def test_support(self):
"""Test getting support value of a node."""
# test nodes with support alone as label
tree = TreeNode.read(['((a,b)75,(c,d)90);'])
node1, node2 = tree.children
self.assertEqual(support(node1), 75.0)
self.assertEqual(support(node2), 90.0)
# test nodes with support and branch length
tree = TreeNode.read(['((a,b)0.85:1.23,(c,d)0.95:4.56);'])
node1, node2 = tree.children
self.assertEqual(support(node1), 0.85)
self.assertEqual(support(node2), 0.95)
# test nodes with support and extra label (not a common scenario but
# can happen)
tree = TreeNode.read(['((a,b)\'80:X\',(c,d)\'60:Y\');'])
node1, node2 = tree.children
self.assertEqual(support(node1), 80.0)
self.assertEqual(support(node2), 60.0)
# test nodes without label, with non-numeric label, and with branch
# length only
tree = TreeNode.read(['((a,b),(c,d)x,(e,f):1.0);'])
for node in tree.children:
self.assertIsNone(support(node))
def func(x):
return support(x) < 75
def func(x):
sup = support(x)
return sup is not None and sup < 75
def test_unpack_by_func(self):
"""Test unpacking nodes by function."""
# unpack internal nodes with branch length <= 1.0
def func(x):
return x.length <= 1.0
# will unpack node 'a', but not tip 'e'
# will add the branch length of 'a' to its child nodes 'c' and 'd'
tree = TreeNode.read(['((c:2,d:3)a:1,(e:1,f:2)b:2);'])
obs = str(unpack_by_func(tree, func)).rstrip()
exp = '((e:1.0,f:2.0)b:2.0,c:3.0,d:4.0);'
self.assertEqual(obs, exp)
# unpack internal nodes with branch length < 2.01
# will unpack both 'a' and 'b'
obs = str(unpack_by_func(tree, lambda x: x.length <= 2.0)).rstrip()
exp = '(c:3.0,d:4.0,e:3.0,f:4.0);'
self.assertEqual(obs, exp)
# unpack two nested nodes 'a' and 'c' simultaneously
tree = TreeNode.read(['(((e:3,f:2)c:1,d:3)a:1,b:4);'])
obs = str(unpack_by_func(tree, lambda x: x.length <= 2.0)).rstrip()
exp = '(b:4.0,d:4.0,e:5.0,f:4.0);'
self.assertEqual(obs, exp)
# test a complicated scenario (unpacking nodes 'g', 'h' and 'm')
def func(x):
return x.length < 2.0
tree = TreeNode.read(['(((a:1.04,b:2.32,c:1.44)d:3.20,'
'(e:3.91,f:2.47)g:1.21)h:1.75,'
'(i:4.14,(j:2.06,k:1.58)l:3.32)m:0.77);'])
obs = str(unpack_by_func(tree, func)).rstrip()
exp = ('((a:1.04,b:2.32,c:1.44)d:4.95,e:6.87,f:5.43,i:4.91,'
'(j:2.06,k:1.58)l:4.09);')
self.assertEqual(obs, exp)
# unpack nodes with support < 75
def func(x):
return support(x) < 75
tree = TreeNode.read(['(((a,b)85,(c,d)78)75,(e,(f,g)64)80);'])
obs = str(unpack_by_func(tree, func)).rstrip()
exp = '(((a,b)85,(c,d)78)75,(e,f,g)80);'
self.assertEqual(obs, exp)
# unpack nodes with support < 85
obs = str(unpack_by_func(tree, lambda x: support(x) < 85)).rstrip()
exp = '((a,b)85,c,d,e,f,g);'
self.assertEqual(obs, exp)
# unpack nodes with support < 0.95
tree = TreeNode.read(['(((a,b)0.97,(c,d)0.98)1.0,(e,(f,g)0.88)0.96);'])
obs = str(unpack_by_func(tree, lambda x: support(x) < 0.95)).rstrip()
exp = '(((a,b)0.97,(c,d)0.98)1.0,(e,f,g)0.96);'
self.assertEqual(obs, exp)
# test a case where there are branch lengths, none support values and
# node labels
def func(x):
sup = support(x)
return sup is not None and sup < 75
tree = TreeNode.read(['(((a:1.02,b:0.33)85:0.12,(c:0.86,d:2.23)'
'70:3.02)75:0.95,(e:1.43,(f:1.69,g:1.92)64:0.20)'
'node:0.35)root;'])
obs = str(unpack_by_func(tree, func)).rstrip()
exp = ('(((a:1.02,b:0.33)85:0.12,c:3.88,d:5.25)75:0.95,'
'(e:1.43,f:1.89,g:2.12)node:0.35)root;')
self.assertEqual(obs, exp)