def join_nodes(parsed):
"""Join the nodes from tips up
expects parsed to go from high -> low similarity, ie:
99, 97, 94, ...
"""
last_lookup, last_nodes = parsed[0]
for lookup, nodes in parsed[1:]:
for n in nodes:
replace_nodes = [last_lookup[c.Name] for c in n.Children]
new_c = []
todelete = set([])
for c in n.Children:
last_lookup[c.Name].Length = c.Length
new_c.append(last_lookup[c.Name])
todelete.add(c)
n.removeDeleted(lambda x: x in todelete)
for c in new_c:
n.append(c)
last_lookup = lookup
last_nodes = nodes
root = PhyloNode()
for c in last_nodes:
root.append(c)
return root
def test_missing_tip_name(self):
"""DndParser should produce the correct tree when missing a name"""
obs = DndParser(missing_tip_name)
exp = PhyloNode()
exp.append(PhyloNode())
exp.append(PhyloNode())
exp.Children[0].append(PhyloNode(Name='a'))
exp.Children[0].append(PhyloNode(Name='b'))
exp.Children[1].append(PhyloNode(Name='c'))
exp.Children[1].append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_nonames(self):
"""DndParser should produce the correct tree when there are no names"""
obs = DndParser(no_names)
exp = PhyloNode()
exp.append(PhyloNode())
exp.append(PhyloNode())
exp.Children[0].append(PhyloNode())
exp.Children[0].append(PhyloNode())
exp.Children[1].append(PhyloNode())
exp.Children[1].append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_missing_tip_name(self):
"""DndParser should produce the correct tree when missing a name"""
obs = DndParser(missing_tip_name)
exp = PhyloNode()
exp.append(PhyloNode())
exp.append(PhyloNode())
exp.Children[0].append(PhyloNode(Name='a'))
exp.Children[0].append(PhyloNode(Name='b'))
exp.Children[1].append(PhyloNode(Name='c'))
exp.Children[1].append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_nonames(self):
"""DndParser should produce the correct tree when there are no names"""
obs = DndParser(no_names)
exp = PhyloNode()
exp.append(PhyloNode())
exp.append(PhyloNode())
exp.Children[0].append(PhyloNode())
exp.Children[0].append(PhyloNode())
exp.Children[1].append(PhyloNode())
exp.Children[1].append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_gops(self):
"""Basic PhyloNode operations should work as expected"""
p = PhyloNode()
self.assertEqual(str(p), ';')
p.Name = 'abc'
self.assertEqual(str(p), 'abc;')
p.Length = 3
self.assertEqual(str(p), 'abc:3;') #don't suppress branch from root
q = PhyloNode()
p.append(q)
self.assertEqual(str(p), '()abc:3;')
r = PhyloNode()
q.append(r)
self.assertEqual(str(p), '(())abc:3;')
r.Name = 'xyz'
self.assertEqual(str(p), '((xyz))abc:3;')
q.Length = 2
self.assertEqual(str(p), '((xyz):2)abc:3;')
def test_gops(self):
"""Basic PhyloNode operations should work as expected"""
p = PhyloNode()
self.assertEqual(str(p), ';')
p.Name = 'abc'
self.assertEqual(str(p), 'abc;')
p.Length = 3
self.assertEqual(str(p), 'abc:3;') #don't suppress branch from root
q = PhyloNode()
p.append(q)
self.assertEqual(str(p), '()abc:3;')
r = PhyloNode()
q.append(r)
self.assertEqual(str(p), '(())abc:3;')
r.Name = 'xyz'
self.assertEqual(str(p), '((xyz))abc:3;')
q.Length = 2
self.assertEqual(str(p), '((xyz):2)abc:3;')
def test_gops(self):
"""Basic PhyloNode operations should work as expected"""
p = PhyloNode()
self.assertEqual(str(p), ";")
p.Name = "abc"
self.assertEqual(str(p), "abc;")
p.Length = 3
self.assertEqual(str(p), "abc:3;") # don't suppress branch from root
q = PhyloNode()
p.append(q)
self.assertEqual(str(p), "()abc:3;")
r = PhyloNode()
q.append(r)
self.assertEqual(str(p), "(())abc:3;")
r.Name = "xyz"
self.assertEqual(str(p), "((xyz))abc:3;")
q.Length = 2
self.assertEqual(str(p), "((xyz):2)abc:3;")
def test_minimal(self):
"""DndParser should produce the correct minimal tree"""
obs = DndParser(minimal)
exp = PhyloNode()
exp.append(PhyloNode())
self.assertEqual(str(obs), str(exp))
def test_minimal(self):
"""DndParser should produce the correct minimal tree"""
obs = DndParser(minimal)
exp = PhyloNode()
exp.append(PhyloNode())
self.assertEqual(str(obs), str(exp))
