def test_restore_rooting(self):
# rooted source
source = TreeNode.read(['(((e,f),g),((c,d),(b,a)));'])
target = TreeNode.read(['(((a,b),(c,d)),(e,f),g);'])
rooted = restore_rooting(source, target)
self.assertTrue(_exact_compare(rooted, source))
# unrooted source
source = TreeNode.read(['(((e,f),g),(a,b),(c,d));'])
unrooted = restore_rooting(source, target)
self.assertTrue(_exact_compare(unrooted, source))
# test support handling
source = TreeNode.read(['(((e,f),g),((c,d),(b,a)));'])
target = TreeNode.read(['(((a,b)95,(c,d)90)80,(e,f)100,g);'])
assign_supports(target)
obs = restore_rooting(source, target)
exp = TreeNode.read(['(((e,f)100,g)80,((c,d)90,(b,a)95)80);'])
assign_supports(exp)
self.assertTrue(_exact_compare(obs, exp))
# taxa don't match
msg = 'Source and target trees have different taxa.'
with self.assertRaisesRegex(ValueError, msg):
restore_rooting(source, TreeNode.read(['((a,b),(c,d));']))
def test_root_above(self):
# test rooted tree
tree1 = TreeNode.read([
'(((a:1.0,b:0.8)c:2.4,(d:0.8,e:0.6)f:1.2)g:0.4,'
'(h:0.5,i:0.7)j:1.8)k;'
])
tree1_cg = root_above(tree1.find('c'))
exp = TreeNode.read([
'((a:1.0,b:0.8)c:1.2,((d:0.8,e:0.6)f:1.2,(h:0.5,'
'i:0.7)j:2.2)g:1.2);'
])
self.assertTrue(_exact_compare(exp, tree1_cg))
tree1_ij = root_above(tree1.find('i'))
exp = TreeNode.read([
'(i:0.35,(h:0.5,((a:1.0,b:0.8)c:2.4,(d:0.8,'
'e:0.6)f:1.2)g:2.2)j:0.35);'
])
self.assertTrue(_exact_compare(exp, tree1_ij))
# test unrooted tree
tree2 = TreeNode.read([
'(((a:0.6,b:0.5)g:0.3,c:0.8)h:0.4,(d:0.4,'
'e:0.5)i:0.5,f:0.9)j;'
])
tree2_ag = root_above(tree2.find('a'))
exp = TreeNode.read([
'(a:0.3,(b:0.5,(c:0.8,((d:0.4,e:0.5)i:0.5,'
'f:0.9)j:0.4)h:0.3)g:0.3);'
])
self.assertTrue(_exact_compare(exp, tree2_ag))
tree2_gh = root_above(tree2.find('g'))
exp = TreeNode.read([
'((a:0.6,b:0.5)g:0.15,(c:0.8,((d:0.4,e:0.5)i:0.5,'
'f:0.9)j:0.4)h:0.15);'
])
self.assertTrue(_exact_compare(exp, tree2_gh))
# test unrooted tree with 1 basal node
tree3 = TreeNode.read(
['(((a:0.4,b:0.3)e:0.1,(c:0.4,'
'd:0.1)f:0.2)g:0.6)h:0.2;'])
tree3_ae = root_above(tree3.find('a'))
exp = TreeNode.read(
['(a:0.2,(b:0.3,((c:0.4,d:0.1)f:0.2,'
'h:0.6)g:0.1)e:0.2);'])
self.assertTrue(_exact_compare(exp, tree3_ae))
def test_root_by_outgroup(self):
tree = TreeNode.read(['((((a,b),(c,d)),(e,f)),g);'])
# outgroup is monophyletic
obs = root_by_outgroup(tree, outgroup=['a', 'b'])
exp = TreeNode.read(['((a,b),((c,d),((e,f),g)));'])
self.assertTrue(_exact_compare(obs, exp))
# outgroup is monophyletic after rotating
obs = root_by_outgroup(tree, outgroup=['e', 'f', 'g'])
exp = TreeNode.read(['(((e,f),g),((c,d),(b,a)));'])
self.assertTrue(_exact_compare(obs, exp))
# outgroup is not monophyletic
msg = 'Outgroup is not monophyletic in tree.'
