def test_uc_w_comments_and_blank_lines(self): """ uc contains comments and blank lines """ actual = _parse_uc(uc_w_comments_and_blank_lines.split('\n')) expected = biom.Table(np.array([[1.0]]), observation_ids=['f2_1539'], sample_ids=['f2']) self.assertEqual(actual, expected)
def test_mixed_hits(self): """ new and library seeds observed """ actual = _parse_uc(uc_mixed_hits.split('\n')) expected = biom.Table(np.array([[2.0, 1.0], [0.0, 1.0], [1.0, 0.0]]), observation_ids=['f2_1539', 'f3_44', '295053'], sample_ids=['f2', 'f3']) self.assertEqual(actual, expected)
def test_seed_hits(self): """ multiple new seeds observed """ actual = _parse_uc(uc_seed_hits.split('\n')) expected = biom.Table(np.array([[2.0, 1.0], [0.0, 1.0]]), observation_ids=['f2_1539', 'f3_44'], sample_ids=['f2', 'f3']) self.assertEqual(actual, expected)
def test_lib_minimal(self): """ single library seed observed """ actual = _parse_uc(uc_lib_minimal.split('\n')) expected = biom.Table(np.array([[1.0]]), observation_ids=['295053'], sample_ids=['f2']) self.assertEqual(actual, expected)
def test_empty(self): """ empty uc file returns empty Table """ actual = _parse_uc(uc_empty.split('\n')) expected = biom.Table(np.array([[]]), observation_ids=[], sample_ids=[]) self.assertEqual(actual, expected)
def test_underscore_in_sample_id(self): """ single new seed observed for sample with underscores in id """ actual = _parse_uc(uc_minimal_w_underscores.split('\n')) expected = biom.Table(np.array([[1.0]]), observation_ids=['sample_id_w_underscores_42'], sample_ids=['sample_id_w_underscores']) print(actual) print(expected) self.assertEqual(actual, expected)