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 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 read_and_encode_splits(dataset, tree_stream):
"""Reads the file-like object `tree_stream` as a source of trees for the
the taxa found in dataset. and then encodes the splits of the nodes of the trees.
This is a convenience function that bridges between dendropy 2 and 3 API's
"""
_LOG.debug("NOT covered in tests")
tree_list = read_trees_into_dataset(dataset, tree_stream)
assert len(tree_list) == 1
delete_outdegree_one(tree_list[0])
return tree_list
def read_and_encode_splits(dataset, tree_stream, starting_tree=False):
"""Reads the file-like object `tree_stream` as a source of trees for the
the taxa found in dataset. and then encodes the splits of the nodes of the trees.
This is a convenience function that bridges between dendropy 2 and 3 API's
"""
_LOG.debug("NOT covered in tests")
tree_list = read_trees_into_dataset(dataset,
tree_stream,
starting_tree=starting_tree)
assert len(tree_list) == 1
delete_outdegree_one(tree_list[0])
return tree_list
