Python PhylogeneticTree.calc_splits Beispiele

Beispiel #1

 def phylogeneticTreeFromFile(self, treefile, file_format):
     dataset = Dataset()
     dataset.read(open(treefile, 'rU'), schema=file_format)
     dendropy_tree = dataset.tree_lists[0][0]
     tree = PhylogeneticTree(dendropy_tree)
     tree.calc_splits()
     delete_outdegree_one(tree._tree)
     return tree

Beispiel #2

Datei: treeholder.py Projekt: SagesWang/pasta

def generate_tree_with_splits_from_tree(t, force_fully_resolved=False):    
    if force_fully_resolved:        
        resolve_polytomies(t, update_splits=False)
    t = PhylogeneticTree(t)
    _LOG.debug("calculating splits")
    t.calc_splits()
    _LOG.debug("end generating tree from string")
    return t

Beispiel #3

def generate_tree_with_splits_from_tree(t, force_fully_resolved=False):
    if force_fully_resolved:
        resolve_polytomies(t, update_splits=False)
    t = PhylogeneticTree(t)
    _LOG.debug("calculating splits")
    t.calc_splits()
    _LOG.debug("end generating tree from string")
    return t

Beispiel #4

Datei: test_phylogenetic_tree.py Projekt: SagesWang/pasta

 def phylogeneticTreeFromFile(self, treefile, file_format):
     dataset = Dataset()
     dataset.read(open(treefile, 'rU'), schema=file_format)
     dendropy_tree = dataset.tree_lists[0][0]
     tree = PhylogeneticTree(dendropy_tree)
     tree.calc_splits()
     delete_outdegree_one(tree._tree)
     return tree