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)
