.assertAlmostEqual(observed["R", "I"], 0.000000000) self.assertAlmostEqual(observed["R", "K"], 0.003257329) self.assertAlmostEqual(observed["R", "L"], 0.000407166) self.assertAlmostEqual(observed["R", "M"], 0.000162866) self.assertAlmostEqual(observed["R", "N"], 0.000325733) self.assertAlmostEqual(observed["R", "P"], 0.000407166) self.assertAlmostEqual(observed["R", "Q"], 0.002361564) self.assertAlmostEqual(observed["R", "R"], 0.040065147) self.assertAlmostEqual(observed["R", "S"], 0.000732899) self.assertAlmostEqual(observed["R", "T"], 0.000244300) self.assertAlmostEqual(observed["R", "V"], 0.000162866) self.assertAlmostEqual(observed["R", "W"], 0.000081433) self.assertAlmostEqual(observed["R", "Y"], 0.000000000) self.assertAlmostEqual(observed["S", "A"], 0.002768730) self.assertAlmostEqual(observed["S", "C"], 0.000244300) self.assertAlmostEqual(observed["S", "D"], 0.000244300) self.assertAlmostEqual(observed["S", "E"], 0.000244300) self.assertAlmostEqual(observed["S", "F"], 0.000732899) self.assertAlmostEqual(observed["S", "G"], 0.001465798) self.assertAlmostEqual(observed["S", "H"], 0.000162866) self.assertAlmostEqual(observed["S", "I"], 0.000325733) self.assertAlmostEqual(observed["S", "K"], 0.000325733) self.assertAlmostEqual(observed["S", "L"], 0.000244300) self.assertAlmostEqual(observed["S", "M"], 0.000000000) self.assertAlmostEqual(observed["S", "N"], 0.002035831) self.assertAlmostEqual(observed["S", "P"], 0.001547231) self.assertAlmostEqual(observed["S", "Q"], 0.000162866) self.assertAlmostEqual(observed["S", "R"], 0.000895765) self.assertAlmostEqual(observed["S", "S"], 0.065390879) self.assertAlmostEqual(observed["S", "T"], 0.002117264) self.assertAlmostEqual(observed["S", "V"], 0.000244300) self.assertAlmostEqual(observed["S", "W"], 0.000162866) self.assertAlmostEqual(observed["S", "Y"], 0.000488599) self.assertAlmostEqual(observed["T", "A"], 0.003501629) self.assertAlmostEqual(observed["T", "C"], 0.000081433) self.assertAlmostEqual(observed["T", "D"], 0.000325733) self.assertAlmostEqual(observed["T", "E"], 0.000081433) self.assertAlmostEqual(observed["T", "F"], 0.000000000) self.assertAlmostEqual(observed["T", "G"], 0.000162866) self.assertAlmostEqual(observed["T", "H"], 0.000081433) self.assertAlmostEqual(observed["T", "I"], 0.001465798) self.assertAlmostEqual(observed["T", "K"], 0.000325733) self.assertAlmostEqual(observed["T", "L"], 0.000325733) self.assertAlmostEqual(observed["T", "M"], 0.001302932) self.assertAlmostEqual(observed["T", "N"], 0.000651466) self.assertAlmostEqual(observed["T", "P"], 0.000732899) self.assertAlmostEqual(observed["T", "Q"], 0.000162866) self.assertAlmostEqual(observed["T", "R"], 0.000162866) self.assertAlmostEqual(observed["T", "S"], 0.002198697) self.assertAlmostEqual(observed["T", "T"], 0.042833876) self.assertAlmostEqual(observed["T", "V"], 0.000488599) self.assertAlmostEqual(observed["T", "W"], 0.000081433) self.assertAlmostEqual(observed["T", "Y"], 0.000081433) self.assertAlmostEqual(observed["V", "A"], 0.002035831) self.assertAlmostEqual(observed["V", "C"], 0.000081433) self.assertAlmostEqual(observed["V", "D"], 0.000244300) self.assertAlmostEqual(observed["V", "E"], 0.000162866) self.assertAlmostEqual(observed["V", "F"], 0.000488599) self.assertAlmostEqual(observed["V", "G"], 0.000732899) self.assertAlmostEqual(observed["V", "H"], 0.000000000) self.assertAlmostEqual(observed["V", "I"], 0.003908795) self.assertAlmostEqual(observed["V", "K"], 0.000081433) self.assertAlmostEqual(observed["V", "L"], 0.001710098) self.assertAlmostEqual(observed["V", "M"], 0.000651466) self.assertAlmostEqual(observed["V", "N"], 0.000081433) self.assertAlmostEqual(observed["V", "P"], 0.000162866) self.assertAlmostEqual(observed["V", "Q"], 0.000081433) self.assertAlmostEqual(observed["V", "R"], 0.000244300) self.assertAlmostEqual(observed["V", "S"], 0.000244300) self.assertAlmostEqual(observed["V", "T"], 0.001058632) self.assertAlmostEqual(observed["V", "V"], 0.050732899) self.assertAlmostEqual(observed["V", "W"], 0.000081433) self.assertAlmostEqual(observed["V", "Y"], 0.000000000) self.assertAlmostEqual(observed["W", "A"], 0.000162866) self.assertAlmostEqual(observed["W", "C"], 0.000081433) self.assertAlmostEqual(observed["W", "D"], 0.000000000) self.assertAlmostEqual(observed["W", "E"], 0.000081433) self.assertAlmostEqual(observed["W", "F"], 0.000000000) self.assertAlmostEqual(observed["W", "G"], 0.000325733) self.assertAlmostEqual(observed["W", "H"], 0.000081433) self.assertAlmostEqual(observed["W", "I"], 0.000081433) self.assertAlmostEqual(observed["W", "K"], 0.000081433) self.assertAlmostEqual(observed["W", "L"], 0.000162866) self.assertAlmostEqual(observed["W", "M"], 0.000081433) self.assertAlmostEqual(observed["W", "N"], 0.000081433) self.assertAlmostEqual(observed["W", "P"], 0.000000000) self.assertAlmostEqual(observed["W", "Q"], 0.000081433) self.assertAlmostEqual(observed["W", "R"], 0.000570033) self.assertAlmostEqual(observed["W", "S"], 0.000000000) self.assertAlmostEqual(observed["W", "T"], 0.000081433) self.assertAlmostEqual(observed["W", "V"], 0.000000000) self.assertAlmostEqual(observed["W", "W"], 0.013843648) self.assertAlmostEqual(observed["W", "Y"], 0.000000000) self.assertAlmostEqual(observed["Y", "A"], 0.000000000) self.assertAlmostEqual(observed["Y", "C"], 0.000325733) self.assertAlmostEqual(observed["Y", "D"], 0.000081433) self.assertAlmostEqual(observed["Y", "E"], 0.000081433) self.assertAlmostEqual(observed["Y", "F"], 0.001058632) self.assertAlmostEqual(observed["Y", "G"], 0.000000000) self.assertAlmostEqual(observed["Y", "H"], 0.001221498) self.assertAlmostEqual(observed["Y", "I"], 0.000000000) self.assertAlmostEqual(observed["Y", "K"], 0.000081433) self.assertAlmostEqual(observed["Y", "L"], 0.000162866) self.assertAlmostEqual(observed["Y", "M"], 0.000000000) self.assertAlmostEqual(observed["Y", "N"], 0.000000000) self.assertAlmostEqual(observed["Y", "P"], 0.000081433) self.assertAlmostEqual(observed["Y", "Q"], 0.000162866) self.assertAlmostEqual(observed["Y", "R"], 0.000081433) self.assertAlmostEqual(observed["Y", "S"], 0.000162866) self.assertAlmostEqual(observed["Y", "T"], 0.000000000) self.assertAlmostEqual(observed["Y", "V"], 0.000081433) self.assertAlmostEqual(observed["Y", "W"], 0.000081433) self.assertAlmostEqual(observed["Y", "Y"], 0.028664495) def test3_observed_symmetric_probabilities(self): observed = self.observed # make a symmetric matrix observed[:, :] = 0.5 * (observed + observed.transpose()) self.assertEqual(observed.alphabet, protein_alphabet) self.assertEqual(observed.shape, (20, 20)) self.assertAlmostEqual(observed["A", "A"], 0.057491857) self.assertAlmostEqual(observed["A", "C"], 0.000040717) self.assertAlmostEqual(observed["A", "D"], 0.000407166) self.assertAlmostEqual(observed["A", "E"], 0.000814332) self.assertAlmostEqual(observed["A", "F"], 0.000040717) self.assertAlmostEqual(observed["A", "G"], 0.001058632) self.assertAlmostEqual(observed["A", "H"], 0.000081433) self.assertAlmostEqual(observed["A", "I"], 0.000366450) self.assertAlmostEqual(observed["A", "K"], 0.000162866) self.assertAlmostEqual(observed["A", "L"], 0.000488599) self.assertAlmostEqual(observed["A", "M"], 0.000203583) self.assertAlmostEqual(observed["A", "N"], 0.000122150) self.assertAlmostEqual(observed["A", "P"], 0.000773616) self.assertAlmostEqual(observed["A", "Q"], 0.000040717) self.assertAlmostEqual(observed["A", "R"], 0.000162866) self.assertAlmostEqual(observed["A", "S"], 0.002280130) self.assertAlmostEqual(observed["A", "T"], 0.003257329) self.assertAlmostEqual(observed["A", "V"], 0.002442997) self.assertAlmostEqual(observed["A", "W"], 0.000081433) self.assertAlmostEqual(observed["A", "Y"], 0.000040717) self.assertAlmostEqual(observed["C", "A"], 0.000040717) self.assertAlmostEqual(observed["C", "C"], 0.022719870) self.assertAlmostEqual(observed["C", "D"], 0.000040717) self.assertAlmostEqual(observed["C", "E"], 0.000040717) self.assertAlmostEqual(observed["C", "F"], 0.000203583) self.assertAlmostEqual(observed["C", "G"], 0.000162866) self.assertAlmostEqual(observed["C", "H"], 0.000040717) self.assertAlmostEqual(observed["C", "I"], 0.000040717) self.assertAlmostEqual(observed["C", "K"], 0.000040717) self.assertAlmostEqual(observed["C", "L"], 0.000081433) self.assertAlmostEqual(observed["C", "M"], 0.000040717) self.assertAlmostEqual(observed["C", "N"], 0.000040717) self.assertAlmostEqual(observed["C", "P"], 0.000081433) self.assertAlmostEqual(observed["C", "Q"], 0.000040717) self.assertAlmostEqual(observed["C", "R"], 0.000366450) self.assertAlmostEqual(observed["C", "S"], 0.000366450) self.assertAlmostEqual(observed["C", "T"], 0.000040717) self.assertAlmostEqual(observed["C", "V"], 0.000081433) self.assertAlmostEqual(observed["C", "W"], 0.000081433) self.assertAlmostEqual(observed["C", "Y"], 0.000407166) self.assertAlmostEqual(observed["D", "A"], 0.000407166) self.assertAlmostEqual(observed["D", "C"], 0.000040717) self.assertAlmostEqual(observed["D", "D"], 0.034771987) self.assertAlmostEqual(observed["D", "E"], 0.002239414) self.assertAlmostEqual(observed["D", "F"], 0.000040717) self.assertAlmostEqual(observed["D", "G"], 0.000732899) self.assertAlmostEqual(observed["D", "H"], 0.000162866) self.assertAlmostEqual(observed["D", "I"], 0.000040717) self.assertAlmostEqual(observed["D", "K"], 0.000081433) self.assertAlmostEqual(observed["D", "L"], 0.000081433) self.assertAlmostEqual(observed["D", "M"], 0.000040717) self.assertAlmostEqual(observed["D", "N"], 