Python NNITreeSearcher._get_neighbors示例

示例#1

文件： test_TreeConstruction.py 项目： thorbenwiese/bachelorarbeit_wiese

 def test_get_neighbors(self):
     tree = Phylo.read('./TreeConstruction/upgma.tre', 'newick')
     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)
     searcher = NNITreeSearcher(scorer)
     trees = searcher._get_neighbors(tree)
     self.assertEqual(len(trees), 2 * (5 - 3))
     Phylo.write(trees, './TreeConstruction/neighbor_trees.tre', 'newick')

示例#2

文件： test_TreeConstruction.py 项目： iriziotis/biopython_bugfixes

 def test_get_neighbors(self):
     tree = Phylo.read("./TreeConstruction/upgma.tre", "newick")
     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)
     searcher = NNITreeSearcher(scorer)
     trees = searcher._get_neighbors(tree)
     self.assertEqual(len(trees), 2 * (5 - 3))
     Phylo.write(trees, os.path.join(temp_dir, "neighbor_trees.tre"), "newick")

示例#3

def NNITreeSurgery(treeStr, schema="newick"):
    tree = Phylo.read(StringIO(treeStr), schema)

    nniTreeSearcher = NNITreeSearcher(Scorer())
    treeList = nniTreeSearcher._get_neighbors(tree)
    allTreeList = []
    for t in treeList:
        tstr = t.format("newick")
        tstr.strip()
        allTreeList.append("[&R] " + tstr[0:len(tstr) - 6] + ";")
    return allTreeList

示例#4

文件： test_TreeConstruction.py 项目： vocessitas/biopython

 def test_get_neighbors(self):
     tree = Phylo.read('./TreeConstruction/upgma.tre', 'newick')
     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)
     searcher = NNITreeSearcher(scorer)
     trees = searcher._get_neighbors(tree)
     self.assertEqual(len(trees), 2 * (5 - 3))
     Phylo.write(trees, './TreeConstruction/neighbor_trees.tre', 'newick')