def test_subset_samples(self):
"""Correctly subsets samples in a table."""
obs = _subset_table(json_table_str=self.biom_str1, axis='sample',
ids=['f4', 'f2'], hdf5_biom=None)
obs = parse_biom_table(list(obs[0]))
self.assertEqual(len(obs.ids()), 2)
self.assertEqual(len(obs.ids(axis='observation')), 14)
self.assertTrue('f4' in obs.ids())
self.assertTrue('f2' in obs.ids())
def test_subset_observations(self):
"""Correctly subsets observations in a table."""
obs = _subset_table(json_table_str=self.biom_str1, axis='observation',
ids=['None2', '879972'], hdf5_biom=None)
obs = parse_biom_table(list(obs[0]))
self.assertEqual(len(obs.ids()), 9)
self.assertEqual(len(obs.ids(axis='observation')), 2)
self.assertTrue('None2' in obs.ids(axis='observation'))
self.assertTrue('879972' in obs.ids(axis='observation'))
def test_subset_samples_hdf5(self):
"""Correctly subsets samples in a hdf5 table"""
cwd = os.getcwd()
if '/' in __file__:
os.chdir(__file__.rsplit('/', 1)[0])
obs = _subset_table(hdf5_biom='test_data/test.biom', axis='sample',
ids=[u'Sample1', u'Sample2', u'Sample3'],
json_table_str=None)
os.chdir(cwd)
obs = obs[0]
self.assertEqual(len(obs.ids()), 3)
self.assertEqual(len(obs.ids(axis='observation')), 5)
self.assertTrue(u'Sample1' in obs.ids())
self.assertTrue(u'Sample2' in obs.ids())
self.assertTrue(u'Sample3' in obs.ids())
def test_invalid_input(self):
"""Correctly raises politically correct error upon invalid input."""
with self.assertRaises(ValueError):
_subset_table(hdf5_biom=None, json_table_str=self.biom_str1, axis='foo',
ids=['f2', 'f4'])
with self.assertRaises(ValueError):
_subset_table(hdf5_biom=None, json_table_str=None, axis='sample', ids=['f2', 'f4'])
with self.assertRaises(ValueError):
_subset_table(json_table_str=self.biom_str1, hdf5_biom='foo',
axis='sample', ids=['f2', 'f4'])
def test_invalid_input(self):
"""Correctly raises politically correct error upon invalid input."""
with self.assertRaises(ValueError):
_subset_table(hdf5_biom=None, json_table_str=self.biom_str1,
axis='foo', ids=['f2', 'f4'])
with self.assertRaises(ValueError):
_subset_table(hdf5_biom=None, json_table_str=None, axis='sample',
ids=['f2', 'f4'])
with self.assertRaises(ValueError):
_subset_table(json_table_str=self.biom_str1, hdf5_biom='foo',
axis='sample', ids=['f2', 'f4'])