def test_Node_custom_length(self):
root = Node.create(length=100., length_formatter="{:0.1e}".format)
self.assertEqual(root.newick, ':1.0e+02')
weird_numbers_tree = "((a:1.e2,b:3j),(c:0x0BEFD6B0,d:003))"
root = loads(weird_numbers_tree, length_parser=None)[0]
self.assertEqual(weird_numbers_tree, root.newick)
with self.assertRaises(ValueError):
root = Node.create(length=1., length_formatter="({:0.1e})".format)
root.newick
def upgma(distance_matrix, names=None):
"""Cluster based on distance matrix dist using UPGMA
That is, the Unweighted Pair Group Method with Arithmetic Mean algorithm
If node names are given (not None), they must be a sequence of the same
length as the size of the square distance_matrix.
The edge lengths in the tree are not useful for the time being.
"""
# Initialize nodes
nodes = [Node(name) for name in (names or range(len(distance_matrix)))]
# Iterate until the number of clusters is k
nc = len(distance_matrix)
while nc > 1:
# Calculate the pairwise distance of each cluster, while searching for pair with least distance
minimum_distance = numpy.inf
i, j = 0, 1
for i in range(nc - 1):
for j in range(i + 1, nc):
dis = distance_matrix[i, j]
if dis < minimum_distance:
minimum_distance = dis
cluster = nodes[i], nodes[j]
indices = i, j
# Merge these two nodes into one new node
i, j = indices
distance_matrix[i] = 0.5 * (distance_matrix[i]) + 0.5 * (
distance_matrix[j])
distance_matrix[:, i] = 0.5 * (distance_matrix[:, i]) + 0.5 * (
distance_matrix[:, j])
nodes[i] = Node.create(descendants=cluster)
for c in cluster:
c.length = distance_matrix[i, i]
distance_matrix = numpy.delete(distance_matrix, j, 0)
distance_matrix = numpy.delete(distance_matrix, j, 1)
del nodes[j]
nc -= 1
return nodes[0]
def test_Node_custom_length():
root = Node.create(length='1e2', length_parser=lambda l: l + 'i')
assert root.length == '1e2i'
root = Node.create(length_formatter=lambda l: 5)
root.length = 10
assert root.length == pytest.approx(5)
def test_Node_custom_length(self):
root = Node.create(length='1e2', length_parser=lambda l: l + 'i')
self.assertEqual(root.length, '1e2i')
root = Node.create(length_formatter=lambda l: 5)
root.length = 10
self.assertAlmostEqual(root.length, 5)
def test_Node_custom_length():
root = Node.create(length='1e2', length_parser=lambda l: l + 'i')
assert root.length == '1e2i'
root = Node.create(length_formatter=lambda l: 5)
root.length = 10
assert root.length == pytest.approx(5)
def test_Node_custom_length(self):
root = Node.create(length='1e2', length_parser=lambda l: l + 'i')
self.assertEqual(root.length, '1e2i')
root = Node.create(length_formatter=lambda l: 5)
root.length = 10
self.assertAlmostEqual(root.length, 5)