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())