0.001628664) self.assertAlmostEqual(observed["D", "P"], 0.000040717) self.assertAlmostEqual(observed["D", "Q"], 0.000040717) self.assertAlmostEqual(observed["D", "R"], 0.000122150) self.assertAlmostEqual(observed["D", "S"], 0.000244300) self.assertAlmostEqual(observed["D", "T"], 0.000203583) self.assertAlmostEqual(observed["D", "V"], 0.000162866) self.assertAlmostEqual(observed["D", "W"], 0.000040717) self.assertAlmostEqual(observed["D", "Y"], 0.000081433) self.assertAlmostEqual(observed["E", "A"], 0.000814332) self.assertAlmostEqual(observed["E", "C"], 0.000040717) self.assertAlmostEqual(observed["E", "D"], 0.002239414) self.assertAlmostEqual(observed["E", "E"], 0.051221498) self.assertAlmostEqual(observed["E", "F"], 0.000040717) self.assertAlmostEqual(observed["E", "G"], 0.001343648) self.assertAlmostEqual(observed["E", "H"], 0.000162866) self.assertAlmostEqual(observed["E", "I"], 0.000122150) self.assertAlmostEqual(observed["E", "K"], 0.001180782) self.assertAlmostEqual(observed["E", "L"], 0.000081433) self.assertAlmostEqual(observed["E", "M"], 0.000040717) self.assertAlmostEqual(observed["E", "N"], 0.000081433) self.assertAlmostEqual(observed["E", "P"], 0.000040717) self.assertAlmostEqual(observed["E", "Q"], 0.000895765) self.assertAlmostEqual(observed["E", "R"], 0.000285016) self.assertAlmostEqual(observed["E", "S"], 0.000244300) self.assertAlmostEqual(observed["E", "T"], 0.000081433) self.assertAlmostEqual(observed["E", "V"], 0.000122150) self.assertAlmostEqual(observed["E", "W"], 0.000040717) self.assertAlmostEqual(observed["E", "Y"], 0.000040717) self.assertAlmostEqual(observed["F", "A"], 0.000040717) self.assertAlmostEqual(observed["F", "C"], 0.000203583) self.assertAlmostEqual(observed["F", "D"], 0.000040717) self.assertAlmostEqual(observed["F", "E"], 0.000040717) self.assertAlmostEqual(observed["F", "F"], 0.040472313) self.assertAlmostEqual(observed["F", "G"], 0.000040717) self.assertAlmostEqual(observed["F", "H"], 0.000081433) self.assertAlmostEqual(observed["F", "I"], 0.000244300) self.assertAlmostEqual(observed["F", "K"], 0.000040717) self.assertAlmostEqual(observed["F", "L"], 0.002117264) self.assertAlmostEqual(observed["F", "M"], 0.000081433) self.assertAlmostEqual(observed["F", "N"], 0.000081433) self.assertAlmostEqual(observed["F", "P"], 0.000040717) self.assertAlmostEqual(observed["F", "Q"], 0.000040717) self.assertAlmostEqual(observed["F", "R"], 0.000040717) self.assertAlmostEqual(observed["F", "S"], 0.000610749) self.assertAlmostEqual(observed["F", "T"], 0.000122150) self.assertAlmostEqual(observed["F", "V"], 0.000407166) self.assertAlmostEqual(observed["F", "W"], 0.000040717) self.assertAlmostEqual(observed["F", "Y"], 0.001017915) self.assertAlmostEqual(observed["G", "A"], 0.001058632) self.assertAlmostEqual(observed["G", "C"], 0.000162866) self.assertAlmostEqual(observed["G", "D"], 0.000732899) self.assertAlmostEqual(observed["G", "E"], 0.001343648) self.assertAlmostEqual(observed["G", "F"], 0.000040717) self.assertAlmostEqual(observed["G", "G"], 0.049837134) self.assertAlmostEqual(observed["G", "H"], 0.000081433) self.assertAlmostEqual(observed["G", "I"], 0.000040717) self.assertAlmostEqual(observed["G", "K"], 0.000122150) self.assertAlmostEqual(observed["G", "L"], 0.000122150) self.assertAlmostEqual(observed["G", "M"], 0.000122150) self.assertAlmostEqual(observed["G", "N"], 0.000285016) self.assertAlmostEqual(observed["G", "P"], 0.000040717) self.assertAlmostEqual(observed["G", "Q"], 0.000040717) self.assertAlmostEqual(observed["G", "R"], 0.001058632) self.assertAlmostEqual(observed["G", "S"], 0.001628664) self.assertAlmostEqual(observed["G", "T"], 0.000122150) self.assertAlmostEqual(observed["G", "V"], 0.000692182) self.assertAlmostEqual(observed["G", "W"], 0.000244300) self.assertAlmostEqual(observed["G", "Y"], 0.000040717) self.assertAlmostEqual(observed["H", "A"], 0.000081433) self.assertAlmostEqual(observed["H", "C"], 0.000040717) self.assertAlmostEqual(observed["H", "D"], 0.000162866) self.assertAlmostEqual(observed["H", "E"], 0.000162866) self.assertAlmostEqual(observed["H", "F"], 0.000081433) self.assertAlmostEqual(observed["H", "G"], 0.000081433) self.assertAlmostEqual(observed["H", "H"], 0.018485342) self.assertAlmostEqual(observed["H", "I"], 0.000040717) self.assertAlmostEqual(observed["H", "K"], 0.000122150) self.assertAlmostEqual(observed["H", "L"], 0.000081433) self.assertAlmostEqual(observed["H", "M"], 0.000040717) self.assertAlmostEqual(observed["H", "N"], 0.000447883) self.assertAlmostEqual(observed["H", "P"], 0.000285016) self.assertAlmostEqual(observed["H", "Q"], 0.000814332) self.assertAlmostEqual(observed["H", "R"], 0.001058632) self.assertAlmostEqual(observed["H", "S"], 0.000203583) self.assertAlmostEqual(observed["H", "T"], 0.000040717) self.assertAlmostEqual(observed["H", "V"], 0.000040717) self.assertAlmostEqual(observed["H", "W"], 0.000040717) self.assertAlmostEqual(observed["H", "Y"], 0.000895765) self.assertAlmostEqual(observed["I", "A"], 0.000366450) self.assertAlmostEqual(observed["I", "C"], 0.000040717) self.assertAlmostEqual(observed["I", "D"], 0.000040717) self.assertAlmostEqual(observed["I", "E"], 0.000122150) self.assertAlmostEqual(observed["I", "F"], 0.000244300) self.assertAlmostEqual(observed["I", "G"], 0.000040717) self.assertAlmostEqual(observed["I", "H"], 0.000040717) self.assertAlmostEqual(observed["I", "I"], 0.045439739) self.assertAlmostEqual(observed["I", "K"], 0.000122150) self.assertAlmostEqual(observed["I", "L"], 0.001750814) self.assertAlmostEqual(observed["I", "M"], 0.001017915) self.assertAlmostEqual(observed["I", "N"], 0.000203583) self.assertAlmostEqual(observed["I", "P"], 0.000040717) self.assertAlmostEqual(observed["I", "Q"], 0.000040717) self.assertAlmostEqual(observed["I", "R"], 0.000040717) self.assertAlmostEqual(observed["I", "S"], 0.000244300) self.assertAlmostEqual(observed["I", "T"], 0.001465798) self.assertAlmostEqual(observed["I", "V"], 0.004438111) self.assertAlmostEqual(observed["I", "W"], 0.000040717) self.assertAlmostEqual(observed["I", "Y"], 0.000040717) self.assertAlmostEqual(observed["K", "A"], 0.000162866) self.assertAlmostEqual(observed["K", "C"], 0.000040717) self.assertAlmostEqual(observed["K", "D"], 0.000081433) self.assertAlmostEqual(observed["K", "E"], 0.001180782) self.assertAlmostEqual(observed["K", "F"], 0.000040717) self.assertAlmostEqual(observed["K", "G"], 0.000122150) self.assertAlmostEqual(observed["K", "H"], 0.000122150) self.assertAlmostEqual(observed["K", "I"], 0.000122150) self.assertAlmostEqual(observed["K", "K"], 0.046661238) self.assertAlmostEqual(observed["K", "L"], 0.000040717) self.assertAlmostEqual(observed["K", "M"], 0.000203583) self.assertAlmostEqual(observed["K", "N"], 0.000773616) self.assertAlmostEqual(observed["K", "P"], 0.000040717) self.assertAlmostEqual(observed["K", "Q"], 0.001058632) self.assertAlmostEqual(observed["K", "R"], 0.003501629) self.assertAlmostEqual(observed["K", "S"], 0.000162866) self.assertAlmostEqual(observed["K", "T"], 0.000529316) self.assertAlmostEqual(observed["K", "V"], 0.000081433) self.assertAlmostEqual(observed["K", "W"], 0.000040717) self.assertAlmostEqual(observed["K", "Y"], 0.000081433) self.assertAlmostEqual(observed["L", "A"], 0.000488599) self.assertAlmostEqual(observed["L", "C"], 0.000081433) self.assertAlmostEqual(observed["L", "D"], 0.000081433) self.assertAlmostEqual(observed["L", "E"], 0.000081433) self.assertAlmostEqual(observed["L", "F"], 0.002117264) self.assertAlmostEqual(observed["L", "G"], 0.000122150) self.assertAlmostEqual(observed["L", "H"], 0.000081433) self.assertAlmostEqual(observed["L", "I"], 0.001750814) self.assertAlmostEqual(observed["L", "K"], 0.000040717) self.assertAlmostEqual(observed["L", "L"], 0.105863192) self.assertAlmostEqual(observed["L", "M"], 0.001506515) self.assertAlmostEqual(observed["L", "N"], 0.000122150) self.assertAlmostEqual(observed["L", "P"], 0.001343648) self.assertAlmostEqual(observed["L", "Q"], 0.000366450) self.assertAlmostEqual(observed["L", "R"], 0.000325733) self.assertAlmostEqual(observed["L", "S"], 0.000488599) self.assertAlmostEqual(observed["L", "T"], 0.000325733) self.assertAlmostEqual(observed["L", "V"], 0.002361564) self.assertAlmostEqual(observed["L", "W"], 0.000162866) self.assertAlmostEqual(observed["L", "Y"], 0.000081433) self.assertAlmostEqual(observed["M", "A"], 0.000203583) self.assertAlmostEqual(observed["M", "C"], 0.000040717) self.assertAlmostEqual(observed["M", "D"], 0.000040717) self.assertAlmostEqual(observed["M", "E"], 0.000040717) self.assertAlmostEqual(observed["M", "F"], 0.000081433) self.assertAlmostEqual(observed["M", "G"], 0.000122150) self.assertAlmostEqual(observed["M", "H"], 0.000040717) self.assertAlmostEqual(observed["M", "I"], 0.001017915) self.assertAlmostEqual(observed["M", "K"], 0.000203583) self.assertAlmostEqual(observed["M", "L"], 0.001506515) self.assertAlmostEqual(observed["M", "M"], 0.021416938) self.assertAlmostEqual(observed["M", "N"], 0.000040717) self.assertAlmostEqual(observed["M", "P"], 0.000040717) self.assertAlmostEqual(observed["M", "Q"], 0.000040717) self.assertAlmostEqual(observed["M", "R"], 0.000122150) self.assertAlmostEqual(observed["M", "S"], 0.000081433) self.assertAlmostEqual(observed["M", "T"], 0.000936482) self.assertAlmostEqual(observed["M", "V"], 0.000570033) self.assertAlmostEqual(observed["M", "W"], 0.000040717) self.assertAlmostEqual(observed["M", "Y"], 0.000040717) self.assertAlmostEqual(observed["N", "A"], 0.000122150) self.assertAlmostEqual(observed["N", "C"], 