def condense_node_order(matrix, smallest_index, node_order):
"""condenses two nodes in node_order based on smallest_index info
This function is used to create a tree while condensing a matrix
with the condense_matrix function. The smallest_index is retrieved
with find_smallest_index. The first index is replaced with a node object
that combines the two nodes corresponding to the indices in node order.
The second index in smallest_index is replaced with None.
Also sets the branch length of the nodes to 1/2 of the distance between
the nodes in the matrix"""
index1 = smallest_index[0]
index2 = smallest_index[1]
node1 = node_order[index1]
node2 = node_order[index2]
#get the distance between the nodes and assign 1/2 the distance to the
#BranchLength property of each node
distance = matrix[index1, index2]
nodes = [node1,node2]
d = distance/2.0
for n in nodes:
if n.Children:
n.BranchLength = d - n.Children[0].TipLength
else:
n.BranchLength = d
n.TipLength = d
#combine the two nodes into a new PhyloNode object
new_node = PhyloNode()
new_node.append(node1)
new_node.append(node2)
#replace the object at index1 with the combined node
node_order[index1] = new_node
#replace the object at index2 with None
node_order[index2] = None
return node_order
def setUp(self):
"""creates inputs"""
#create a list of PhyloNode objects
a = PhyloNode()
a.Data = 'a'
b = PhyloNode()
b.Data = 'b'
c = PhyloNode()
c.Data = 'c'
d = PhyloNode()
d.Data = 'd'
e = PhyloNode()
e.Data = 'e'
self.node_order = [a, b, c, d, e]
#create a Numeric matrix object to cluster
self.matrix = array(([9999999, 1, 4, 20, 22], \
[1, 9999999, 5, 21, 23], \
[4, 5, 9999999, 10, 12], \
[20, 21, 10, 9999999, 2], \
[22, 23, 12, 2, 9999999]), Float)
def test_ops(self):
"""Basic PhyloNode operations should work as expected"""
p = PhyloNode()
self.assertEqual(str(p), "()")
p.Data = "abc"
self.assertEqual(str(p), "()abc")
p.BranchLength = 3
self.assertEqual(str(p), "()abc") # suppress branch from root
q = PhyloNode()
p.append(q)
self.assertEqual(str(p), "(None)abc")
r = PhyloNode()
q.append(r)
self.assertEqual(str(p), "((None))abc")
r.Data = "xyz"
self.assertEqual(str(p), "((xyz))abc")
q.BranchLength = 2
self.assertEqual(str(p), "((xyz):2)abc")
