add calcTree tests to confirm not broken

Author: jamesmkrieger

prody/tests/utilities/test_catchall.py

@@ -0,0 +1,53 @@
+"""This module contains some unit tests for :mod:`prody.utilities.catchall` module,
+starting with calcTree."""
+
+import numpy as np
+
+from prody.tests import unittest
+from prody.utilities import calcTree
+
+class TestCalcTree(unittest.TestCase):
+
+    def testCalcTreeUPGMA(self):
+        """Test calcTree with UPGMA method."""
+        names = ['A', 'B', 'C', 'D']
+        distance_matrix = np.array([[0,   1,   2, 1],
+                                    [1,   0, 1.5, 2],
+                                    [2, 1.5,   0, 2],
+                                    [1,   2,   2, 0]])
+        tree = calcTree(names, distance_matrix, method='upgma')
+        self.assertIsNotNone(tree)
+        # Check that tree has 4 leaves and they include the names
+        leaves = tree.get_terminals()
+        self.assertEqual(len(leaves), 4)
+        self.assertEqual(set([leaf.name for leaf in leaves]), set(names))
+        # Check that the tree has split evenly as expected for UPGMA
+        self.assertEqual(len(tree.root.clades), 2)
+
+    def testCalcTreeNJ(self):
+        """Test calcTree with NJ method."""
+        names = ['A', 'B', 'C', 'D']
+        distance_matrix = np.array([[0,   1,   2, 1],
+                                    [1,   0, 1.5, 2],
+                                    [2, 1.5,   0, 2],
+                                    [1,   2,   2, 0]])
+        tree = calcTree(names, distance_matrix, method='nj')
+        self.assertIsNotNone(tree)
+        leaves = tree.get_terminals()
+        # Check that tree has 4 leaves and they include the names
+        self.assertEqual(len(leaves), 4)
+        self.assertEqual(set([leaf.name for leaf in leaves]), set(names))
+        # Check that the tree has split unevenly as expected for NJ
+        self.assertEqual(len(tree.root.clades), 3)
+
+    def testCalcTreeMismatchSize(self):
+        """Test calcTree with mismatched names and matrix sizes."""
+        names = ['A', 'B']
+        distance_matrix = np.array([[0, 1, 2],
+                                    [1, 0, 1.5],
+                                    [2, 1.5, 0]])
+        with self.assertRaises(ValueError):
+            calcTree(names, distance_matrix)
+
+if __name__ == '__main__':
+    unittest.main()