0.000040717) self.assertAlmostEqual(observed["N", "D"], 0.001628664) self.assertAlmostEqual(observed["N", "E"], 0.000081433) self.assertAlmostEqual(observed["N", "F"], 0.000081433) self.assertAlmostEqual(observed["N", "G"], 0.000285016) self.assertAlmostEqual(observed["N", "H"], 0.000447883) self.assertAlmostEqual(observed["N", "I"], 0.000203583) self.assertAlmostEqual(observed["N", "K"], 0.000773616) self.assertAlmostEqual(observed["N", "L"], 0.000122150) self.assertAlmostEqual(observed["N", "M"], 0.000040717) self.assertAlmostEqual(observed["N", "N"], 0.029315961) self.assertAlmostEqual(observed["N", "P"], 0.000040717) self.assertAlmostEqual(observed["N", "Q"], 0.000203583) self.assertAlmostEqual(observed["N", "R"], 0.000203583) self.assertAlmostEqual(observed["N", "S"], 0.001628664) self.assertAlmostEqual(observed["N", "T"], 0.000651466) self.assertAlmostEqual(observed["N", "V"], 0.000040717) self.assertAlmostEqual(observed["N", "W"], 0.000040717) self.assertAlmostEqual(observed["N", "Y"], 0.000081433) self.assertAlmostEqual(observed["P", "A"], 0.000773616) self.assertAlmostEqual(observed["P", "C"], 0.000081433) self.assertAlmostEqual(observed["P", "D"], 0.000040717) self.assertAlmostEqual(observed["P", "E"], 0.000040717) self.assertAlmostEqual(observed["P", "F"], 0.000040717) self.assertAlmostEqual(observed["P", "G"], 0.000040717) self.assertAlmostEqual(observed["P", "H"], 0.000285016) self.assertAlmostEqual(observed["P", "I"], 0.000040717) self.assertAlmostEqual(observed["P", "K"], 0.000040717) self.assertAlmostEqual(observed["P", "L"], 0.001343648) self.assertAlmostEqual(observed["P", "M"], 0.000040717) self.assertAlmostEqual(observed["P", "N"], 0.000040717) self.assertAlmostEqual(observed["P", "P"], 0.044869707) self.assertAlmostEqual(observed["P", "Q"], 0.000162866) self.assertAlmostEqual(observed["P", "R"], 0.000285016) self.assertAlmostEqual(observed["P", "S"], 0.001750814) self.assertAlmostEqual(observed["P", "T"], 0.000651466) self.assertAlmostEqual(observed["P", "V"], 0.000162866) self.assertAlmostEqual(observed["P", "W"], 0.000040717) self.assertAlmostEqual(observed["P", "Y"], 0.000040717) self.assertAlmostEqual(observed["Q", "A"], 0.000040717) self.assertAlmostEqual(observed["Q", "C"], 0.000040717) self.assertAlmostEqual(observed["Q", "D"], 0.000040717) self.assertAlmostEqual(observed["Q", "E"], 0.000895765) self.assertAlmostEqual(observed["Q", "F"], 0.000040717) self.assertAlmostEqual(observed["Q", "G"], 0.000040717) self.assertAlmostEqual(observed["Q", "H"], 0.000814332) self.assertAlmostEqual(observed["Q", "I"], 0.000040717) self.assertAlmostEqual(observed["Q", "K"], 0.001058632) self.assertAlmostEqual(observed["Q", "L"], 0.000366450) self.assertAlmostEqual(observed["Q", "M"], 0.000040717) self.assertAlmostEqual(observed["Q", "N"], 0.000203583) self.assertAlmostEqual(observed["Q", "P"], 0.000162866) self.assertAlmostEqual(observed["Q", "Q"], 0.033306189) self.assertAlmostEqual(observed["Q", "R"], 0.001913681) self.assertAlmostEqual(observed["Q", "S"], 0.000122150) self.assertAlmostEqual(observed["Q", "T"], 0.000081433) self.assertAlmostEqual(observed["Q", "V"], 0.000081433) self.assertAlmostEqual(observed["Q", "W"], 0.000040717) self.assertAlmostEqual(observed["Q", "Y"], 0.000081433) self.assertAlmostEqual(observed["R", "A"], 0.000162866) self.assertAlmostEqual(observed["R", "C"], 0.000366450) self.assertAlmostEqual(observed["R", "D"], 0.000122150) self.assertAlmostEqual(observed["R", "E"], 0.000285016) self.assertAlmostEqual(observed["R", "F"], 0.000040717) self.assertAlmostEqual(observed["R", "G"], 0.001058632) self.assertAlmostEqual(observed["R", "H"], 0.001058632) self.assertAlmostEqual(observed["R", "I"], 0.000040717) self.assertAlmostEqual(observed["R", "K"], 0.003501629) self.assertAlmostEqual(observed["R", "L"], 0.000325733) self.assertAlmostEqual(observed["R", "M"], 0.000122150) self.assertAlmostEqual(observed["R", "N"], 0.000203583) self.assertAlmostEqual(observed["R", "P"], 0.000285016) self.assertAlmostEqual(observed["R", "Q"], 0.001913681) self.assertAlmostEqual(observed["R", "R"], 0.040065147) self.assertAlmostEqual(observed["R", "S"], 0.000814332) self.assertAlmostEqual(observed["R", "T"], 0.000203583) self.assertAlmostEqual(observed["R", "V"], 0.000203583) self.assertAlmostEqual(observed["R", "W"], 0.000325733) self.assertAlmostEqual(observed["R", "Y"], 0.000040717) self.assertAlmostEqual(observed["S", "A"], 0.002280130) self.assertAlmostEqual(observed["S", "C"], 0.000366450) self.assertAlmostEqual(observed["S", "D"], 0.000244300) self.assertAlmostEqual(observed["S", "E"], 0.000244300) self.assertAlmostEqual(observed["S", "F"], 0.000610749) self.assertAlmostEqual(observed["S", "G"], 0.001628664) self.assertAlmostEqual(observed["S", "H"], 0.000203583) self.assertAlmostEqual(observed["S", "I"], 0.000244300) self.assertAlmostEqual(observed["S", "K"], 0.000162866) self.assertAlmostEqual(observed["S", "L"], 0.000488599) self.assertAlmostEqual(observed["S", "M"], 0.000081433) self.assertAlmostEqual(observed["S", "N"], 0.001628664) self.assertAlmostEqual(observed["S", "P"], 0.001750814) self.assertAlmostEqual(observed["S", "Q"], 0.000122150) self.assertAlmostEqual(observed["S", "R"], 0.000814332) self.assertAlmostEqual(observed["S", "S"], 0.065390879) self.assertAlmostEqual(observed["S", "T"], 0.002157980) self.assertAlmostEqual(observed["S", "V"], 0.000244300) self.assertAlmostEqual(observed["S", "W"], 0.000081433) self.assertAlmostEqual(observed["S", "Y"], 0.000325733) self.assertAlmostEqual(observed["T", "A"], 0.003257329) self.assertAlmostEqual(observed["T", "C"], 0.000040717) self.assertAlmostEqual(observed["T", "D"], 0.000203583) self.assertAlmostEqual(observed["T", "E"], 0.000081433) self.assertAlmostEqual(observed["T", "F"], 0.000122150) self.assertAlmostEqual(observed["T", "G"], 0.000122150) self.assertAlmostEqual(observed["T", "H"], 0.000040717) self.assertAlmostEqual(observed["T", "I"], 0.001465798) self.assertAlmostEqual(observed["T", "K"], 0.000529316) self.assertAlmostEqual(observed["T", "L"], 0.000325733) self.assertAlmostEqual(observed["T", "M"], 0.000936482) self.assertAlmostEqual(observed["T", "N"], 0.000651466) self.assertAlmostEqual(observed["T", "P"], 0.000651466) self.assertAlmostEqual(observed["T", "Q"], 0.000081433) self.assertAlmostEqual(observed["T", "R"], 0.000203583) self.assertAlmostEqual(observed["T", "S"], 0.002157980) self.assertAlmostEqual(observed["T", "T"], 0.042833876) self.assertAlmostEqual(observed["T", "V"], 0.000773616) self.assertAlmostEqual(observed["T", "W"], 0.000081433) self.assertAlmostEqual(observed["T", "Y"], 0.000040717) self.assertAlmostEqual(observed["V", "A"], 0.002442997) self.assertAlmostEqual(observed["V", "C"], 0.000081433) self.assertAlmostEqual(observed["V", "D"], 0.000162866) self.assertAlmostEqual(observed["V", "E"], 0.000122150) self.assertAlmostEqual(observed["V", "F"], 0.000407166) self.assertAlmostEqual(observed["V", "G"], 0.000692182) self.assertAlmostEqual(observed["V", "H"], 0.000040717) self.assertAlmostEqual(observed["V", "I"], 0.004438111) self.assertAlmostEqual(observed["V", "K"], 0.000081433) self.assertAlmostEqual(observed["V", "L"], 0.002361564) self.assertAlmostEqual(observed["V", "M"], 0.000570033) self.assertAlmostEqual(observed["V", "N"], 0.000040717) self.assertAlmostEqual(observed["V", "P"], 0.000162866) self.assertAlmostEqual(observed["V", "Q"], 0.000081433) self.assertAlmostEqual(observed["V", "R"], 0.000203583) self.assertAlmostEqual(observed["V", "S"], 0.000244300) self.assertAlmostEqual(observed["V", "T"], 0.000773616) self.assertAlmostEqual(observed["V", "V"], 0.050732899) self.assertAlmostEqual(observed["V", "W"], 0.000040717) self.assertAlmostEqual(observed["V", "Y"], 0.000040717) self.assertAlmostEqual(observed["W", "A"], 0.000081433) self.assertAlmostEqual(observed["W", "C"], 0.000081433) self.assertAlmostEqual(observed["W", "D"], 0.000040717) self.assertAlmostEqual(observed["W", "E"], 0.000040717) self.assertAlmostEqual(observed["W", "F"], 0.000040717) self.assertAlmostEqual(observed["W", "G"], 0.000244300) self.assertAlmostEqual(observed["W", "H"], 0.000040717) self.assertAlmostEqual(observed["W", "I"], 0.000040717) self.assertAlmostEqual(observed["W", "K"], 0.000040717) self.assertAlmostEqual(observed["W", "L"], 0.000162866) self.assertAlmostEqual(observed["W", "M"], 0.000040717) self.assertAlmostEqual(observed["W", "N"], 0.000040717) self.assertAlmostEqual(observed["W", "P"], 0.000040717) self.assertAlmostEqual(observed["W", "Q"], 0.000040717) self.assertAlmostEqual(observed["W", "R"], 0.000325733) self.assertAlmostEqual(observed["W", "S"], 0.000081433) self.assertAlmostEqual(observed["W", "T"], 0.000081433) self.assertAlmostEqual(observed["W", "V"], 0.000040717) self.assertAlmostEqual(observed["W", "W"], 0.013843648) self.assertAlmostEqual(observed["W", "Y"], 0.000040717) self.assertAlmostEqual(observed["Y", "A"], 0.000040717) self.assertAlmostEqual(observed["Y", "C"], 0.000407166) self.assertAlmostEqual(observed["Y", "D"], 0.000081433) self.assertAlmostEqual(observed["Y", "E"], 0.000040717) self.assertAlmostEqual(observed["Y", "F"], 0.001017915) self.assertAlmostEqual(observed["Y", "G"], 0.000040717) self.assertAlmostEqual(observed["Y", "H"], 0.000895765) self.assertAlmostEqual(observed["Y", "I"], 0.000040717) self.assertAlmostEqual(observed["Y", "K"], 0.000081433) self.assertAlmostEqual(observed["Y", "L"], 0.000081433) self.assertAlmostEqual(observed["Y", "M"], 0.000040717) self.assertAlmostEqual(observed["Y", "N"], 