Python _count_matrix Examples

Example #1

File: test_balances.py Project: biocore/gneiss

    def test_count_matrix_base_case(self):
        tree = u"(a,b);"
        t = TreeNode.read([tree])
        res, _ = _count_matrix(t)
        exp = {'k': 0, 'l': 1, 'r': 1, 't': 0, 'tips': 2}
        self.assertEqual(res[t], exp)

        exp = {'k': 0, 'l': 0, 'r': 0, 't': 0, 'tips': 1}
        self.assertEqual(res[t[0]], exp)

        exp = {'k': 0, 'l': 0, 'r': 0, 't': 0, 'tips': 1}
        self.assertEqual(res[t[1]], exp)

Example #2

File: test_balances.py Project: thermokarst-forks/gneiss

    def test_count_matrix_base_case(self):
        tree = u"(a,b);"
        t = TreeNode.read([tree])
        res, _ = _count_matrix(t)
        exp = {'k': 0, 'l': 1, 'r': 1, 't': 0, 'tips': 2}
        self.assertEqual(res[t], exp)

        exp = {'k': 0, 'l': 0, 'r': 0, 't': 0, 'tips': 1}
        self.assertEqual(res[t[0]], exp)

        exp = {'k': 0, 'l': 0, 'r': 0, 't': 0, 'tips': 1}
        self.assertEqual(res[t[1]], exp)

Example #3

File: test_balances.py Project: thermokarst-forks/gneiss

    def test_count_matrix_unbalanced(self):
        tree = u"((a,b)c, d);"
        t = TreeNode.read([tree])
        res, _ = _count_matrix(t)

        exp = {'k': 0, 'l': 2, 'r': 1, 't': 0, 'tips': 3}
        self.assertEqual(res[t], exp)
        exp = {'k': 1, 'l': 1, 'r': 1, 't': 0, 'tips': 2}
        self.assertEqual(res[t[0]], exp)

        exp = {'k': 0, 'l': 0, 'r': 0, 't': 0, 'tips': 1}
        self.assertEqual(res[t[1]], exp)
        self.assertEqual(res[t[0][0]], exp)
        self.assertEqual(res[t[0][1]], exp)

Example #4

File: test_balances.py Project: biocore/gneiss

    def test_count_matrix_unbalanced(self):
        tree = u"((a,b)c, d);"
        t = TreeNode.read([tree])
        res, _ = _count_matrix(t)

        exp = {'k': 0, 'l': 2, 'r': 1, 't': 0, 'tips': 3}
        self.assertEqual(res[t], exp)
        exp = {'k': 1, 'l': 1, 'r': 1, 't': 0, 'tips': 2}
        self.assertEqual(res[t[0]], exp)

        exp = {'k': 0, 'l': 0, 'r': 0, 't': 0, 'tips': 1}
        self.assertEqual(res[t[1]], exp)
        self.assertEqual(res[t[0][0]], exp)
        self.assertEqual(res[t[0][1]], exp)

Example #5

File: test_balances.py Project: thermokarst-forks/gneiss

 def test_count_matrix_trifurcating_error(self):
     with self.assertRaises(ValueError):
         tree = u"((a,b,e)c, d);"
         t = TreeNode.read([tree])
         _count_matrix(t)

Example #6

File: test_balances.py Project: thermokarst-forks/gneiss

 def test_count_matrix_singleton_error(self):
     with self.assertRaises(ValueError):
         tree = u"(((a,b)c, d)root);"
         t = TreeNode.read([tree])
         _count_matrix(t)

Example #7

File: test_balances.py Project: biocore/gneiss

 def test_count_matrix_trifurcating_error(self):
     with self.assertRaises(ValueError):
         tree = u"((a,b,e)c, d);"
         t = TreeNode.read([tree])
         _count_matrix(t)

Example #8

File: test_balances.py Project: biocore/gneiss

 def test_count_matrix_singleton_error(self):
     with self.assertRaises(ValueError):
         tree = u"(((a,b)c, d)root);"
         t = TreeNode.read([tree])
         _count_matrix(t)