def test_addChildren(self):
"""RangeNode add_children should add specified # children to list"""
t = RangeNode()
t2 = RangeNode(Parent=t)
t.addChildren(5)
self.assertEqual(len(t.Children), 6)
assert t.Children[0] is t2
for c in t.Children:
assert c.Parent is t
def test_addChildren(self):
"""RangeNode add_children should add specified # children to list"""
t = RangeNode()
t2 = RangeNode(Parent=t)
t.addChildren(5)
self.assertEqual(len(t.Children), 6)
assert t.Children[0] is t2
for c in t.Children:
assert c.Parent is t
def __init__(self, Length=0, Array=None, *args, **kwargs):
"""Returns new MicroarrayNode object.
Length: float giving the branch length (sd to add to data)
Array: array of float giving the expression vector, or None
Additional args for superclass:
Name: usually a text label giving the name of the node
LeafRange: range of leaves that the node spans
Id: unique numeric identifier from the node
Children: list of Node objects specifying the children
Parent: Node object specifying the parent
"""
RangeNode.__init__(self, *args, **kwargs)
self.Length = Length
self.Array = Array
def __init__(self, Length=0, Array=None, *args, **kwargs):
"""Returns new MicroarrayNode object.
Length: float giving the branch length (sd to add to data)
Array: array of float giving the expression vector, or None
Additional args for superclass:
Name: usually a text label giving the name of the node
LeafRange: range of leaves that the node spans
Id: unique numeric identifier from the node
Children: list of Node objects specifying the children
Parent: Node object specifying the parent
"""
RangeNode.__init__(self, *args, **kwargs)
self.Length = Length
self.Array = Array
def test_init(self):
"""Make sure keyword arguments are being passed to baseclass"""
node = RangeNode(LeafRange=1, Id=2, Name='foo', Length=42)
self.assertEqual(node.LeafRange, 1)
self.assertEqual(node.Id, 2)
self.assertEqual(node.Name, 'foo')
self.assertEqual(node.Length, 42)
def test_str(self):
"""RangeNode should round-trip Newick string corrrectly."""
r = RangeNode()
self.assertEqual(str(r), '()')
#should work for tree with branch lengths set
t = DndParser(self.sample_tree_string, RangeNode)
expected = self.sample_tree_string.replace('\n', '')
expected = expected.replace(' ', '')
self.assertEqual(str(t), expected)
#self.assertEqual(t.getNewick(with_distances=True), expected)
#should also work for tree w/o branch lengths
t2 = DndParser(self.sample_string_2, RangeNode)
self.assertEqual(str(t2), self.sample_string_2)
def test_fromBreakpoints(self):
"""RangeNode fromBreakpoints should have correct topology"""
breakpoints = [4, 2, 1, 0, 3, 6, 5]
t = RangeNode.fromBreakpoints(breakpoints)
#check number of leaves
self.assertEqual(len(list(t.traverse())), 8)
self.assertEqual(len(list(t.traverse(self_before=True))), 15)
#check that leaves were created in right order
self.assertEqual([i.Id for i in t.traverse()], range(8))
#check that whole toplogy is right wrt ids...
nodes = list(t.traverse(self_before=True))
obs = [i.Id for i in nodes]
exp = [8, 9, 11, 13, 0, 1, 2, 12, 3, 4, 10, 14, 5, 6, 7]
self.assertEqual(obs, exp)
#...and ranges
obs = [i.LeafRange for i in nodes]
exp = [(0,8),(0,5),(0,3),(0,2),(0,1),(1,2),(2,3),(3,5),(3,4),(4,5), \
(5,8),(5,7),(5,6),(6,7),(7,8)]
self.assertEqual(obs, exp)
def test_fromBreakpoints(self):
"""RangeNode fromBreakpoints should have correct topology"""
breakpoints = [4,2,1,0,3,6,5]
t = RangeNode.fromBreakpoints(breakpoints)
#check number of leaves
self.assertEqual(len(list(t.traverse())), 8)
self.assertEqual(len(list(t.traverse(self_before=True))), 15)
#check that leaves were created in right order
self.assertEqual([i.Id for i in t.traverse()], range(8))
#check that whole toplogy is right wrt ids...
nodes = list(t.traverse(self_before=True))
obs = [i.Id for i in nodes]
exp = [8, 9, 11, 13, 0, 1, 2, 12, 3, 4, 10, 14, 5, 6, 7]
self.assertEqual(obs, exp)
#...and ranges
obs = [i.LeafRange for i in nodes]
exp = [(0,8),(0,5),(0,3),(0,2),(0,1),(1,2),(2,3),(3,5),(3,4),(4,5), \
(5,8),(5,7),(5,6),(6,7),(7,8)]
self.assertEqual(obs, exp)
def make_tree_arb_safe(t):
"""Gives a second child to all single descendent nodes"""
for n in t.nontips(include_self=True):
if len(n.Children) == 1:
n.append(RangeNode(Name="X",Length=0.0))