0.000081433) self.assertAlmostEqual(observed["Y", "P"], 0.000040717) self.assertAlmostEqual(observed["Y", "Q"], 0.000081433) self.assertAlmostEqual(observed["Y", "R"], 0.000040717) self.assertAlmostEqual(observed["Y", "S"], 0.000325733) self.assertAlmostEqual(observed["Y", "T"], 0.000040717) self.assertAlmostEqual(observed["Y", "V"], 0.000040717) self.assertAlmostEqual(observed["Y", "W"], 0.000040717) self.assertAlmostEqual(observed["Y", "Y"], 0.028664495) def test4_aminoacid_probabilities(self): observed = self.observed # calculate probabilities expected under a null model probabilities = numpy.sum(observed, 0) # Be sure to use numpy"s sum self.assertEqual(probabilities.shape, (20,)) self.assertAlmostEqual(probabilities["A"], 0.070358306) self.assertAlmostEqual(probabilities["C"], 0.024959283) self.assertAlmostEqual(probabilities["D"], 0.041205212) self.assertAlmostEqual(probabilities["E"], 0.059120521) self.assertAlmostEqual(probabilities["F"], 0.045806189) self.assertAlmostEqual(probabilities["G"], 0.057817590) self.assertAlmostEqual(probabilities["H"], 0.023208469) self.assertAlmostEqual(probabilities["I"], 0.055781759) self.assertAlmostEqual(probabilities["K"], 0.055048860) self.assertAlmostEqual(probabilities["L"], 0.117793160) self.assertAlmostEqual(probabilities["M"], 0.026628664) self.assertAlmostEqual(probabilities["N"], 0.036034202) self.assertAlmostEqual(probabilities["P"], 0.050773616) self.assertAlmostEqual(probabilities["Q"], 0.039413681) self.assertAlmostEqual(probabilities["R"], 0.051140065) self.assertAlmostEqual(probabilities["S"], 0.079071661) self.assertAlmostEqual(probabilities["T"], 0.054600977) self.assertAlmostEqual(probabilities["V"], 0.063721498) self.assertAlmostEqual(probabilities["W"], 0.015390879) self.assertAlmostEqual(probabilities["Y"], 0.032125407) TestScoringMatrices.probabilities = probabilities def test5_expected_probabilities(self): probabilities = self.probabilities expected = numpy.dot(probabilities[:, None], probabilities[None, :]) self.assertEqual(expected.alphabet, protein_alphabet) self.assertEqual(expected.shape, (20, 20)) self.assertAlmostEqual(expected["A", "A"], 0.004950291) self.assertAlmostEqual(expected["A", "C"], 0.001756093) self.assertAlmostEqual(expected["A", "D"], 0.002899129) self.assertAlmostEqual(expected["A", "E"], 0.004159620) self.assertAlmostEqual(expected["A", "F"], 0.003222846) self.assertAlmostEqual(expected["A", "G"], 0.004067948) self.assertAlmostEqual(expected["A", "H"], 0.001632909) self.assertAlmostEqual(expected["A", "I"], 0.003924710) self.assertAlmostEqual(expected["A", "K"], 0.003873145) self.assertAlmostEqual(expected["A", "L"], 0.008287727) self.assertAlmostEqual(expected["A", "M"], 0.001873548) self.assertAlmostEqual(expected["A", "N"], 0.002535305) self.assertAlmostEqual(expected["A", "P"], 0.003572346) self.assertAlmostEqual(expected["A", "Q"], 0.002773080) self.assertAlmostEqual(expected["A", "R"], 0.003598128) self.assertAlmostEqual(expected["A", "S"], 0.005563348) self.assertAlmostEqual(expected["A", "T"], 0.003841632) self.assertAlmostEqual(expected["A", "V"], 0.004483337) self.assertAlmostEqual(expected["A", "W"], 0.001082876) self.assertAlmostEqual(expected["A", "Y"], 0.002260289) self.assertAlmostEqual(expected["C", "A"], 0.001756093) self.assertAlmostEqual(expected["C", "C"], 0.000622966) self.assertAlmostEqual(expected["C", "D"], 0.001028453) self.assertAlmostEqual(expected["C", "E"], 0.001475606) self.assertAlmostEqual(expected["C", "F"], 0.001143290) self.assertAlmostEqual(expected["C", "G"], 0.001443086) self.assertAlmostEqual(expected["C", "H"], 0.000579267) self.assertAlmostEqual(expected["C", "I"], 0.001392273) self.assertAlmostEqual(expected["C", "K"], 0.001373980) self.assertAlmostEqual(expected["C", "L"], 0.002940033) self.assertAlmostEqual(expected["C", "M"], 0.000664632) self.assertAlmostEqual(expected["C", "N"], 0.000899388) self.assertAlmostEqual(expected["C", "P"], 0.001267273) self.assertAlmostEqual(expected["C", "Q"], 0.000983737) self.assertAlmostEqual(expected["C", "R"], 0.001276419) self.assertAlmostEqual(expected["C", "S"], 0.001973572) self.assertAlmostEqual(expected["C", "T"], 0.001362801) self.assertAlmostEqual(expected["C", "V"], 0.001590443) self.assertAlmostEqual(expected["C", "W"], 0.000384145) self.assertAlmostEqual(expected["C", "Y"], 0.000801827) self.assertAlmostEqual(expected["D", "A"], 0.002899129) self.assertAlmostEqual(expected["D", "C"], 0.001028453) self.assertAlmostEqual(expected["D", "D"], 0.001697869) self.assertAlmostEqual(expected["D", "E"], 0.002436074) self.assertAlmostEqual(expected["D", "F"], 0.001887454) self.assertAlmostEqual(expected["D", "G"], 0.002382386) self.assertAlmostEqual(expected["D", "H"], 0.000956310) self.assertAlmostEqual(expected["D", "I"], 0.002298499) self.assertAlmostEqual(expected["D", "K"], 0.002268300) self.assertAlmostEqual(expected["D", "L"], 0.004853692) self.assertAlmostEqual(expected["D", "M"], 0.001097240) self.assertAlmostEqual(expected["D", "N"], 0.001484797) self.assertAlmostEqual(expected["D", "P"], 0.002092138) self.assertAlmostEqual(expected["D", "Q"], 0.001624049) self.assertAlmostEqual(expected["D", "R"], 0.002107237) self.assertAlmostEqual(expected["D", "S"], 0.003258165) self.assertAlmostEqual(expected["D", "T"], 0.002249845) self.assertAlmostEqual(expected["D", "V"], 0.002625658) self.assertAlmostEqual(expected["D", "W"], 0.000634184) self.assertAlmostEqual(expected["D", "Y"], 0.001323734) self.assertAlmostEqual(expected["E", "A"], 0.004159620) self.assertAlmostEqual(expected["E", "C"], 0.001475606) self.assertAlmostEqual(expected["E", "D"], 0.002436074) self.assertAlmostEqual(expected["E", "E"], 0.003495236) self.assertAlmostEqual(expected["E", "F"], 0.002708086) self.assertAlmostEqual(expected["E", "G"], 0.003418206) self.assertAlmostEqual(expected["E", "H"], 0.001372097) self.assertAlmostEqual(expected["E", "I"], 0.003297847) self.assertAlmostEqual(expected["E", "K"], 0.003254517) self.assertAlmostEqual(expected["E", "L"], 0.006963993) self.assertAlmostEqual(expected["E", "M"], 0.001574301) self.assertAlmostEqual(expected["E", "N"], 0.002130361) self.assertAlmostEqual(expected["E", "P"], 0.003001763) self.assertAlmostEqual(expected["E", "Q"], 0.002330157) self.assertAlmostEqual(expected["E", "R"], 0.003023427) self.assertAlmostEqual(expected["E", "S"], 0.004674758) self.assertAlmostEqual(expected["E", "T"], 0.003228038) self.assertAlmostEqual(expected["E", "V"], 0.003767248) self.assertAlmostEqual(expected["E", "W"], 0.000909917) self.assertAlmostEqual(expected["E", "Y"], 0.001899271) self.assertAlmostEqual(expected["F", "A"], 0.003222846) self.assertAlmostEqual(expected["F", "C"], 0.001143290) self.assertAlmostEqual(expected["F", "D"], 0.001887454) self.assertAlmostEqual(expected["F", "E"], 0.002708086) self.assertAlmostEqual(expected["F", "F"], 0.002098207) self.assertAlmostEqual(expected["F", "G"], 0.002648403) self.assertAlmostEqual(expected["F", "H"], 0.001063092) self.assertAlmostEqual(expected["F", "I"], 0.002555150) self.assertAlmostEqual(expected["F", "K"], 0.002521578) self.assertAlmostEqual(expected["F", "L"], 0.005395656) self.assertAlmostEqual(expected["F", "M"], 0.001219758) self.assertAlmostEqual(expected["F", "N"], 0.001650589) self.assertAlmostEqual(expected["F", "P"], 0.002325746) self.assertAlmostEqual(expected["F", "Q"], 0.001805391) self.assertAlmostEqual(expected["F", "R"], 0.002342531) self.assertAlmostEqual(expected["F", "S"], 0.003621971) self.assertAlmostEqual(expected["F", "T"], 0.002501063) self.assertAlmostEqual(expected["F", "V"], 0.002918839) self.assertAlmostEqual(expected["F", "W"], 0.000704998) self.assertAlmostEqual(expected["F", "Y"], 0.001471542) self.assertAlmostEqual(expected["G", "A"], 0.004067948) self.assertAlmostEqual(expected["G", "C"], 0.001443086) self.assertAlmostEqual(expected["G", "D"], 0.002382386) self.assertAlmostEqual(expected["G", "E"], 0.003418206) self.assertAlmostEqual(expected["G", "F"], 0.002648403) self.assertAlmostEqual(expected["G", "G"], 0.003342874) self.assertAlmostEqual(expected["G", "H"], 0.001341858) self.assertAlmostEqual(expected["G", "I"], 0.003225167) self.assertAlmostEqual(expected["G", "K"], 0.003182792) self.assertAlmostEqual(expected["G", "L"], 0.006810517) self.assertAlmostEqual(expected["G", "M"], 0.001539605) self.assertAlmostEqual(expected["G", "N"], 0.002083411) self.assertAlmostEqual(expected["G", "P"], 0.002935608) self.assertAlmostEqual(expected["G", "Q"], 0.002278804) self.assertAlmostEqual(expected["G", "R"], 0.002956795) self.assertAlmostEqual(expected["G", "S"], 0.004571733) self.assertAlmostEqual(expected["G", "T"], 0.003156897) self.assertAlmostEqual(expected["G", "V"], 0.003684223) self.assertAlmostEqual(expected["G", "W"], 0.000889864) self.assertAlmostEqual(expected["G", "Y"], 0.001857414) self.assertAlmostEqual(expected["H", "A"], 0.001632909) self.assertAlmostEqual(expected["H", "C"], 0.000579267) self.assertAlmostEqual(expected["H", "D"], 0.000956310) self.assertAlmostEqual(expected["H", "E"], 0.001372097) self.assertAlmostEqual(expected["H", "F"], 0.001063092) self.assertAlmostEqual(expected["H", "G"], 0.001341858) self.assertAlmostEqual(expected["H", "H"], 0.000538633) self.assertAlmostEqual(expected["H", "I"], 0.001294609) self.assertAlmostEqual(expected["H", "K"], 0.001277600) self.assertAlmostEqual(expected["H", "L"], 0.002733799) self.assertAlmostEqual(expected["H", "M"], 0.000618011) self.assertAlmostEqual(expected["H", "N"], 