def _data_to_object(self, data, schema=None):
"""Attaches a DendroPy tree object"""
schemas = [
"newick",
"nexus"
]
# If schemas is not given, try each schema until one works.
if schema is None:
for s in schemas:
# Try different schemas until a tree works
try:
tree = DendropyTree.get(data=data, schema=s)
except:
pass
else:
tree = DendropyTree.get(data=data, schema=schema)
# Check that a tree was made.
try:
self._Tree._DendroPy = tree
self._Tree._construct()
except NameError:
raise Exception("""Tree data doesn't seem to be in a format that DendroPy can read.""")
return self._Tree
def _data_to_object(self, data, schema=None):
"""Attaches a DendroPy tree object"""
schemas = ["newick", "nexus"]
# If schemas is not given, try each schema until one works.
if schema is None:
for s in schemas:
# Try different schemas until a tree works
try:
tree = DendropyTree.get(data=data, schema=s)
except:
pass
else:
tree = DendropyTree.get(data=data, schema=schema)
# Check that a tree was made.
try:
self._Tree._DendroPy = tree
self._Tree._construct()
except NameError:
raise Exception(
"""Tree data doesn't seem to be in a format that DendroPy can read."""
)
return self._Tree
def add_outgroup(tree, relative_additional_height):
desired_height = (
1 + relative_additional_height) * tree.seed_node.distance_from_tip()
outgroup = Node(taxon=Taxon("outgroup"), edge_length=desired_height)
tns = deepcopy(tree.taxon_namespace)
tns.add_taxon(outgroup.taxon)
new_root = Node()
new_root.add_child(outgroup)
new_root.add_child(tree.seed_node)
new_tree = Tree(taxon_namespace=tns)
new_tree.seed_node = new_root
# Despite my best efforts, I was getting taxon namespace errors. So we round trip
# from Newick. ¯\_(ツ)_/¯
new_newick = str(new_tree) + ";"
return Tree.get(data=new_newick, schema="newick")
def nexus(self, data):
Tree = DendropyTree.get(data=data, schema="nexus")
return self._data_to_object(Tree)
def nexus(self, data):
Tree = DendropyTree.get(data=data, schema="nexus")
return self._data_to_object(Tree)
