def test_neighbor_joining():
"""
Compare the results of `neighbor_join()` with a known tree.
"""
dist = np.array([
[0, 5, 4, 7, 6, 8],
[5, 0, 7, 10, 9, 11],
[4, 7, 0, 7, 6, 8],
[7, 10, 7, 0, 5, 9],
[6, 9, 6, 5, 0, 8],
[8, 11, 8, 9, 8, 0],
])
ref_tree = phylo.Tree(
phylo.TreeNode([
phylo.TreeNode([
phylo.TreeNode([
phylo.TreeNode(index=0),
phylo.TreeNode(index=1),
], [1, 4]),
phylo.TreeNode(index=2),
], [1, 2]),
phylo.TreeNode([
phylo.TreeNode(index=3),
phylo.TreeNode(index=4),
], [3, 2]),
phylo.TreeNode(index=5),
], [1, 1, 5]))
test_tree = phylo.neighbor_joining(dist)
assert test_tree == ref_tree
def test_clustalo_tree(sequences):
leaves = [phylo.TreeNode(index=i) for i in range(len(sequences))]
inter1 = phylo.TreeNode([leaves[0], leaves[1]], [1.0, 1.0])
inter2 = phylo.TreeNode([leaves[2], leaves[3]], [2.5, 2.5])
root = phylo.TreeNode([inter1, inter2], [3.5, 2])
tree = phylo.Tree(root)
# You cannot simultaneously set and get a tree in ClustalOmega
# -> Test whether both is possible in separate calls
app = ClustalOmegaApp(sequences)
app.set_guide_tree(tree)
app.start()
app.join()
app = ClustalOmegaApp(sequences)
app.start()
app.join()
assert app.get_guide_tree() is not None
def test_equality(tree):
"""
Assert that equal trees equal each other, and non-equal trees do not
equal each other.
"""
assert tree == tree.copy()
# Order of children is not important
assert tree == phylo.Tree(
phylo.TreeNode(
[tree.root.children[1].copy(), tree.root.children[0].copy()],
[tree.root.children[1].distance, tree.root.children[0].distance]))
# Different distance -> Unequal tree
assert tree != phylo.Tree(
phylo.TreeNode(
[tree.root.children[0].copy(), tree.root.children[1].copy()],
[tree.root.children[0].distance, 42]))
# Additional node -> Unequal tree
assert tree != phylo.Tree(
phylo.TreeNode([
tree.root.children[0].copy(), tree.root.children[1].copy(),
phylo.TreeNode(index=len(tree))
], [
tree.root.children[0].distance, tree.root.children[1].distance, 42
]))
# When a :class:`TreeNode` is created, you have to provide either child
# nodes and their distances to this node (intermediate node) or a
# reference index (leaf node).
# This reference index is dependent on the context and can refer to
# anything: sequences, organisms, etc.
#
# The childs and the reference index cannot be changed after object
# creation.
# Also the parent can only be set once - when the node is used as child
# in the creation of a new node.
import biotite.sequence.phylo as phylo
# The reference objects
fruits = ["Apple", "Pear", "Orange", "Lemon", "Banana"]
# Create nodes
apple = phylo.TreeNode(index=fruits.index("Apple"))
pear = phylo.TreeNode(index=fruits.index("Pear"))
orange = phylo.TreeNode(index=fruits.index("Orange"))
lemon = phylo.TreeNode(index=fruits.index("Lemon"))
banana = phylo.TreeNode(index=fruits.index("Banana"))
intermediate1 = phylo.TreeNode(children=(apple, pear), distances=(2.0, 2.0))
intermediate2 = phylo.TreeNode((orange, lemon), (1.0, 1.0))
intermediate3 = phylo.TreeNode((intermediate2, banana), (2.0, 3.0))
root = phylo.TreeNode((intermediate1, intermediate3), (2.0, 1.0))
# Create tree from root node
tree = phylo.Tree(root=root)
# Trees can be converted into Newick notation
print("Tree:", tree.to_newick(labels=fruits))
# Distances can be omitted
print("Tree w/o distances:",
tree.to_newick(labels=fruits, include_distance=False))
def test_immutability():
node = phylo.TreeNode(index=0)
# Attributes are not writable
with pytest.raises(AttributeError):
node.children = None
with pytest.raises(AttributeError):
node.parent = None
with pytest.raises(AttributeError):
node.index = None
# A root node cannot be child
node1 = phylo.TreeNode(index=0)
node2 = phylo.TreeNode(index=1)
node1.as_root()
with pytest.raises(phylo.TreeError):
phylo.TreeNode([node1, node2], [0, 0])
# A child node cannot be root
node1 = phylo.TreeNode(index=0)
node2 = phylo.TreeNode(index=1)
phylo.TreeNode([node1, node2], [0, 0])
with pytest.raises(phylo.TreeError):
node1.as_root()
# A node cannot be child of a two nodes
node1 = phylo.TreeNode(index=0)
node2 = phylo.TreeNode(index=1)
phylo.TreeNode([node1, node2], [0, 0])
with pytest.raises(phylo.TreeError):
phylo.TreeNode([node1, node2], [0, 0])
# Tree cannot be constructed from child nodes
node1 = phylo.TreeNode(index=0)
node2 = phylo.TreeNode(index=0)
# node1 and node2 have now a parent
phylo.TreeNode([node1, node2], [0, 0])
with pytest.raises(phylo.TreeError):
phylo.Tree(node1)
