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 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, index2 = smallest_index
node1 = node_order[index1]
node2 = node_order[index2]
#get the distance between the nodes and assign 1/2 the distance to the
#Length property of each node
distance = matrix[index1, index2]
nodes = [node1, node2]
d = distance / 2.0
for n in nodes:
if n.Children:
n.Length = d - n.Children[0].TipLength
else:
n.Length = d
n.TipLength = d
#combine the two nodes into a new PhyloNode object
new_node = PhyloNode()
new_node.Children.append(node1)
new_node.Children.append(node2)
node1.Parent = new_node
node2.Parent = new_node
#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 make_nodes(otu_map, length, level):
"""returns nodes that have been created outta the map"""
nodedist = length / 2.0
nodes = []
lookup = {}
for clusterid, seqids in otu_map:
rep = seqids[0]
children = []
for id_ in seqids:
node = PhyloNode(Name=id_, Length=nodedist)
children.append(node)
parent = PhyloNode(Name="_".join(map(str, [level,clusterid,rep])),
Length=None, Children=children)
nodes.append(parent)
lookup[rep] = parent
return lookup,nodes
def inputs_from_dict2D(dict2d_matrix):
"""makes inputs for UPGMA_cluster from a Dict2D object
Dict2D object is a distance matrix with labeled Rows. The diagonal
elements should have a very large positive number assigned (e.g.1e305).
The returned array is a numpy array with the distances.
PhyloNode_order is a list of PhyloNode objects with the Data property
assigned from the Dict2D Row order.
"""
matrix_lists = list(dict2d_matrix.Rows)
matrix = array(matrix_lists, Float)
row_order = dict2d_matrix.RowOrder
PhyloNode_order = []
for i in row_order:
PhyloNode_order.append(PhyloNode(Name=i))
return matrix, PhyloNode_order
def test_make_nodes(self):
"""makes nodes..."""
exp_99_0_10 = PhyloNode(Name="10",Length=0.005)
exp_99_0_20 = PhyloNode(Name="20",Length=0.005)
exp_99_0_30 = PhyloNode(Name="30",Length=0.005)
exp_99_0 = PhyloNode(Name="99_0_10",Length=None, Children=\
[exp_99_0_10,exp_99_0_20,exp_99_0_30])
exp_99_1_1 = PhyloNode(Name="1",Length=0.005)
exp_99_1_6 = PhyloNode(Name="6",Length=0.005)
exp_99_1 = PhyloNode(Name="99_1_1",Length=None, Children=\
[exp_99_1_1,exp_99_1_6])
exp_99_2_3 = PhyloNode(Name="3", Length=0.005)
exp_99_2 = PhyloNode(Name="99_2_3", Length=None, Children=[exp_99_2_3])
exp_99_3_8 = PhyloNode(Name="8", Length=0.005)
exp_99_3_7 = PhyloNode(Name="7", Length=0.005)
exp_99_3 = PhyloNode(Name="99_3_8", Length=None, Children=\
[exp_99_3_8,exp_99_3_7])
exp_lookup = {'10':exp_99_0,'1':exp_99_1,'3':exp_99_2,'8':exp_99_3}
lookup, nodes = make_nodes(self.clst_99, 0.01, 99)
self.assertEqual(nodes[0].getNewick(with_distances=True),
exp_99_0.getNewick(with_distances=True))
self.assertEqual(nodes[1].getNewick(with_distances=True),
exp_99_1.getNewick(with_distances=True))
self.assertEqual(nodes[2].getNewick(with_distances=True),
exp_99_2.getNewick(with_distances=True))
self.assertEqual(nodes[3].getNewick(with_distances=True),
exp_99_3.getNewick(with_distances=True))
self.assertEqual(len(nodes), 4)
self.assertEqual(lookup.keys(), exp_lookup.keys())
self.assertEqual(map(str, lookup.values()),
map(str,exp_lookup.values()))
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_make_nodes(self):
"""makes nodes..."""
exp_99_0_10 = PhyloNode(Name="10", Length=0.005)
exp_99_0_20 = PhyloNode(Name="20", Length=0.005)
exp_99_0_30 = PhyloNode(Name="30", Length=0.005)
exp_99_0 = PhyloNode(Name="99_0_10",Length=None, Children=\
[exp_99_0_10,exp_99_0_20,exp_99_0_30])
exp_99_1_1 = PhyloNode(Name="1", Length=0.005)
exp_99_1_6 = PhyloNode(Name="6", Length=0.005)
exp_99_1 = PhyloNode(Name="99_1_1",Length=None, Children=\
[exp_99_1_1,exp_99_1_6])
exp_99_2_3 = PhyloNode(Name="3", Length=0.005)
exp_99_2 = PhyloNode(Name="99_2_3", Length=None, Children=[exp_99_2_3])
exp_99_3_8 = PhyloNode(Name="8", Length=0.005)
exp_99_3_7 = PhyloNode(Name="7", Length=0.005)
exp_99_3 = PhyloNode(Name="99_3_8", Length=None, Children=\
[exp_99_3_8,exp_99_3_7])
exp_lookup = {
'10': exp_99_0,
'1': exp_99_1,
'3': exp_99_2,
'8': exp_99_3
}
lookup, nodes = make_nodes(self.clst_99, 0.01, 99)
self.assertEqual(nodes[0].getNewick(with_distances=True),
exp_99_0.getNewick(with_distances=True))
self.assertEqual(nodes[1].getNewick(with_distances=True),
exp_99_1.getNewick(with_distances=True))
self.assertEqual(nodes[2].getNewick(with_distances=True),
exp_99_2.getNewick(with_distances=True))
self.assertEqual(nodes[3].getNewick(with_distances=True),
exp_99_3.getNewick(with_distances=True))
self.assertEqual(len(nodes), 4)
self.assertEqual(lookup.keys(), exp_lookup.keys())
self.assertEqual(map(str, lookup.values()),
map(str, exp_lookup.values()))
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_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;")