with self.assertRaisesRegex(ValueError, msg):
root_by_outgroup(tree, outgroup=['a', 'c'])
# outgroup is single taxon
obs = root_by_outgroup(tree, outgroup=['a'])
exp = TreeNode.read(['(a,(b,((c,d),((e,f),g))));'])
self.assertTrue(_exact_compare(obs, exp))
# outgroup has extra taxa
obs = root_by_outgroup(tree, outgroup=['a', 'b', 'x'])
exp = TreeNode.read(['((a,b),((c,d),((e,f),g)));'])
self.assertTrue(_exact_compare(obs, exp))
# outgroup has extra taxa but strict mode
msg = 'Outgroup is not a subset of tree taxa.'
with self.assertRaisesRegex(ValueError, msg):
root_by_outgroup(tree, outgroup=['a', 'b', 'x'], strict=True)
# outgroup is not in tree
msg = 'None of outgroup taxa are present in tree.'
with self.assertRaisesRegex(ValueError, msg):
root_by_outgroup(tree, outgroup=['x', 'y'])
# outgroup is the whole tree
msg = 'Outgroup constitutes the entire tree.'
with self.assertRaisesRegex(ValueError, msg):
root_by_outgroup(tree, outgroup='abcdefg')
# generate unrooted tree
obs = root_by_outgroup(tree, outgroup=['a', 'b'], unroot=True)
exp = TreeNode.read(['(((e,f),g),(a,b),(c,d));'])
self.assertTrue(_exact_compare(obs, exp))
def test_restore_node_labels(self):
# simple case
source = TreeNode.read(['((a,b)x,(c,d)y);'])
target = TreeNode.read(['((a:0.5,b:0.6):1.2,(c:1.0,d:1.4):0.4);'])
obs = restore_node_labels(source, target)
exp = TreeNode.read(['((a:0.5,b:0.6)x:1.2,(c:1.0,d:1.4)y:0.4);'])
self.assertTrue(_exact_compare(obs, exp))
# complex case with missing label, extra taxa, label overwrittern
source = TreeNode.read(['(((a,b)85,c)90,((d,e)98,(f,g)93));'])
target = TreeNode.read(['((((g,f),(e,d))x,(c,(a,b))y),h);'])
obs = restore_node_labels(source, target)
exp = TreeNode.read(['((((g,f)93,(e,d)98)x,(c,(a,b)85)90),h);'])
self.assertTrue(_exact_compare(obs, exp))
# a duplicated node label
msg = 'Duplicated node label "x" found.'
with self.assertRaisesRegex(ValueError, msg):
restore_node_labels(TreeNode.read(['((a,b)x,(c,d)x);']), target)
def test_unroot_at(self):
# sample example from doctest of scikit-bio's `root_at`
tree = TreeNode.read(['(((a,b)c,(d,e)f)g,h)i;'])
obs = unroot_at(tree.find('c'))
exp = TreeNode.read(['(((d,e)f,h)g,a,b)c;'])
self.assertTrue(_exact_compare(obs, exp))
# test branch support handling
tree.find('c').support = 95
tree.find('f').support = 99
obs = unroot_at(tree.find('c'))
exp = TreeNode.read(["(((d,e)'99:f',h)'95:g',a,b)c;"])
assign_supports(exp)
self.assertTrue(_exact_compare(obs, exp))
# test branch length handling
tree = TreeNode.read(
['(((a:1.1,b:2.2)c:1.3,(d:1.4,e:0.8)f:0.6)g:0.4,h:3.1)i;'])
obs = unroot_at(tree.find('c'))
exp = TreeNode.read(
['(((d:1.4,e:0.8)f:0.6,h:3.5)g:1.3,a:1.1,b:2.2)c;'])
self.assertTrue(_exact_compare(obs, exp))
def test_restore_node_order(self):
source = TreeNode.read(['(((a,b),(c,d)),((e,f),g));'])
target = TreeNode.read(['((g,(e,f)100),((d,c)80,(a,b)90));'])
obs = restore_node_order(source, target)
exp = TreeNode.read(['(((a,b)90,(c,d)80),((e,f)100,g));'])
self.assertTrue(_exact_compare(obs, exp))
msg = 'Two trees have different sizes.'
with self.assertRaisesRegex(ValueError, msg):
restore_node_order(TreeNode.read(['((a,b),(c,d));']), target)
msg = 'Two trees have different topologies.'