0.000836299) self.assertAlmostEqual(expected["H", "P"], 0.001178378) self.assertAlmostEqual(expected["H", "Q"], 0.000914731) self.assertAlmostEqual(expected["H", "R"], 0.001186883) self.assertAlmostEqual(expected["H", "S"], 0.001835132) self.assertAlmostEqual(expected["H", "T"], 0.001267205) self.assertAlmostEqual(expected["H", "V"], 0.001478878) self.assertAlmostEqual(expected["H", "W"], 0.000357199) self.assertAlmostEqual(expected["H", "Y"], 0.000745582) self.assertAlmostEqual(expected["I", "A"], 0.003924710) self.assertAlmostEqual(expected["I", "C"], 0.001392273) self.assertAlmostEqual(expected["I", "D"], 0.002298499) self.assertAlmostEqual(expected["I", "E"], 0.003297847) self.assertAlmostEqual(expected["I", "F"], 0.002555150) self.assertAlmostEqual(expected["I", "G"], 0.003225167) self.assertAlmostEqual(expected["I", "H"], 0.001294609) self.assertAlmostEqual(expected["I", "I"], 0.003111605) self.assertAlmostEqual(expected["I", "K"], 0.003070722) self.assertAlmostEqual(expected["I", "L"], 0.006570710) self.assertAlmostEqual(expected["I", "M"], 0.001485394) self.assertAlmostEqual(expected["I", "N"], 0.002010051) self.assertAlmostEqual(expected["I", "P"], 0.002832242) self.assertAlmostEqual(expected["I", "Q"], 0.002198564) self.assertAlmostEqual(expected["I", "R"], 0.002852683) self.assertAlmostEqual(expected["I", "S"], 0.004410756) self.assertAlmostEqual(expected["I", "T"], 0.003045739) self.assertAlmostEqual(expected["I", "V"], 0.003554497) self.assertAlmostEqual(expected["I", "W"], 0.000858530) self.assertAlmostEqual(expected["I", "Y"], 0.001792012) self.assertAlmostEqual(expected["K", "A"], 0.003873145) self.assertAlmostEqual(expected["K", "C"], 0.001373980) self.assertAlmostEqual(expected["K", "D"], 0.002268300) self.assertAlmostEqual(expected["K", "E"], 0.003254517) self.assertAlmostEqual(expected["K", "F"], 0.002521578) self.assertAlmostEqual(expected["K", "G"], 0.003182792) self.assertAlmostEqual(expected["K", "H"], 0.001277600) self.assertAlmostEqual(expected["K", "I"], 0.003070722) self.assertAlmostEqual(expected["K", "K"], 0.003030377) self.assertAlmostEqual(expected["K", "L"], 0.006484379) self.assertAlmostEqual(expected["K", "M"], 0.001465878) self.assertAlmostEqual(expected["K", "N"], 0.001983642) self.assertAlmostEqual(expected["K", "P"], 0.002795030) self.assertAlmostEqual(expected["K", "Q"], 0.002169678) self.assertAlmostEqual(expected["K", "R"], 0.002815202) self.assertAlmostEqual(expected["K", "S"], 0.004352805) self.assertAlmostEqual(expected["K", "T"], 0.003005722) self.assertAlmostEqual(expected["K", "V"], 0.003507796) self.assertAlmostEqual(expected["K", "W"], 0.000847250) self.assertAlmostEqual(expected["K", "Y"], 0.001768467) self.assertAlmostEqual(expected["L", "A"], 0.008287727) self.assertAlmostEqual(expected["L", "C"], 0.002940033) self.assertAlmostEqual(expected["L", "D"], 0.004853692) self.assertAlmostEqual(expected["L", "E"], 0.006963993) self.assertAlmostEqual(expected["L", "F"], 0.005395656) self.assertAlmostEqual(expected["L", "G"], 0.006810517) self.assertAlmostEqual(expected["L", "H"], 0.002733799) self.assertAlmostEqual(expected["L", "I"], 0.006570710) self.assertAlmostEqual(expected["L", "K"], 0.006484379) self.assertAlmostEqual(expected["L", "L"], 0.013875228) self.assertAlmostEqual(expected["L", "M"], 0.003136675) self.assertAlmostEqual(expected["L", "N"], 0.004244583) self.assertAlmostEqual(expected["L", "P"], 0.005980785) self.assertAlmostEqual(expected["L", "Q"], 0.004642662) self.assertAlmostEqual(expected["L", "R"], 0.006023950) self.assertAlmostEqual(expected["L", "S"], 0.009314101) self.assertAlmostEqual(expected["L", "T"], 0.006431622) self.assertAlmostEqual(expected["L", "V"], 0.007505957) self.assertAlmostEqual(expected["L", "W"], 0.001812940) self.assertAlmostEqual(expected["L", "Y"], 0.003784153) self.assertAlmostEqual(expected["M", "A"], 0.001873548) self.assertAlmostEqual(expected["M", "C"], 0.000664632) self.assertAlmostEqual(expected["M", "D"], 0.001097240) self.assertAlmostEqual(expected["M", "E"], 0.001574301) self.assertAlmostEqual(expected["M", "F"], 0.001219758) self.assertAlmostEqual(expected["M", "G"], 0.001539605) self.assertAlmostEqual(expected["M", "H"], 0.000618011) self.assertAlmostEqual(expected["M", "I"], 0.001485394) self.assertAlmostEqual(expected["M", "K"], 0.001465878) self.assertAlmostEqual(expected["M", "L"], 0.003136675) self.assertAlmostEqual(expected["M", "M"], 0.000709086) self.assertAlmostEqual(expected["M", "N"], 0.000959543) self.assertAlmostEqual(expected["M", "P"], 0.001352034) self.assertAlmostEqual(expected["M", "Q"], 0.001049534) self.assertAlmostEqual(expected["M", "R"], 0.001361792) self.assertAlmostEqual(expected["M", "S"], 0.002105573) self.assertAlmostEqual(expected["M", "T"], 0.001453951) self.assertAlmostEqual(expected["M", "V"], 0.001696818) self.assertAlmostEqual(expected["M", "W"], 0.000409839) self.assertAlmostEqual(expected["M", "Y"], 0.000855457) self.assertAlmostEqual(expected["N", "A"], 0.002535305) self.assertAlmostEqual(expected["N", "C"], 0.000899388) self.assertAlmostEqual(expected["N", "D"], 0.001484797) self.assertAlmostEqual(expected["N", "E"], 0.002130361) self.assertAlmostEqual(expected["N", "F"], 0.001650589) self.assertAlmostEqual(expected["N", "G"], 0.002083411) self.assertAlmostEqual(expected["N", "H"], 0.000836299) self.assertAlmostEqual(expected["N", "I"], 0.002010051) self.assertAlmostEqual(expected["N", "K"], 0.001983642) self.assertAlmostEqual(expected["N", "L"], 0.004244583) self.assertAlmostEqual(expected["N", "M"], 0.000959543) self.assertAlmostEqual(expected["N", "N"], 0.001298464) self.assertAlmostEqual(expected["N", "P"], 0.001829587) self.assertAlmostEqual(expected["N", "Q"], 0.001420241) self.assertAlmostEqual(expected["N", "R"], 0.001842791) self.assertAlmostEqual(expected["N", "S"], 0.002849284) self.assertAlmostEqual(expected["N", "T"], 0.001967503) self.assertAlmostEqual(expected["N", "V"], 0.002296153) self.assertAlmostEqual(expected["N", "W"], 0.000554598) self.assertAlmostEqual(expected["N", "Y"], 0.001157613) self.assertAlmostEqual(expected["P", "A"], 0.003572346) self.assertAlmostEqual(expected["P", "C"], 0.001267273) self.assertAlmostEqual(expected["P", "D"], 0.002092138) self.assertAlmostEqual(expected["P", "E"], 0.003001763) self.assertAlmostEqual(expected["P", "F"], 0.002325746) self.assertAlmostEqual(expected["P", "G"], 0.002935608) self.assertAlmostEqual(expected["P", "H"], 0.001178378) self.assertAlmostEqual(expected["P", "I"], 0.002832242) self.assertAlmostEqual(expected["P", "K"], 0.002795030) self.assertAlmostEqual(expected["P", "L"], 0.005980785) self.assertAlmostEqual(expected["P", "M"], 0.001352034) self.assertAlmostEqual(expected["P", "N"], 0.001829587) self.assertAlmostEqual(expected["P", "P"], 0.002577960) self.assertAlmostEqual(expected["P", "Q"], 0.002001175) self.assertAlmostEqual(expected["P", "R"], 0.002596566) self.assertAlmostEqual(expected["P", "S"], 0.004014754) self.assertAlmostEqual(expected["P", "T"], 0.002772289) self.assertAlmostEqual(expected["P", "V"], 0.003235371) self.assertAlmostEqual(expected["P", "W"], 0.000781451) self.assertAlmostEqual(expected["P", "Y"], 0.001631123) self.assertAlmostEqual(expected["Q", "A"], 0.002773080) self.assertAlmostEqual(expected["Q", "C"], 0.000983737) self.assertAlmostEqual(expected["Q", "D"], 0.001624049) self.assertAlmostEqual(expected["Q", "E"], 0.002330157) self.assertAlmostEqual(expected["Q", "F"], 0.001805391) self.assertAlmostEqual(expected["Q", "G"], 0.002278804) self.assertAlmostEqual(expected["Q", "H"], 0.000914731) self.assertAlmostEqual(expected["Q", "I"], 0.002198564) self.assertAlmostEqual(expected["Q", "K"], 0.002169678) self.assertAlmostEqual(expected["Q", "L"], 0.004642662) self.assertAlmostEqual(expected["Q", "M"], 0.001049534) self.assertAlmostEqual(expected["Q", "N"], 0.001420241) self.assertAlmostEqual(expected["Q", "P"], 0.002001175) self.assertAlmostEqual(expected["Q", "Q"], 0.001553438) self.assertAlmostEqual(expected["Q", "R"], 0.002015618) self.assertAlmostEqual(expected["Q", "S"], 0.003116505) self.assertAlmostEqual(expected["Q", "T"], 0.002152025) self.assertAlmostEqual(expected["Q", "V"], 0.002511499) self.assertAlmostEqual(expected["Q", "W"], 0.000606611) self.assertAlmostEqual(expected["Q", "Y"], 0.001266181) self.assertAlmostEqual(expected["R", "A"], 0.003598128) self.assertAlmostEqual(expected["R", "C"], 0.001276419) self.assertAlmostEqual(expected["R", "D"], 0.002107237) self.assertAlmostEqual(expected["R", "E"], 0.003023427) self.assertAlmostEqual(expected["R", "F"], 0.002342531) self.assertAlmostEqual(expected["R", "G"], 0.002956795) self.assertAlmostEqual(expected["R", "H"], 0.001186883) self.assertAlmostEqual(expected["R", "I"], 0.002852683) self.assertAlmostEqual(expected["R", "K"], 0.002815202) self.assertAlmostEqual(expected["R", "L"], 0.006023950) self.assertAlmostEqual(expected["R", "M"], 0.001361792) self.assertAlmostEqual(expected["R", "N"], 0.001842791) self.assertAlmostEqual(expected["R", "P"], 0.002596566) self.assertAlmostEqual(expected["R", "Q"], 0.002015618) self.assertAlmostEqual(expected["R", "R"], 0.002615306) self.assertAlmostEqual(expected["R", "S"], 0.004043730) self.assertAlmostEqual(expected["R", "T"], 0.002792298) self.assertAlmostEqual(expected["R", "V"], 0.003258722) self.assertAlmostEqual(expected["R", "W"], 0.000787091) self.assertAlmostEqual(expected["R", "Y"], 0.001642895) self.assertAlmostEqual(expected["S", "A"], 0.005563348) self.assertAlmostEqual(expected["S", "C"], 