def testLength(self):
"""midpoint rooting."""
for tree in self.trees:
t = Tree(tree)
t.root_midpoint()
# test 1: only two children for root
s = t.node(t.root).succ
self.assertEqual(len(s), 2)
# calculate tree length on either side of tree
d2leaves = [0] * (max(t.chain.keys()) + 1)
def dist2leaves(node_id):
node = t.node(node_id)
if node.succ:
d2leaves[node_id] = max([
d2leaves[s] + t.node(s).data.branchlength
for s in node.succ
])
t.dfs(t.root, post_function=dist2leaves)
d1 = d2leaves[s[0]] + t.node(s[0]).data.branchlength
d2 = d2leaves[s[1]] + t.node(s[1]).data.branchlength
# test 2: distance to children equal on both sides
self.assertAlmostEqual(
d1, d2, 5, "assertion error: %s != %s for tree %s -> %s" %
(str(d1), str(d2), tree, t.to_string(branchlengths_only=True)))
def testNegativeBranchLengths(self):
for tree in self.trees:
t = Tree(tree)
t.root_midpoint()
for n, node in t.chain.items():
self.failIf(node.data.branchlength < 0,
"assertion error: negative branchlength for tree %s -> %s" %
(tree, t.to_string(branchlengths_only=True)))
def testNegativeBranchLengths(self):
for tree in self.trees:
t = Tree(tree)
t.root_midpoint()
for n, node in t.chain.items():
self.failIf(
node.data.branchlength < 0,
"assertion error: negative branchlength for tree %s -> %s"
% (tree, t.to_string(branchlengths_only=True)))
def testLength(self):
"""midpoint rooting."""
for tree in self.trees:
t = Tree(tree)
t.root_midpoint()
# test 1: only two children for root
s = t.node(t.root).succ
self.assertEqual(len(s), 2)
# calculate tree length on either side of tree
d2leaves = [0] * (max(t.chain.keys()) + 1)
def dist2leaves(node_id):
node = t.node(node_id)
if node.succ:
d2leaves[node_id] = max(
[d2leaves[s] + t.node(s).data.branchlength for s in node.succ])
t.dfs(t.root, post_function=dist2leaves)
d1 = d2leaves[s[0]] + t.node(s[0]).data.branchlength
d2 = d2leaves[s[1]] + t.node(s[1]).data.branchlength
# test 2: distance to children equal on both sides
self.assertAlmostEqual(d1, d2, 5,
"assertion error: %s != %s for tree %s -> %s" %
(str(d1), str(d2),
tree, t.to_string(branchlengths_only=True)))
def testTruncate(self):
t = Tree("(A:1,((B:1,C:1):1,D:1):1,(E:1,F:1):1);")
t.truncate(7, "E+F")
result = t.to_string(branchlengths_only=True,
branchlength_format="%i",
format="nh")
self.assertEqual(result, "(A:1,((B:1,C:1):1,D:1):1,E+F:1);")
t = Tree("(A:1,((B:1,C:1):1,D:1):1,(E:1,F:1):1);")
t.truncate(8)
result = t.to_string(branchlengths_only=True,
branchlength_format="%i",
format="nh")
self.assertEqual(result, "(A:1,((B:1,C:1):1,D:1):1,F:1);")
def testTruncate(self):
t = Tree("(A:1,((B:1,C:1):1,D:1):1,(E:1,F:1):1);")
t.truncate(7, "E+F")
result = t.to_string(branchlengths_only=True,
branchlength_format="%i",
format="nh")
self.assertEqual(result, "(A:1,((B:1,C:1):1,D:1):1,E+F:1);")
t = Tree("(A:1,((B:1,C:1):1,D:1):1,(E:1,F:1):1);")
t.truncate(8)
result = t.to_string(branchlengths_only=True,
branchlength_format="%i",
format="nh")
self.assertEqual(result, "(A:1,((B:1,C:1):1,D:1):1,F:1);")