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 generate_tree_with_splits_from_str(tree_str, dataset):
'''Uses `tree_str` and `dataset` to create a PhylogeneticTree object
and calls `calc_splits` on the object before returning it.
'''
tree_stream = StringIO(tree_str)
tree_list = read_and_encode_splits(dataset, tree_stream)
t = PhylogeneticTree(tree_list[0])
t.calc_splits()
return t
def generate_tree_with_splits_from_str(tree_str, dataset, force_fully_resolved=False):
'''Uses `tree_str` and `dataset` to create a PhylogeneticTree object
and calls `calc_splits` on the object before returning it.
'''
tree_stream = StringIO(tree_str)
tree_list = read_and_encode_splits(dataset, tree_stream)
t = tree_list[0]
if force_fully_resolved:
resolve_polytomies(t, update_splits=True)
t = PhylogeneticTree(t)
t.calc_splits()
return t
def generate_tree_with_splits_from_str(tree_str,
dataset,
force_fully_resolved=False):
'''Uses `tree_str` and `dataset` to create a PhylogeneticTree object
and calls `calc_splits` on the object before returning it.
'''
tree_stream = StringIO(tree_str)
tree_list = read_and_encode_splits(dataset, tree_stream)
t = tree_list[0]
if force_fully_resolved:
resolve_polytomies(t, update_splits=True)
t = PhylogeneticTree(t)
t.calc_splits()
return t
def testCentroidEdge(self):
sd = SequenceDataset()
fp = data_source_path('100T.fasta')
sd.read(open(fp, 'rU'), file_format='FASTA', datatype='DNA')
fp = data_source_path('100T.tree')
tree_list = read_and_encode_splits(sd.dataset, open(fp, "rU"))
self.assertEqual(len(tree_list), 1)
t = PhylogeneticTree(tree_list[0])
self._do_test_centroid(t)