0.001973572) self.assertAlmostEqual(expected["S", "D"], 0.003258165) self.assertAlmostEqual(expected["S", "E"], 0.004674758) self.assertAlmostEqual(expected["S", "F"], 0.003621971) self.assertAlmostEqual(expected["S", "G"], 0.004571733) self.assertAlmostEqual(expected["S", "H"], 0.001835132) self.assertAlmostEqual(expected["S", "I"], 0.004410756) self.assertAlmostEqual(expected["S", "K"], 0.004352805) self.assertAlmostEqual(expected["S", "L"], 0.009314101) self.assertAlmostEqual(expected["S", "M"], 0.002105573) self.assertAlmostEqual(expected["S", "N"], 0.002849284) self.assertAlmostEqual(expected["S", "P"], 0.004014754) self.assertAlmostEqual(expected["S", "Q"], 0.003116505) self.assertAlmostEqual(expected["S", "R"], 0.004043730) self.assertAlmostEqual(expected["S", "S"], 0.006252328) self.assertAlmostEqual(expected["S", "T"], 0.004317390) self.assertAlmostEqual(expected["S", "V"], 0.005038565) self.assertAlmostEqual(expected["S", "W"], 0.001216982) self.assertAlmostEqual(expected["S", "Y"], 0.002540209) self.assertAlmostEqual(expected["T", "A"], 0.003841632) self.assertAlmostEqual(expected["T", "C"], 0.001362801) self.assertAlmostEqual(expected["T", "D"], 0.002249845) self.assertAlmostEqual(expected["T", "E"], 0.003228038) self.assertAlmostEqual(expected["T", "F"], 0.002501063) self.assertAlmostEqual(expected["T", "G"], 0.003156897) self.assertAlmostEqual(expected["T", "H"], 0.001267205) self.assertAlmostEqual(expected["T", "I"], 0.003045739) self.assertAlmostEqual(expected["T", "K"], 0.003005722) self.assertAlmostEqual(expected["T", "L"], 0.006431622) self.assertAlmostEqual(expected["T", "M"], 0.001453951) self.assertAlmostEqual(expected["T", "N"], 0.001967503) self.assertAlmostEqual(expected["T", "P"], 0.002772289) self.assertAlmostEqual(expected["T", "Q"], 0.002152025) self.assertAlmostEqual(expected["T", "R"], 0.002792298) self.assertAlmostEqual(expected["T", "S"], 0.004317390) self.assertAlmostEqual(expected["T", "T"], 0.002981267) self.assertAlmostEqual(expected["T", "V"], 0.003479256) self.assertAlmostEqual(expected["T", "W"], 0.000840357) self.assertAlmostEqual(expected["T", "Y"], 0.001754079) self.assertAlmostEqual(expected["V", "A"], 0.004483337) self.assertAlmostEqual(expected["V", "C"], 0.001590443) self.assertAlmostEqual(expected["V", "D"], 0.002625658) self.assertAlmostEqual(expected["V", "E"], 0.003767248) self.assertAlmostEqual(expected["V", "F"], 0.002918839) self.assertAlmostEqual(expected["V", "G"], 0.003684223) self.assertAlmostEqual(expected["V", "H"], 0.001478878) self.assertAlmostEqual(expected["V", "I"], 0.003554497) self.assertAlmostEqual(expected["V", "K"], 0.003507796) self.assertAlmostEqual(expected["V", "L"], 0.007505957) self.assertAlmostEqual(expected["V", "M"], 0.001696818) self.assertAlmostEqual(expected["V", "N"], 0.002296153) self.assertAlmostEqual(expected["V", "P"], 0.003235371) self.assertAlmostEqual(expected["V", "Q"], 0.002511499) self.assertAlmostEqual(expected["V", "R"], 0.003258722) self.assertAlmostEqual(expected["V", "S"], 0.005038565) self.assertAlmostEqual(expected["V", "T"], 0.003479256) self.assertAlmostEqual(expected["V", "V"], 0.004060429) self.assertAlmostEqual(expected["V", "W"], 0.000980730) self.assertAlmostEqual(expected["V", "Y"], 0.002047079) self.assertAlmostEqual(expected["W", "A"], 0.001082876) self.assertAlmostEqual(expected["W", "C"], 0.000384145) self.assertAlmostEqual(expected["W", "D"], 0.000634184) self.assertAlmostEqual(expected["W", "E"], 0.000909917) self.assertAlmostEqual(expected["W", "F"], 0.000704998) self.assertAlmostEqual(expected["W", "G"], 0.000889864) self.assertAlmostEqual(expected["W", "H"], 0.000357199) self.assertAlmostEqual(expected["W", "I"], 0.000858530) self.assertAlmostEqual(expected["W", "K"], 0.000847250) self.assertAlmostEqual(expected["W", "L"], 0.001812940) self.assertAlmostEqual(expected["W", "M"], 0.000409839) self.assertAlmostEqual(expected["W", "N"], 0.000554598) self.assertAlmostEqual(expected["W", "P"], 0.000781451) self.assertAlmostEqual(expected["W", "Q"], 0.000606611) self.assertAlmostEqual(expected["W", "R"], 0.000787091) self.assertAlmostEqual(expected["W", "S"], 0.001216982) self.assertAlmostEqual(expected["W", "T"], 0.000840357) self.assertAlmostEqual(expected["W", "V"], 0.000980730) self.assertAlmostEqual(expected["W", "W"], 0.000236879) self.assertAlmostEqual(expected["W", "Y"], 0.000494438) self.assertAlmostEqual(expected["Y", "A"], 0.002260289) self.assertAlmostEqual(expected["Y", "C"], 0.000801827) self.assertAlmostEqual(expected["Y", "D"], 0.001323734) self.assertAlmostEqual(expected["Y", "E"], 0.001899271) self.assertAlmostEqual(expected["Y", "F"], 0.001471542) self.assertAlmostEqual(expected["Y", "G"], 0.001857414) self.assertAlmostEqual(expected["Y", "H"], 0.000745582) self.assertAlmostEqual(expected["Y", "I"], 0.001792012) self.assertAlmostEqual(expected["Y", "K"], 0.001768467) self.assertAlmostEqual(expected["Y", "L"], 0.003784153) self.assertAlmostEqual(expected["Y", "M"], 0.000855457) self.assertAlmostEqual(expected["Y", "N"], 0.001157613) self.assertAlmostEqual(expected["Y", "P"], 0.001631123) self.assertAlmostEqual(expected["Y", "Q"], 0.001266181) self.assertAlmostEqual(expected["Y", "R"], 0.001642895) self.assertAlmostEqual(expected["Y", "S"], 0.002540209) self.assertAlmostEqual(expected["Y", "T"], 0.001754079) self.assertAlmostEqual(expected["Y", "V"], 0.002047079) self.assertAlmostEqual(expected["Y", "W"], 0.000494438) self.assertAlmostEqual(expected["Y", "Y"], 0.001032042) TestScoringMatrices.expected = expected def test6_scores(self): observed = self.observed expected = self.expected # calculate the log-ratio scores = numpy.log2(observed / expected) self.assertEqual(scores.alphabet, protein_alphabet) self.assertEqual(scores.shape, (20, 20)) self.assertAlmostEqual(scores["A", "A"], 3.537772309) self.assertAlmostEqual(scores["A", "C"], -5.430607826) self.assertAlmostEqual(scores["A", "D"], -2.831930042) self.assertAlmostEqual(scores["A", "E"], -2.352762205) self.assertAlmostEqual(scores["A", "F"], -6.306573848) self.assertAlmostEqual(scores["A", "G"], -1.942100058) self.assertAlmostEqual(scores["A", "H"], -4.325682671) self.assertAlmostEqual(scores["A", "I"], -3.420899738) self.assertAlmostEqual(scores["A", "K"], -4.571743998) self.assertAlmostEqual(scores["A", "L"], -4.084252669) self.assertAlmostEqual(scores["A", "M"], -3.202083293) self.assertAlmostEqual(scores["A", "N"], -4.375435706) self.assertAlmostEqual(scores["A", "P"], -2.207182798) self.assertAlmostEqual(scores["A", "Q"], -6.089727799) self.assertAlmostEqual(scores["A", "R"], -4.465485311) self.assertAlmostEqual(scores["A", "S"], -1.286837125) self.assertAlmostEqual(scores["A", "T"], -0.238029989) self.assertAlmostEqual(scores["A", "V"], -0.875920908) self.assertAlmostEqual(scores["A", "W"], -3.733106986) self.assertAlmostEqual(scores["A", "Y"], -5.794746052) self.assertAlmostEqual(scores["C", "A"], -5.430607826) self.assertAlmostEqual(scores["C", "C"], 5.188657725) self.assertAlmostEqual(scores["C", "D"], -4.658713898) self.assertAlmostEqual(scores["C", "E"], -5.179546061) self.assertAlmostEqual(scores["C", "F"], -2.489501515) self.assertAlmostEqual(scores["C", "G"], -3.147395538) self.assertAlmostEqual(scores["C", "H"], -3.830538432) self.assertAlmostEqual(scores["C", "I"], -5.095680501) self.assertAlmostEqual(scores["C", "K"], -5.076599760) self.assertAlmostEqual(scores["C", "L"], -5.174070931) self.assertAlmostEqual(scores["C", "M"], -4.028867149) self.assertAlmostEqual(scores["C", "N"], -4.465253968) self.assertAlmostEqual(scores["C", "P"], -3.959966073) self.assertAlmostEqual(scores["C", "Q"], -4.594583561) self.assertAlmostEqual(scores["C", "R"], -1.800416071) self.assertAlmostEqual(scores["C", "S"], -2.429122807) self.assertAlmostEqual(scores["C", "T"], -5.064813845) self.assertAlmostEqual(scores["C", "V"], -4.287667265) self.assertAlmostEqual(scores["C", "W"], -2.237962748) self.assertAlmostEqual(scores["C", "Y"], -0.977673719) self.assertAlmostEqual(scores["D", "A"], -2.831930042) self.assertAlmostEqual(scores["D", "C"], -4.658713898) self.assertAlmostEqual(scores["D", "D"], 4.356128050) self.assertAlmostEqual(scores["D", "E"], -0.121436659) self.assertAlmostEqual(scores["D", "F"], -5.534679921) self.assertAlmostEqual(scores["D", "G"], -1.700720847) self.assertAlmostEqual(scores["D", "H"], -2.553788743) self.assertAlmostEqual(scores["D", "I"], -5.818930812) self.assertAlmostEqual(scores["D", "K"], -4.799850071) self.assertAlmostEqual(scores["D", "L"], -5.897321242) self.assertAlmostEqual(scores["D", "M"], -4.752117460) self.assertAlmostEqual(scores["D", "N"], 0.133423815) self.assertAlmostEqual(scores["D", "P"], -5.683216384) self.assertAlmostEqual(scores["D", "Q"], -5.317833872) self.assertAlmostEqual(scores["D", "R"], -4.108628883) self.assertAlmostEqual(scores["D", "S"], -3.737335619) self.assertAlmostEqual(scores["D", "T"], -3.466136061) self.assertAlmostEqual(scores["D", "V"], -4.010917576) self.assertAlmostEqual(scores["D", "W"], -3.961213059) self.assertAlmostEqual(scores["D", "Y"], -4.022852124) self.assertAlmostEqual(scores["E", "A"], -2.352762205) self.assertAlmostEqual(scores["E", "C"], -5.179546061) self.assertAlmostEqual(scores["E", "D"], -0.121436659) self.assertAlmostEqual(scores["E", "E"], 