def test_get_score(self): aln = AlignIO.read('TreeConstruction/msa.phy', 'phylip') tree = Phylo.read('./TreeConstruction/upgma.tre', 'newick') scorer = ParsimonyScorer() score = scorer.get_score(tree, aln) self.assertEqual(score, 2 + 1 + 2 + 2 + 1 + 1 + 1 + 3) alphabet = ['A', 'T', 'C', 'G'] step_matrix = [[0], [2.5, 0], [2.5, 1, 0], [1, 2.5, 2.5, 0]] matrix = _Matrix(alphabet, step_matrix) scorer = ParsimonyScorer(matrix) score = scorer.get_score(tree, aln) self.assertEqual(score, 3.5 + 2.5 + 3.5 + 3.5 + 2.5 + 1 + 2.5 + 4.5) alphabet = [ 'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', '1', '2', 'T', 'V', 'W', 'Y', '*', '-' ] step_matrix = [ [0], [2, 0], [1, 2, 0], [1, 2, 1, 0], [2, 1, 2, 2, 0], [1, 1, 1, 1, 2, 0], [2, 2, 1, 2, 2, 2, 0], [2, 2, 2, 2, 1, 2, 2, 0], [2, 2, 2, 1, 2, 2, 2, 1, 0], [2, 2, 2, 2, 1, 2, 1, 1, 2, 0], [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 0], [2, 2, 1, 2, 2, 2, 1, 1, 1, 2, 2, 0], [1, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 0], [2, 2, 2, 1, 2, 2, 1, 2, 1, 1, 2, 2, 1, 0], [2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 0], [1, 1, 2, 2, 1, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 0], [2, 1, 2, 2, 2, 1, 2, 1, 2, 2, 2, 1, 2, 2, 1, 2, 0], [1, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 0], [1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 0], [2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 2, 3, 2, 2, 1, 1, 2, 2, 2, 0], [2, 1, 1, 2, 1, 2, 1, 2, 2, 2, 3, 1, 2, 2, 2, 1, 2, 2, 2, 2, 0], [2, 1, 2, 1, 2, 1, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 0], [ 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0 ] ] matrix = _Matrix(alphabet, step_matrix) scorer = ParsimonyScorer(matrix) score = scorer.get_score(tree, aln) self.assertEqual(score, 3 + 1 + 3 + 3 + 2 + 1 + 2 + 5)
def test_get_score(self): aln = AlignIO.read('TreeConstruction/msa.phy', 'phylip') tree = Phylo.read('./TreeConstruction/upgma.tre', 'newick') scorer = ParsimonyScorer() score = scorer.get_score(tree, aln) self.assertEqual(score, 2 + 1 + 2 + 2 + 1 + 1 + 1 + 3) alphabet = ['A', 'T', 'C', 'G'] step_matrix = [[0], [2.5, 0], [2.5, 1, 0], [1, 2.5, 2.5, 0]] matrix = _Matrix(alphabet, step_matrix) scorer = ParsimonyScorer(matrix) score = scorer.get_score(tree, aln) self.assertEqual(score, 3.5 + 2.5 + 3.5 + 3.5 + 2.5 + 1 + 2.5 + 4.5) alphabet = ['A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', '1', '2', 'T', 'V', 'W', 'Y', '*', '-'] step_matrix = [[0], [2, 0], [1, 2, 0], [1, 2, 1, 0], [2, 1, 2, 2, 0], [1, 1, 1, 1, 2, 0], [2, 2, 1, 2, 2, 2, 0], [2, 2, 2, 2, 1, 2, 2, 0], [2, 2, 2, 1, 2, 2, 2, 1, 0], [2, 2, 2, 2, 1, 2, 1, 1, 2, 0], [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 0], [2, 2, 1, 2, 2, 2, 1, 1, 1, 2, 2, 0], [1, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 0], [2, 2, 2, 1, 2, 2, 1, 2, 1, 1, 2, 2, 1, 0], [2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 0], [1, 1, 2, 2, 1, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 0], [2, 1, 2, 2, 2, 1, 2, 1, 2, 2, 2, 1, 2, 2, 1, 2, 0], [1, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 0], [1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 0], [2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 2, 3, 2, 2, 1, 1, 2, 2, 2, 0], [2, 1, 1, 2, 1, 2, 1, 2, 2, 2, 3, 1, 2, 2, 2, 1, 2, 2, 2, 2, 0], [2, 1, 2, 1, 2, 1, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 0], [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0]] matrix = _Matrix(alphabet, step_matrix) scorer = ParsimonyScorer(matrix) score = scorer.get_score(tree, aln) self.assertEqual(score, 3 + 1 + 3 + 3 + 2 + 1 + 2 + 5)
def test_get_score(self): aln = AlignIO.read("TreeConstruction/msa.phy", "phylip") tree = Phylo.read("./TreeConstruction/upgma.tre", "newick") scorer = ParsimonyScorer() score = scorer.get_score(tree, aln) self.assertEqual(score, 2 + 1 + 2 + 2 + 1 + 1 + 1 + 3) alphabet = ["A", "T", "C", "G"] step_matrix = [[0], [2.5, 0], [2.5, 1, 0], [1, 2.5, 2.5, 0]] matrix = _Matrix(alphabet, step_matrix) scorer = ParsimonyScorer(matrix) score = scorer.get_score(tree, aln) self.assertEqual(score, 3.5 + 2.5 + 3.5 + 3.5 + 2.5 + 1 + 2.5 + 4.5) alphabet = [ "A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M", "N", "P", "Q", "R", "1", "2", "T", "V", "W", "Y", "*", "-", ] step_matrix = [ [0], [2, 0], [1, 2, 0], [1, 2, 1, 0], [2, 1, 2, 2, 0], [1, 1, 1, 1, 2, 0], [2, 2, 1, 2, 2, 2, 0], [2, 2, 2, 2, 1, 2, 2, 0], [2, 2, 2, 1, 2, 2, 2, 1, 0], [2, 2, 2, 2, 1, 2, 1, 1, 2, 0], [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 0], [2, 2, 1, 2, 2, 2, 1, 1, 1, 2, 2, 0], [1, 2, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 0], [2, 2, 2, 1, 2, 2, 1, 2, 1, 1, 2, 2, 1, 0], [2, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 1, 1, 0], [1, 1, 2, 2, 1, 2, 2, 2, 2, 1, 2, 2, 1, 2, 2, 0], [2, 1, 2, 2, 2, 1, 2, 1, 2, 2, 2, 1, 2, 2, 1, 2, 0], [1, 2, 2, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1, 0], [1, 2, 1, 1, 1, 1, 2, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 0], [2, 1, 2, 2, 2, 1, 2, 2, 2, 1, 2, 3, 2, 2, 1, 1, 2, 2, 2, 0], [2, 1, 1, 2, 1, 2, 1, 2, 2, 2, 3, 1, 2, 2, 2, 1, 2, 2, 2, 2, 0], [2, 1, 2, 1, 2, 1, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 0], [ 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 0 ], ] matrix = _Matrix(alphabet, step_matrix) scorer = ParsimonyScorer(matrix) score = scorer.get_score(tree, aln) self.assertEqual(score, 3 + 1 + 3 + 3 + 2 + 1 + 2 + 5)