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
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