def test_setup_master_tree_missingtips(self):
"""tests setup_master_tree"""
master_tree = parse_newick('((a:2,b:3):2,(c:1,d:2)foo:7);')
t1 = parse_newick('((a:6,b:8.2):2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,c:33):2,d:7);') # where's b?
support_tree_tipnames = ['a', 'c', 'd']
exp = "((c:1.0,d:2.0)foo:7.0,a:4.0)node0;"
new_master = tc.setup_master_tree(master_tree, [t1, t2])
self.assertEqual(new_master.getNewick(with_distances=True), exp)
desc_tips_root = frozenset(['a', 'c', 'd'])
desc_tips_c1 = frozenset(['a'])
desc_tips_c0 = frozenset(['c', 'd'])
desc_tips_c0c0 = frozenset(['c'])
desc_tips_c0c1 = frozenset(['d'])
self.assertEqual(frozenset(new_master.getTipNames()), desc_tips_root)
self.assertEqual(
frozenset(new_master.Children[0].getTipNames()),
desc_tips_c0)
self.assertEqual(
frozenset(new_master.Children[1].getTipNames()),
desc_tips_c1)
c0 = new_master.Children[0]
self.assertEqual(
frozenset(c0.Children[0].getTipNames()),
desc_tips_c0c0)
self.assertEqual(
frozenset(c0.Children[1].getTipNames()),
desc_tips_c0c1)
def test_setup_master_tree_alltips(self):
"""tests setup_master_tree"""
master_tree = parse_newick('((a:2,b:3):2,(c:1,d:2)foo:7);')
t1 = parse_newick('((a:6,b:8.2):2,(c:1,d:2):7);') # same structure
t2 = parse_newick('((a:2,b:3,c:33):2,d:7);') # abc are siblings
support_tree_tipnames = ['a','b','c','d']
exp = "((a:2.0,b:3.0)node1:2.0,(c:1.0,d:2.0)foo:7.0)node0;"
new_master = tc.setup_master_tree(master_tree, [t1,t2])
self.assertEqual(new_master.getNewick(with_distances=True),exp)
desc_tips_root = frozenset(['a','b','c','d'])
desc_tips_c0 = frozenset(['a','b'])
desc_tips_c1 = frozenset(['c','d'])
desc_tips_c0c0 = frozenset(['a'])
desc_tips_c0c1 = frozenset(['b'])
desc_tips_c1c0 = frozenset(['c'])
desc_tips_c1c1 = frozenset(['d'])
self.assertEqual(frozenset(new_master.getTipNames()), desc_tips_root)
self.assertEqual(frozenset(new_master.Children[0].getTipNames()), desc_tips_c0)
self.assertEqual(frozenset(new_master.Children[1].getTipNames()), desc_tips_c1)
c0 = master_tree.Children[0]
c1 = master_tree.Children[1]
self.assertEqual(frozenset(c0.Children[0].getTipNames()), desc_tips_c0c0)
self.assertEqual(frozenset(c0.Children[1].getTipNames()), desc_tips_c0c1)
self.assertEqual(frozenset(c1.Children[0].getTipNames()), desc_tips_c1c0)
self.assertEqual(frozenset(c1.Children[1].getTipNames()), desc_tips_c1c1)
def test_setup_master_tree_alltips(self):
"""tests setup_master_tree"""
master_tree = parse_newick("((a:2,b:3):2,(c:1,d:2)foo:7);")
t1 = parse_newick("((a:6,b:8.2):2,(c:1,d:2):7);") # same structure
t2 = parse_newick("((a:2,b:3,c:33):2,d:7);") # abc are siblings
support_tree_tipnames = ["a", "b", "c", "d"]
exp = "((a:2.0,b:3.0)node1:2.0,(c:1.0,d:2.0)foo:7.0)node0;"
new_master = tc.setup_master_tree(master_tree, [t1, t2])
self.assertEqual(new_master.getNewick(with_distances=True), exp)
desc_tips_root = frozenset(["a", "b", "c", "d"])
desc_tips_c0 = frozenset(["a", "b"])
desc_tips_c1 = frozenset(["c", "d"])
desc_tips_c0c0 = frozenset(["a"])
desc_tips_c0c1 = frozenset(["b"])
desc_tips_c1c0 = frozenset(["c"])
desc_tips_c1c1 = frozenset(["d"])
self.assertEqual(frozenset(new_master.getTipNames()), desc_tips_root)
self.assertEqual(frozenset(new_master.Children[0].getTipNames()), desc_tips_c0)
self.assertEqual(frozenset(new_master.Children[1].getTipNames()), desc_tips_c1)
c0 = master_tree.Children[0]
c1 = master_tree.Children[1]
self.assertEqual(frozenset(c0.Children[0].getTipNames()), desc_tips_c0c0)
self.assertEqual(frozenset(c0.Children[1].getTipNames()), desc_tips_c0c1)
self.assertEqual(frozenset(c1.Children[0].getTipNames()), desc_tips_c1c0)
self.assertEqual(frozenset(c1.Children[1].getTipNames()), desc_tips_c1c1)