def test_meta_unifrac_unbalanced(self):
with self.assertRaisesRegex(ValueError, ("Number of trees and tables "
"must be the same.")):
meta(('a', ), ('a', 'b'))
with self.assertRaisesRegex(ValueError, ("Number of trees and tables "
"must be the same.")):
meta(('a', 'b'), ('a', ))
def test_meta_unifrac(self):
"""meta_unifrac should give correct result on sample trees"""
t1 = self.get_data_path('t1.newick')
t2 = self.get_data_path('t2.newick')
e1 = self.get_data_path('e1.biom')
e2 = self.get_data_path('e2.biom')
result = meta([e1, e2], [t1, t2],
weights=[1, 1],
consolidation='skipping-missing-values',
method='unweighted')
u1_distances = np.array([[0, 10 / 16.,
8 / 13.], [10 / 16., 0, 8 / 17.],
[8 / 13., 8 / 17., 0]])
u2_distances = np.array([[0, 11 / 14.,
6 / 13.], [11 / 14., 0, 7 / 13.],
[6 / 13., 7 / 13., 0]])
exp = (u1_distances + u2_distances) / 2
npt.assert_almost_equal(exp, result.data)
self.assertEqual(tuple('ABC'), result.ids)
def test_meta_unifrac_alpha_not_generalized(self):
with self.assertRaisesRegex(ValueError, "The alpha parameter can"):
meta(('a', ), ('b', ),
method='generalized',
alpha=1,
consolidation='skipping_missing_matrices')
def test_meta_unifrac_bad_consolidation(self):
with self.assertRaisesRegex(ValueError,
"Consolidation \(foo\) unrecognized."):
meta(('a', ), ('b', ), method='unweighted', consolidation='foo')
def test_meta_unifrac_bad_method(self):
with self.assertRaisesRegex(ValueError, "Method \(bar\) "
"unrecognized."):
meta(('a', ), ('b', ), method='bar')
def test_meta_unifrac_no_consolidation(self):
with self.assertRaisesRegex(ValueError, "No consolidation specified."):
meta(('a', ), ('b', ), method='unweighted')
def test_meta_unifrac_no_method(self):
with self.assertRaisesRegex(ValueError, "No method specified."):
meta(('a', ), ('b', ))
def test_meta_unifrac_missing(self):
with self.assertRaisesRegex(ValueError, "No trees specified."):
meta(('a', ), tuple())
with self.assertRaisesRegex(ValueError, "No tables specified."):
meta(tuple(), ('a', ))
def test_meta_unifrac_unbalanced_weights(self):
with self.assertRaisesRegex(
ValueError, "Number of weights does not "
"match number of trees and "
"tables."):
meta(('c', 'd'), ('a', 'b'), weights=(1, 2, 3))