def test_bioenv_zero_variance_column(self): dm = skbio.DistanceMatrix( [[0.00, 0.25, 0.25], [0.25, 0.00, 0.00], [0.25, 0.00, 0.00]], ids=['sample1', 'sample2', 'sample3']) md = qiime2.Metadata( pd.DataFrame([['1.0', '2.0'], ['2.0', '2.0'], ['3.0', '2.0']], index=['sample1', 'sample2', 'sample3'], columns=['metadata1', 'metadata2'])) with tempfile.TemporaryDirectory() as output_dir: bioenv(output_dir, dm, md) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue('metadata1' in open(index_fp).read()) self.assertTrue('no variance' in open(index_fp).read()) self.assertTrue('<strong>metadata2' in open(index_fp).read()) self.assertFalse('Warning' in open(index_fp).read())
def test_bioenv_exclude_missing_data(self): dm = skbio.DistanceMatrix( [[0.00, 0.25, 0.25], [0.25, 0.00, 0.00], [0.25, 0.00, 0.00]], ids=['sample1', 'sample2', 'sample3']) md = qiime2.Metadata( pd.DataFrame([['1.0', '2.0'], ['2.0', ''], ['3.0', '42.0']], index=['sample1', 'sample2', 'sample3'], columns=['metadata1', 'metadata2'])) with tempfile.TemporaryDirectory() as output_dir: bioenv(output_dir, dm, md) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) self.assertTrue('metadata1' in open(index_fp).read()) self.assertTrue('metadata2' in open(index_fp).read()) self.assertTrue('Warning' in open(index_fp).read()) self.assertTrue('contained 3 samples' in open(index_fp).read()) self.assertTrue('2 samples' in open(index_fp).read())
def test_bioenv_zero_variance_column(self): dm = skbio.DistanceMatrix([[0.00, 0.25, 0.25], [0.25, 0.00, 0.00], [0.25, 0.00, 0.00]], ids=['sample1', 'sample2', 'sample3']) md = qiime2.Metadata( pd.DataFrame([['1.0', '2.0'], ['2.0', '2.0'], ['3.0', '2.0']], index=['sample1', 'sample2', 'sample3'], columns=['metadata1', 'metadata2'])) with tempfile.TemporaryDirectory() as output_dir: bioenv(output_dir, dm, md) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue('metadata1' in open(index_fp).read()) self.assertTrue('no variance' in open(index_fp).read()) self.assertTrue('<strong>metadata2' in open(index_fp).read()) self.assertFalse('Warning' in open(index_fp).read())
def test_bioenv_exclude_missing_data(self): dm = skbio.DistanceMatrix([[0.00, 0.25, 0.25], [0.25, 0.00, 0.00], [0.25, 0.00, 0.00]], ids=['sample1', 'sample2', 'sample3']) md = qiime2.Metadata( pd.DataFrame([['1.0', '2.0'], ['2.0', ''], ['3.0', '42.0']], index=['sample1', 'sample2', 'sample3'], columns=['metadata1', 'metadata2'])) with tempfile.TemporaryDirectory() as output_dir: bioenv(output_dir, dm, md) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) self.assertTrue('metadata1' in open(index_fp).read()) self.assertTrue('metadata2' in open(index_fp).read()) self.assertTrue('Warning' in open(index_fp).read()) self.assertTrue('contained 3 samples' in open(index_fp).read()) self.assertTrue('2 samples' in open(index_fp).read())
def test_bioenv(self): dm = skbio.DistanceMatrix( [[0.00, 0.25, 0.25], [0.25, 0.00, 0.00], [0.25, 0.00, 0.00]], ids=['sample1', 'sample2', 'sample3']) md = qiime2.Metadata( pd.DataFrame([[1.0, 'a'], [2.0, 'b'], [3.0, 'c']], index=pd.Index(['sample1', 'sample2', 'sample3'], name='id'), columns=['metadata1', 'metadata2'])) with tempfile.TemporaryDirectory() as output_dir: bioenv(output_dir, dm, md) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) self.assertTrue('metadata1' in open(index_fp).read()) self.assertTrue('not numeric:' in open(index_fp).read()) self.assertTrue('<strong>metadata2' in open(index_fp).read()) self.assertFalse('Warning' in open(index_fp).read())
def test_bioenv(self): dm = skbio.DistanceMatrix([[0.00, 0.25, 0.25], [0.25, 0.00, 0.00], [0.25, 0.00, 0.00]], ids=['sample1', 'sample2', 'sample3']) md = qiime2.Metadata( pd.DataFrame( [[1.0, 'a'], [2.0, 'b'], [3.0, 'c']], index=pd.Index(['sample1', 'sample2', 'sample3'], name='id'), columns=['metadata1', 'metadata2'])) with tempfile.TemporaryDirectory() as output_dir: bioenv(output_dir, dm, md) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) self.assertTrue('metadata1' in open(index_fp).read()) self.assertTrue('not numeric:' in open(index_fp).read()) self.assertTrue('<strong>metadata2' in open(index_fp).read()) self.assertFalse('Warning' in open(index_fp).read())