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)