3.873287671) self.assertAlmostEqual(scores["E", "F"], -6.055512084) self.assertAlmostEqual(scores["E", "G"], -1.347083893) self.assertAlmostEqual(scores["E", "H"], -3.074620907) self.assertAlmostEqual(scores["E", "I"], -4.754800475) self.assertAlmostEqual(scores["E", "K"], -1.462701239) self.assertAlmostEqual(scores["E", "L"], -6.418153406) self.assertAlmostEqual(scores["E", "M"], -5.272949623) self.assertAlmostEqual(scores["E", "N"], -4.709336443) self.assertAlmostEqual(scores["E", "P"], -6.204048548) self.assertAlmostEqual(scores["E", "Q"], -1.379234416) self.assertAlmostEqual(scores["E", "R"], -3.407068625) self.assertAlmostEqual(scores["E", "S"], -4.258167782) self.assertAlmostEqual(scores["E", "T"], -5.308896320) self.assertAlmostEqual(scores["E", "V"], -4.946787239) self.assertAlmostEqual(scores["E", "W"], -4.482045222) self.assertAlmostEqual(scores["E", "Y"], -5.543684288) self.assertAlmostEqual(scores["F", "A"], -6.306573848) self.assertAlmostEqual(scores["F", "C"], -2.489501515) self.assertAlmostEqual(scores["F", "D"], -5.534679921) self.assertAlmostEqual(scores["F", "E"], -6.055512084) self.assertAlmostEqual(scores["F", "F"], 4.269706410) self.assertAlmostEqual(scores["F", "G"], -6.023361560) self.assertAlmostEqual(scores["F", "H"], -3.706504455) self.assertAlmostEqual(scores["F", "I"], -3.386684023) self.assertAlmostEqual(scores["F", "K"], -5.952565782) self.assertAlmostEqual(scores["F", "L"], -1.349597236) self.assertAlmostEqual(scores["F", "M"], -3.904833171) self.assertAlmostEqual(scores["F", "N"], -4.341219991) self.assertAlmostEqual(scores["F", "P"], -5.835932096) self.assertAlmostEqual(scores["F", "Q"], -5.470549583) self.assertAlmostEqual(scores["F", "R"], -5.846307095) self.assertAlmostEqual(scores["F", "S"], -2.568123236) self.assertAlmostEqual(scores["F", "T"], -4.355817367) self.assertAlmostEqual(scores["F", "V"], -2.841705193) self.assertAlmostEqual(scores["F", "W"], -4.113928770) self.assertAlmostEqual(scores["F", "Y"], -0.531711646) self.assertAlmostEqual(scores["G", "A"], -1.942100058) self.assertAlmostEqual(scores["G", "C"], -3.147395538) self.assertAlmostEqual(scores["G", "D"], -1.700720847) self.assertAlmostEqual(scores["G", "E"], -1.347083893) self.assertAlmostEqual(scores["G", "F"], -6.023361560) self.assertAlmostEqual(scores["G", "G"], 3.898060354) self.assertAlmostEqual(scores["G", "H"], -4.042470383) self.assertAlmostEqual(scores["G", "I"], -6.307612452) self.assertAlmostEqual(scores["G", "K"], -4.703569210) self.assertAlmostEqual(scores["G", "L"], -5.801040381) self.assertAlmostEqual(scores["G", "M"], -3.655836599) self.assertAlmostEqual(scores["G", "N"], -2.869830997) self.assertAlmostEqual(scores["G", "P"], -6.171898024) self.assertAlmostEqual(scores["G", "Q"], -5.806515511) self.assertAlmostEqual(scores["G", "R"], -1.481833305) self.assertAlmostEqual(scores["G", "S"], -1.489051665) self.assertAlmostEqual(scores["G", "T"], -4.691783295) self.assertAlmostEqual(scores["G", "V"], -2.412136375) self.assertAlmostEqual(scores["G", "W"], -1.864932198) self.assertAlmostEqual(scores["G", "Y"], -5.511533764) self.assertAlmostEqual(scores["H", "A"], -4.325682671) self.assertAlmostEqual(scores["H", "C"], -3.830538432) self.assertAlmostEqual(scores["H", "D"], -2.553788743) self.assertAlmostEqual(scores["H", "E"], -3.074620907) self.assertAlmostEqual(scores["H", "F"], -3.706504455) self.assertAlmostEqual(scores["H", "G"], -4.042470383) self.assertAlmostEqual(scores["H", "H"], 5.100935209) self.assertAlmostEqual(scores["H", "I"], -4.990755347) self.assertAlmostEqual(scores["H", "K"], -3.386712104) self.assertAlmostEqual(scores["H", "L"], -5.069145777) self.assertAlmostEqual(scores["H", "M"], -3.923941994) self.assertAlmostEqual(scores["H", "N"], -0.900897195) self.assertAlmostEqual(scores["H", "P"], -2.047685997) self.assertAlmostEqual(scores["H", "Q"], -0.167730311) self.assertAlmostEqual(scores["H", "R"], -0.164976200) self.assertAlmostEqual(scores["H", "S"], -3.172194559) self.assertAlmostEqual(scores["H", "T"], -4.959888691) self.assertAlmostEqual(scores["H", "V"], -5.182742111) self.assertAlmostEqual(scores["H", "W"], -3.133037593) self.assertAlmostEqual(scores["H", "Y"], 0.264754960) self.assertAlmostEqual(scores["I", "A"], -3.420899738) self.assertAlmostEqual(scores["I", "C"], -5.095680501) self.assertAlmostEqual(scores["I", "D"], -5.818930812) self.assertAlmostEqual(scores["I", "E"], -4.754800475) self.assertAlmostEqual(scores["I", "F"], -3.386684023) self.assertAlmostEqual(scores["I", "G"], -6.307612452) self.assertAlmostEqual(scores["I", "H"], -4.990755347) self.assertAlmostEqual(scores["I", "I"], 3.868223896) self.assertAlmostEqual(scores["I", "K"], -4.651854173) self.assertAlmostEqual(scores["I", "L"], -1.908023091) self.assertAlmostEqual(scores["I", "M"], -0.545227873) self.assertAlmostEqual(scores["I", "N"], -3.303542788) self.assertAlmostEqual(scores["I", "P"], -6.120182987) self.assertAlmostEqual(scores["I", "Q"], -5.754800475) self.assertAlmostEqual(scores["I", "R"], -6.130557986) self.assertAlmostEqual(scores["I", "S"], -4.174302222) self.assertAlmostEqual(scores["I", "T"], -1.055105758) self.assertAlmostEqual(scores["I", "V"], 0.320300145) self.assertAlmostEqual(scores["I", "W"], -4.398179662) self.assertAlmostEqual(scores["I", "Y"], -5.459818728) self.assertAlmostEqual(scores["K", "A"], -4.571743998) self.assertAlmostEqual(scores["K", "C"], -5.076599760) self.assertAlmostEqual(scores["K", "D"], -4.799850071) self.assertAlmostEqual(scores["K", "E"], -1.462701239) self.assertAlmostEqual(scores["K", "F"], -5.952565782) self.assertAlmostEqual(scores["K", "G"], -4.703569210) self.assertAlmostEqual(scores["K", "H"], -3.386712104) self.assertAlmostEqual(scores["K", "I"], -4.651854173) self.assertAlmostEqual(scores["K", "K"], 3.944655396) self.assertAlmostEqual(scores["K", "L"], -7.315207104) self.assertAlmostEqual(scores["K", "M"], -2.848075227) self.assertAlmostEqual(scores["K", "N"], -1.358462628) self.assertAlmostEqual(scores["K", "P"], -6.101102246) self.assertAlmostEqual(scores["K", "Q"], -1.035280015) self.assertAlmostEqual(scores["K", "R"], 0.314787510) self.assertAlmostEqual(scores["K", "S"], -4.740183981) self.assertAlmostEqual(scores["K", "T"], -2.505510300) self.assertAlmostEqual(scores["K", "V"], -5.428803438) self.assertAlmostEqual(scores["K", "W"], -4.379098920) self.assertAlmostEqual(scores["K", "Y"], -4.440737986) self.assertAlmostEqual(scores["L", "A"], -4.084252669) self.assertAlmostEqual(scores["L", "C"], -5.174070931) self.assertAlmostEqual(scores["L", "D"], -5.897321242) self.assertAlmostEqual(scores["L", "E"], -6.418153406) self.assertAlmostEqual(scores["L", "F"], -1.349597236) self.assertAlmostEqual(scores["L", "G"], -5.801040381) self.assertAlmostEqual(scores["L", "H"], -5.069145777) self.assertAlmostEqual(scores["L", "I"], -1.908023091) self.assertAlmostEqual(scores["L", "K"], -7.315207104) self.assertAlmostEqual(scores["L", "L"], 2.931617632) self.assertAlmostEqual(scores["L", "M"], -1.058021128) self.assertAlmostEqual(scores["L", "N"], -5.118898812) self.assertAlmostEqual(scores["L", "P"], -2.154179298) self.assertAlmostEqual(scores["L", "Q"], -3.663265904) self.assertAlmostEqual(scores["L", "R"], -4.208948417) self.assertAlmostEqual(scores["L", "S"], -4.252692652) self.assertAlmostEqual(scores["L", "T"], -4.303421190) self.assertAlmostEqual(scores["L", "V"], -1.668293614) self.assertAlmostEqual(scores["L", "W"], -3.476570092) self.assertAlmostEqual(scores["L", "Y"], -5.538209158) self.assertAlmostEqual(scores["M", "A"], -3.202083293) self.assertAlmostEqual(scores["M", "C"], -4.028867149) self.assertAlmostEqual(scores["M", "D"], -4.752117460) self.assertAlmostEqual(scores["M", "E"], -5.272949623) self.assertAlmostEqual(scores["M", "F"], -3.904833171) self.assertAlmostEqual(scores["M", "G"], -3.655836599) self.assertAlmostEqual(scores["M", "H"], -3.923941994) self.assertAlmostEqual(scores["M", "I"], -0.545227873) self.assertAlmostEqual(scores["M", "K"], -2.848075227) self.assertAlmostEqual(scores["M", "L"], -1.058021128) self.assertAlmostEqual(scores["M", "M"], 4.916648279) self.assertAlmostEqual(scores["M", "N"], -4.558657530) self.assertAlmostEqual(scores["M", "P"], -5.053369635) self.assertAlmostEqual(scores["M", "Q"], -4.687987123) self.assertAlmostEqual(scores["M", "R"], -3.478782133) self.assertAlmostEqual(scores["M", "S"], -4.692451371) self.assertAlmostEqual(scores["M", "T"], -0.634655451) self.assertAlmostEqual(scores["M", "V"], -1.573715905) self.assertAlmostEqual(scores["M", "W"], -3.331366309) self.assertAlmostEqual(scores["M", "Y"], -4.393005375) self.assertAlmostEqual(scores["N", "A"], -4.375435706) self.assertAlmostEqual(scores["N", "C"], -4.465253968) self.assertAlmostEqual(scores["N", "D"], 0.133423815) self.assertAlmostEqual(scores["N", "E"], -4.709336443) self.assertAlmostEqual(scores["N", "F"], -4.341219991) self.assertAlmostEqual(scores["N", "G"], -2.869830997) self.assertAlmostEqual(scores["N", "H"], -0.900897195) self.assertAlmostEqual(scores["N", "I"], -3.303542788) self.assertAlmostEqual(scores["N", "K"], -1.358462628) self.assertAlmostEqual(scores["N", "L"], -5.118898812) self.assertAlmostEqual(scores["N", "M"], -4.558657530) self.assertAlmostEqual(scores["N", "N"], 