Exemplo n.º 1
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 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())
Exemplo n.º 2
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 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'))
Exemplo n.º 3
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 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())
Exemplo n.º 4
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    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'])
Exemplo n.º 5
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    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'])