class TestNodeDescendantsFunctionality(unittest.TestCase):
def setUp(self):
self.test_obj = Node("A", "1.0")
self.test_descendant = Node("D", "2.0")
self.lengths = ["2.0", "3.0", "4.0"]
@data(["D1.1", "D1.2", "D1.3"], ["D", "", ""], ["", "", ""])
def test_node_representation_with_deeper_descendants(self, test_data):
"""
:param test_data: names of descendants
Procedure:
1. Make simple tree with one descendant having two another descendants inside
2. Verify if it's newick representation is correct in comparision to parsed
"proper_result"
:return:
"""
single_nodes_reprs = [
"{0}:{1}".format(name, length)
for name, length in zip(test_data, self.lengths)
]
proper_result = "(({1},{2}){0})A:1.0".format(*single_nodes_reprs)
d1, d2, d3 = [
Node(name, length) for name, length in zip(test_data, self.lengths)
]
d1.add_descendant(d2)
d1.add_descendant(d3)
self.test_obj.add_descendant(d1)
self.assertEqual(proper_result, self.test_obj.newick)
def test_node_as_descendants_list(self):
self.test_obj.add_descendant(self.test_descendant)
self.assertListEqual([self.test_descendant], self.test_obj.descendants)
class TestNodeDescendantsFunctionality(unittest.TestCase):
def setUp(self):
self.test_obj = Node("A", "1.0")
self.test_descendant = Node("D", "2.0")
self.lengths = ["2.0", "3.0", "4.0"]
@data(["D1.1", "D1.2", "D1.3"], ["D", "", ""], ["", "", ""])
def test_node_representation_with_deeper_descendants(self, test_data):
"""
:param test_data: names of descendants
Procedure:
1. Make simple tree with one descendant having two another descendants inside
2. Verify if it's newick representation is correct in comparision to parsed
"proper_result"
:return:
"""
single_nodes_reprs = [
"{0}:{1}".format(name, length)
for name, length in zip(test_data, self.lengths)]
proper_result = "(({1},{2}){0})A:1.0".format(*single_nodes_reprs)
d1, d2, d3 = [Node(name, length) for name, length in zip(test_data, self.lengths)]
d1.add_descendant(d2)
d1.add_descendant(d3)
self.test_obj.add_descendant(d1)
self.assertEqual(proper_result, self.test_obj.newick)
def test_node_as_descendants_list(self):
self.test_obj.add_descendant(self.test_descendant)
self.assertListEqual([self.test_descendant], self.test_obj.descendants)
def newick_node(self, nodes=None, template=None):
template = template or self._newick_default_template
n = Node(name=template.format(l=self), length='1') # noqa: E741
children = self.children if nodes is None else self.children_from_nodemap(
nodes)
for nn in sorted(children, key=lambda nn: nn.name):
n.add_descendant(nn.newick_node(nodes=nodes, template=template))
return n
def newick_node(self, nodes=None):
label = '{0} [{1}]'.format(
self.name.replace(',', '/').replace('(', '{').replace(')', '}'),
self.id)
if self.iso:
label += '[%s]' % self.iso
if self.level == Level.language:
label += '-l-'
n = Node(name="'{0}'".format(label), length='1')
children = self.children if nodes is None else self.children_from_nodemap(
nodes)
for nn in sorted(children, key=lambda nn: nn.name):
n.add_descendant(nn.newick_node(nodes=nodes))
return n
def newick_node(self, nodes=None, template=None, maxlevel=None, level=0) -> Node:
"""
Return a `newick.Node` representing the subtree of the Glottolog classification starting
at the languoid.
:param template: Python format string accepting the `Languoid` instance as single \
variable named `l`, used to format node labels.
"""
template = template or self._newick_default_template
n = Node(name=template.format(l=self), length='1') # noqa: E741
children = self.children if nodes is None else self.children_from_nodemap(nodes)
for nn in sorted(children, key=lambda nn: nn.name):
if maxlevel:
if (isinstance(maxlevel, config.LanguoidLevel) and nn.level > maxlevel) or \
(not isinstance(maxlevel, config.LanguoidLevel) and level > maxlevel):
continue
n.add_descendant(
nn.newick_node(nodes=nodes, template=template, maxlevel=maxlevel, level=level + 1))
return n
def _add_leaf(node: Node, target: str, leaf: str):
if PhyTree._is_group(node.name):
if node.name == target:
node.add_descendant(Node(f"{{{leaf}}}"))
else:
if PhyTree._is_group(target):
expected_leaves = set(PhyTree._get_group_leaves(target))
else:
expected_leaves = {target}
for child in node.descendants:
if PhyTree._is_group(child.name):
child_leaves = set(
PhyTree._get_group_leaves(child.name))
if expected_leaves <= child_leaves:
PhyTree._add_leaf(child, target, leaf)
break
elif PhyTree._is_leaf(child.name):
if child.name in expected_leaves:
PhyTree._add_leaf(child, target, leaf)
else:
raise ValueError(f"Couldn't find {target}")
elif PhyTree._is_leaf(node.name):
if node.name == target:
if node.name != '{}':
node.add_descendant(Node(node.name))
node.add_descendant(Node(f"{{{leaf}}}"))
else:
node.name = f"{{{leaf}}}"
return
else:
raise ValueError(f"Unexpected leaf: {node.name}")
else:
raise ValueError(f"Couldn't recognize {leaf} as a leaf or a group")
node.name = node.name.replace("}", f" {leaf}}}")
def clone_node(n):
c = Node(name=n.name)
for nn in n.descendants:
c.add_descendant(clone_node(nn))
return c
def clone_node(n):
c = Node(name=n.name)
for nn in n.descendants:
c.add_descendant(clone_node(nn))
return c