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import io
from unittest import TestCase, main
from skbio import DistanceMatrix, TreeNode
from skbio.tree._upgma import (
upgma
)
class UpgmaTests(TestCase):
def setUp(self):
data = [[0, 5, 9, 9, 8],
[5, 0, 10, 10, 9],
[9, 10, 0, 8, 7],
[9, 10, 8, 0, 3],
[8, 9, 7, 3, 0]]
ids = list('abcde')
self.dm = DistanceMatrix(data, ids)
# Note that upgma and wpgma have different edge
# estimations, even with small examples.
self.expected_str_upgma = (
"((a:2.5,b:2.5):2.083333333333333,(c:3.75,(d:1.5,e:1.5):2.25):0.833333333333333);")
self.expected_str_wpgma = (
"((a:2.5,b:2.5):2.125,(c:3.75,(d:1.5,e:1.5):2.25):0.875);")
self.expected_TreeNode_upgma = TreeNode.read(
io.StringIO(self.expected_str_upgma))
self.expected_TreeNode_wpgma = TreeNode.read(
io.StringIO(self.expected_str_wpgma))
def test_upgma_dm(self):
actual_TreeNode = upgma(self.dm)
self.assertAlmostEqual(actual_TreeNode.compare_cophenet(
self.expected_TreeNode_upgma), 0.0, places=10)
def test_wpgma_dm(self):
actual_TreeNode = upgma(self.dm, weighted=True)
self.assertAlmostEqual(actual_TreeNode.compare_cophenet(
self.expected_TreeNode_wpgma), 0.0, places=10)
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