4.496808747) self.assertAlmostEqual(scores["N", "P"], -5.489756455) self.assertAlmostEqual(scores["N", "Q"], -2.802445847) self.assertAlmostEqual(scores["N", "R"], -3.178203359) self.assertAlmostEqual(scores["N", "S"], -0.806910095) self.assertAlmostEqual(scores["N", "T"], -1.594604227) self.assertAlmostEqual(scores["N", "V"], -5.817457647) self.assertAlmostEqual(scores["N", "W"], -3.767753129) self.assertAlmostEqual(scores["N", "Y"], -3.829392195) self.assertAlmostEqual(scores["P", "A"], -2.207182798) self.assertAlmostEqual(scores["P", "C"], -3.959966073) self.assertAlmostEqual(scores["P", "D"], -5.683216384) self.assertAlmostEqual(scores["P", "E"], -6.204048548) self.assertAlmostEqual(scores["P", "F"], -5.835932096) self.assertAlmostEqual(scores["P", "G"], -6.171898024) self.assertAlmostEqual(scores["P", "H"], -2.047685997) self.assertAlmostEqual(scores["P", "I"], -6.120182987) self.assertAlmostEqual(scores["P", "K"], -6.101102246) self.assertAlmostEqual(scores["P", "L"], -2.154179298) self.assertAlmostEqual(scores["P", "M"], -5.053369635) self.assertAlmostEqual(scores["P", "N"], -5.489756455) self.assertAlmostEqual(scores["P", "P"], 4.121439949) self.assertAlmostEqual(scores["P", "Q"], -3.619086047) self.assertAlmostEqual(scores["P", "R"], -3.187488636) self.assertAlmostEqual(scores["P", "S"], -1.197285540) self.assertAlmostEqual(scores["P", "T"], -2.089316331) self.assertAlmostEqual(scores["P", "V"], -4.312169751) self.assertAlmostEqual(scores["P", "W"], -4.262465234) self.assertAlmostEqual(scores["P", "Y"], -5.324104300) self.assertAlmostEqual(scores["Q", "A"], -6.089727799) self.assertAlmostEqual(scores["Q", "C"], -4.594583561) self.assertAlmostEqual(scores["Q", "D"], -5.317833872) self.assertAlmostEqual(scores["Q", "E"], -1.379234416) self.assertAlmostEqual(scores["Q", "F"], -5.470549583) self.assertAlmostEqual(scores["Q", "G"], -5.806515511) self.assertAlmostEqual(scores["Q", "H"], -0.167730311) self.assertAlmostEqual(scores["Q", "I"], -5.754800475) self.assertAlmostEqual(scores["Q", "K"], -1.035280015) self.assertAlmostEqual(scores["Q", "L"], -3.663265904) self.assertAlmostEqual(scores["Q", "M"], -4.687987123) self.assertAlmostEqual(scores["Q", "N"], -2.802445847) self.assertAlmostEqual(scores["Q", "P"], -3.619086047) self.assertAlmostEqual(scores["Q", "Q"], 4.422253499) self.assertAlmostEqual(scores["Q", "R"], -0.074872194) self.assertAlmostEqual(scores["Q", "S"], -4.673205282) self.assertAlmostEqual(scores["Q", "T"], -4.723933819) self.assertAlmostEqual(scores["Q", "V"], -4.946787239) self.assertAlmostEqual(scores["Q", "W"], -3.897082721) self.assertAlmostEqual(scores["Q", "Y"], -3.958721787) self.assertAlmostEqual(scores["R", "A"], -4.465485311) self.assertAlmostEqual(scores["R", "C"], -1.800416071) self.assertAlmostEqual(scores["R", "D"], -4.108628883) self.assertAlmostEqual(scores["R", "E"], -3.407068625) self.assertAlmostEqual(scores["R", "F"], -5.846307095) self.assertAlmostEqual(scores["R", "G"], -1.481833305) self.assertAlmostEqual(scores["R", "H"], -0.164976200) self.assertAlmostEqual(scores["R", "I"], -6.130557986) self.assertAlmostEqual(scores["R", "K"], 0.314787510) self.assertAlmostEqual(scores["R", "L"], -4.208948417) self.assertAlmostEqual(scores["R", "M"], -3.478782133) self.assertAlmostEqual(scores["R", "N"], -3.178203359) self.assertAlmostEqual(scores["R", "P"], -3.187488636) self.assertAlmostEqual(scores["R", "Q"], -0.074872194) self.assertAlmostEqual(scores["R", "R"], 3.937295948) self.assertAlmostEqual(scores["R", "S"], -2.311997199) self.assertAlmostEqual(scores["R", "T"], -3.777763236) self.assertAlmostEqual(scores["R", "V"], -4.000616656) self.assertAlmostEqual(scores["R", "W"], -1.272840233) self.assertAlmostEqual(scores["R", "Y"], -5.334479299) self.assertAlmostEqual(scores["S", "A"], -1.286837125) self.assertAlmostEqual(scores["S", "C"], -2.429122807) self.assertAlmostEqual(scores["S", "D"], -3.737335619) self.assertAlmostEqual(scores["S", "E"], -4.258167782) self.assertAlmostEqual(scores["S", "F"], -2.568123236) self.assertAlmostEqual(scores["S", "G"], -1.489051665) self.assertAlmostEqual(scores["S", "H"], -3.172194559) self.assertAlmostEqual(scores["S", "I"], -4.174302222) self.assertAlmostEqual(scores["S", "K"], -4.740183981) self.assertAlmostEqual(scores["S", "L"], -4.252692652) self.assertAlmostEqual(scores["S", "M"], -4.692451371) self.assertAlmostEqual(scores["S", "N"], -0.806910095) self.assertAlmostEqual(scores["S", "P"], -1.197285540) self.assertAlmostEqual(scores["S", "Q"], -4.673205282) self.assertAlmostEqual(scores["S", "R"], -2.311997199) self.assertAlmostEqual(scores["S", "S"], 3.386624147) self.assertAlmostEqual(scores["S", "T"], -1.000477613) self.assertAlmostEqual(scores["S", "V"], -4.366288986) self.assertAlmostEqual(scores["S", "W"], -3.901546969) self.assertAlmostEqual(scores["S", "Y"], -2.963186035) self.assertAlmostEqual(scores["T", "A"], -0.238029989) self.assertAlmostEqual(scores["T", "C"], -5.064813845) self.assertAlmostEqual(scores["T", "D"], -3.466136061) self.assertAlmostEqual(scores["T", "E"], -5.308896320) self.assertAlmostEqual(scores["T", "F"], -4.355817367) self.assertAlmostEqual(scores["T", "G"], -4.691783295) self.assertAlmostEqual(scores["T", "H"], -4.959888691) self.assertAlmostEqual(scores["T", "I"], -1.055105758) self.assertAlmostEqual(scores["T", "K"], -2.505510300) self.assertAlmostEqual(scores["T", "L"], -4.303421190) self.assertAlmostEqual(scores["T", "M"], -0.634655451) self.assertAlmostEqual(scores["T", "N"], -1.594604227) self.assertAlmostEqual(scores["T", "P"], -2.089316331) self.assertAlmostEqual(scores["T", "Q"], -4.723933819) self.assertAlmostEqual(scores["T", "R"], -3.777763236) self.assertAlmostEqual(scores["T", "S"], -1.000477613) self.assertAlmostEqual(scores["T", "T"], 3.844754886) self.assertAlmostEqual(scores["T", "V"], -2.169090010) self.assertAlmostEqual(scores["T", "W"], -3.367313006) self.assertAlmostEqual(scores["T", "Y"], -5.428952072) self.assertAlmostEqual(scores["V", "A"], -0.875920908) self.assertAlmostEqual(scores["V", "C"], -4.287667265) self.assertAlmostEqual(scores["V", "D"], -4.010917576) self.assertAlmostEqual(scores["V", "E"], -4.946787239) self.assertAlmostEqual(scores["V", "F"], -2.841705193) self.assertAlmostEqual(scores["V", "G"], -2.412136375) self.assertAlmostEqual(scores["V", "H"], -5.182742111) self.assertAlmostEqual(scores["V", "I"], 0.320300145) self.assertAlmostEqual(scores["V", "K"], -5.428803438) self.assertAlmostEqual(scores["V", "L"], -1.668293614) self.assertAlmostEqual(scores["V", "M"], -1.573715905) self.assertAlmostEqual(scores["V", "N"], -5.817457647) self.assertAlmostEqual(scores["V", "P"], -4.312169751) self.assertAlmostEqual(scores["V", "Q"], -4.946787239) self.assertAlmostEqual(scores["V", "R"], -4.000616656) self.assertAlmostEqual(scores["V", "S"], -4.366288986) self.assertAlmostEqual(scores["V", "T"], -2.169090010) self.assertAlmostEqual(scores["V", "V"], 3.643217410) self.assertAlmostEqual(scores["V", "W"], -4.590166426) self.assertAlmostEqual(scores["V", "Y"], -5.651805492) self.assertAlmostEqual(scores["W", "A"], -3.733106986) self.assertAlmostEqual(scores["W", "C"], -2.237962748) self.assertAlmostEqual(scores["W", "D"], -3.961213059) self.assertAlmostEqual(scores["W", "E"], -4.482045222) self.assertAlmostEqual(scores["W", "F"], -4.113928770) self.assertAlmostEqual(scores["W", "G"], -1.864932198) self.assertAlmostEqual(scores["W", "H"], -3.133037593) self.assertAlmostEqual(scores["W", "I"], -4.398179662) self.assertAlmostEqual(scores["W", "K"], -4.379098920) self.assertAlmostEqual(scores["W", "L"], -3.476570092) self.assertAlmostEqual(scores["W", "M"], -3.331366309) self.assertAlmostEqual(scores["W", "N"], -3.767753129) self.assertAlmostEqual(scores["W", "P"], -4.262465234) self.assertAlmostEqual(scores["W", "Q"], -3.897082721) self.assertAlmostEqual(scores["W", "R"], -1.272840233) self.assertAlmostEqual(scores["W", "S"], -3.901546969) self.assertAlmostEqual(scores["W", "T"], -3.367313006) self.assertAlmostEqual(scores["W", "V"], -4.590166426) self.assertAlmostEqual(scores["W", "W"], 5.868929028) self.assertAlmostEqual(scores["W", "Y"], -3.602100974) self.assertAlmostEqual(scores["Y", "A"], -5.794746052) self.assertAlmostEqual(scores["Y", "C"], -0.977673719) self.assertAlmostEqual(scores["Y", "D"], -4.022852124) self.assertAlmostEqual(scores["Y", "E"], -5.543684288) self.assertAlmostEqual(scores["Y", "F"], -0.531711646) self.assertAlmostEqual(scores["Y", "G"], -5.511533764) self.assertAlmostEqual(scores["Y", "H"], 0.264754960) self.assertAlmostEqual(scores["Y", "I"], -5.459818728) self.assertAlmostEqual(scores["Y", "K"], -4.440737986) self.assertAlmostEqual(scores["Y", "L"], -5.538209158) self.assertAlmostEqual(scores["Y", "M"], -4.393005375) self.assertAlmostEqual(scores["Y", "N"], -3.829392195) self.assertAlmostEqual(scores["Y", "P"], -5.324104300) self.assertAlmostEqual(scores["Y", "Q"], -3.958721787) self.assertAlmostEqual(scores["Y", "R"], -5.334479299) self.assertAlmostEqual(scores["Y", "S"], -2.963186035) self.assertAlmostEqual(scores["Y", "T"], -5.428952072) self.assertAlmostEqual(scores["Y", "V"], -5.651805492) self.assertAlmostEqual(scores["Y", "W"], -3.602100974) self.assertAlmostEqual(scores["Y", "Y"], 4.795691579) def test_ident(self): # Calculate the +6/-1 matrix as an approximation of the BLOSUM62 matrix. # Steven Henikoff & Jorja G. Henikoff: # Amino acid substitution matrices from protein blocks. # Proceedings of the National Academy of Sciences USA 89(2): # 10915-10919 (1992). from Bio.Data.IUPACData import protein_letters as alphabet from Bio.Align import substitution_matrices m = substitution_matrices.load("BLOSUM62") self.assertEqual(alphabet, "ACDEFGHIKLMNPQRSTVWY") match_score = round(numpy.mean([m[c, c] for c in alphabet])) mismatch_score = round( numpy.mean([m[c1, c2] for c1 in alphabet for c2 in alphabet if c1 != c2]) ) self.assertAlmostEqual(match_score, 6.0) self.assertAlmostEqual(mismatch_score, -1.0) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)