with self.assertRaisesRegex(ValueError, msg):
restore_node_order(TreeNode.read(['((((a,b),c),d),(e,(f,g)));']),
target)
def test_exact_compare(self):
# test name
tree0 = TreeNode.read(['((e,d)f,(c,(a,b)));'])
tree1 = TreeNode.read(['(((a,b),c),(d,e)f);'])
self.assertTrue(_exact_compare(tree1, tree1))
self.assertFalse(_exact_compare(tree0, tree1))
# test length
tree2 = TreeNode.read(['(((a:1,b):2,c:1),(d:1,e:2)f:1);'])
self.assertTrue(_exact_compare(tree2, tree2))
self.assertFalse(_exact_compare(tree1, tree2))
tree3 = TreeNode.read(['(((a:1,b:0.0):2,c:1):0.0,(d:1,e:2)f:1);'])
self.assertTrue(_exact_compare(tree3, tree3))
self.assertFalse(_exact_compare(tree2, tree3))
# test support
tree4 = TreeNode.read(['(((a:1,b:1)95:2,c:1)98:3,(d:1,e:2)0.0:1);'])
tree5 = TreeNode.read(['(((a:1,b:1)95:2,c:1)98:3,(d:1,e:2):1);'])
assign_supports(tree4)
self.assertTrue(_exact_compare(tree4, tree4))
self.assertFalse(_exact_compare(tree4, tree5))
assign_supports(tree5)
self.assertFalse(_exact_compare(tree4, tree5))
def test_walk_copy(self):
tree1 = TreeNode.read([
'(((a:1.0,b:0.8)c:2.4,(d:0.8,e:0.6)f:1.2)g:0.4,'
'(h:0.5,i:0.7)j:1.8)k;'
])
# test pos = root
msg = 'Cannot walk from root of a rooted tree.'
with self.assertRaisesRegex(ValueError, msg):
walk_copy(tree1.find('k'), tree1.find('j'))
msg = 'Source and node are not neighbors.'
# test pos = derived
with self.assertRaisesRegex(ValueError, msg):
walk_copy(tree1.find('a'), tree1.find('b'))
with self.assertRaisesRegex(ValueError, msg):
walk_copy(tree1.find('c'), tree1.find('f'))
with self.assertRaisesRegex(ValueError, msg):
walk_copy(tree1.find('f'), tree1.find('j'))
with self.assertRaisesRegex(ValueError, msg):
walk_copy(tree1.find('f'), tree1.find('k'))
# test pos = basal
with self.assertRaisesRegex(ValueError, msg):
walk_copy(tree1.find('g'), tree1.find('a'))
with self.assertRaisesRegex(ValueError, msg):
walk_copy(tree1.find('g'), tree1.find('k'))
# pos = derived, move = up
exp = TreeNode.read(
['(b:0.8,((d:0.8,e:0.6)f:1.2,(h:0.5,i:0.7)j:2.2)'
'g:2.4)c:1.0;'])
obs = walk_copy(tree1.find('c'), tree1.find('a'))
self.assertTrue(_exact_compare(exp, obs))
# pos = derived, move = down
exp = TreeNode.read(['(d:0.8,e:0.6)f:1.2;'])
obs = walk_copy(tree1.find('f'), tree1.find('g'))
self.assertTrue(_exact_compare(exp, obs))
# pos = basal, move = top
exp = TreeNode.read(['((d:0.8,e:0.6)f:1.2,(h:0.5,i:0.7)j:2.2)g:2.4;'])
obs = walk_copy(tree1.find('g'), tree1.find('c'))
self.assertTrue(_exact_compare(exp, obs))
# pos = basal, move = bottom
exp = TreeNode.read(['(h:0.5,i:0.7)j:2.2;'])
obs = walk_copy(tree1.find('j'), tree1.find('g'))
self.assertTrue(_exact_compare(exp, obs))
tree2 = TreeNode.read(
['(((a:1.0,b:0.8)c:2.4,d:0.8)e:0.6,f:1.2,'
'g:0.4)h:0.5;'])
# pos = basal, move = down
exp = TreeNode.read(['((a:1.0,b:0.8)c:2.4,d:0.8)e:0.6;'])
obs = walk_copy(tree2.find('e'), tree2.find('h'))
self.assertTrue(_exact_compare(exp, obs))
# pos = basal, move = up
exp = TreeNode.read(['(d:0.8,(f:1.2,g:0.4)h:0.6)e:2.4;'])
obs = walk_copy(tree2.find('e'), tree2.find('c'))
self.assertTrue(_exact_compare(exp, obs))