def test_alpha_rarefaction_with_filtered_metadata_columns(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
# Empty column and numeric column should both be filtered.
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut', 'summer'],
'foo': [np.nan, np.nan, np.nan, 'bar'],
'bar': [42, 4.2, 99.9, 100.0]},
index=pd.Index(['S1', 'S2', 'S3', 'S4'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp, 'r') as fh:
contents = fh.read()
self.assertTrue('observed_otus' in contents)
self.assertTrue('shannon' in contents)
self.assertTrue('didn\'t contain categorical data' in contents)
self.assertTrue('consisted only of missing values:' in contents)
self.assertTrue('<strong>bar, foo' in contents)
metric_fp = os.path.join(output_dir, 'shannon-pet.jsonp')
with open(metric_fp) as metric_fh:
self.assertTrue('summer' not in metric_fh.read())
self.assertFalse(
os.path.exists(os.path.join(output_dir, 'shannon-foo.jsonp')))
self.assertFalse(
os.path.exists(os.path.join(output_dir, 'shannon-bar.jsonp')))
def test_alpha_rarefaction_with_filtered_metadata_columns(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
# Empty column and numeric column should both be filtered.
md = qiime2.Metadata(
pd.DataFrame(
{
'pet': ['russ', 'milo', 'peanut', 'summer'],
'foo': [np.nan, np.nan, np.nan, 'bar'],
'bar': [42, 4.2, 99.9, 100.0]
},
index=pd.Index(['S1', 'S2', 'S3', 'S4'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp, 'r') as fh:
contents = fh.read()
self.assertTrue('observed_features' in contents)
self.assertTrue('shannon' in contents)
self.assertTrue('didn\'t contain categorical data' in contents)
self.assertTrue('consisted only of missing values:' in contents)
self.assertTrue('<strong>bar, foo' in contents)
metric_fp = os.path.join(output_dir, 'shannon-pet.jsonp')
with open(metric_fp) as metric_fh:
self.assertTrue('summer' not in metric_fh.read())
self.assertFalse(
os.path.exists(
os.path.join(output_dir, 'shannon_entropy-foo.jsonp')))
self.assertFalse(
os.path.exists(
os.path.join(output_dir, 'shannon_entropy-bar.jsonp')))
def test_alpha_rarefaction_without_metadata(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue('observed_otus' in open(index_fp).read())
self.assertTrue('shannon' in open(index_fp).read())
def test_alpha_rarefaction_without_metadata(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp) as index_fh:
index_content = index_fh.read()
self.assertTrue('observed_features' in index_content)
self.assertTrue('shannon' in index_content)
def test_alpha_rarefaction_with_fully_filtered_metadata_columns(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
# All columns should both be filtered and raise an error
md = qiime2.Metadata(
pd.DataFrame({'foo': [np.nan, np.nan, np.nan, 'bar'],
'bar': [42, 4.2, 99.9, 100.0]},
index=pd.Index(['S1', 'S2', 'S3', 'S4'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
with self.assertRaisesRegex(ValueError, "non-categorical"):
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
def test_alpha_rarefaction_with_fully_filtered_metadata_columns(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
# All columns should both be filtered and raise an error
md = qiime2.Metadata(
pd.DataFrame({'foo': [np.nan, np.nan, np.nan, 'bar'],
'bar': [42, 4.2, 99.9, 100.0]},
index=pd.Index(['S1', 'S2', 'S3', 'S4'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
with self.assertRaisesRegex(ValueError, "non-categorical"):
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
def test_alpha_rarefaction_with_metadata(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut']},
index=['S1', 'S2', 'S3']))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue('observed_otus' in open(index_fp).read())
self.assertTrue('shannon' in open(index_fp).read())
def test_alpha_rarefaction_with_phylogeny(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
p = skbio.TreeNode.read(io.StringIO(
'((O1:0.25, O2:0.50):0.25, O3:0.75)root;'))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, phylogeny=p)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue('observed_otus' in open(index_fp).read())
self.assertTrue('shannon' in open(index_fp).read())
self.assertTrue('faith_pd' in open(index_fp).read())
def test_alpha_rarefaction_with_metadata(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp) as index_fh:
index_content = index_fh.read()
self.assertTrue('observed_features' in index_content)
self.assertTrue('shannon' in index_content)
def test_alpha_rarefaction_with_phylogeny(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
p = skbio.TreeNode.read(
io.StringIO('((O1:0.25, O2:0.50):0.25, O3:0.75)root;'))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, phylogeny=p)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp) as index_fh:
index_content = index_fh.read()
self.assertTrue('observed_otus' in index_content)
self.assertTrue('shannon' in index_content)
self.assertTrue('faith_pd' in index_content)
def test_alpha_rarefaction_with_metric_set(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
metrics = set(['observed_otus', 'shannon', 'pielou_e'])
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, metrics=metrics,
max_depth=200)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp) as index_fh:
index_content = index_fh.read()
self.assertTrue('observed_otus' in index_content)
self.assertTrue('shannon' in index_content)
self.assertTrue('pielou_e' in index_content)
def test_alpha_rarefaction_with_metadata_column_with_spaces(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
md = qiime2.Metadata(
pd.DataFrame({'pet name': ['russ', 'milo', 'peanut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp) as index_fh:
self.assertTrue('pet%2520name' in index_fh.read())
jsonp_fp = os.path.join(output_dir, 'shannon-pet%20name.jsonp')
self.assertTrue(os.path.exists(jsonp_fp))
with open(jsonp_fp) as jsonp_fh:
self.assertTrue('pet name' in jsonp_fh.read())
def test_alpha_rarefaction_with_metadata_column_with_spaces(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
md = qiime2.Metadata(
pd.DataFrame({'pet name': ['russ', 'milo', 'peanut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp) as index_fh:
self.assertTrue('pet%2520name' in index_fh.read())
jsonp_fp = os.path.join(output_dir, 'shannon-pet%20name.jsonp')
self.assertTrue(os.path.exists(jsonp_fp))
with open(jsonp_fp) as jsonp_fh:
self.assertTrue('pet name' in jsonp_fh.read())
def test_alpha_rarefaction_with_superset_metadata(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut', 'summer']},
index=pd.Index(['S1', 'S2', 'S3', 'S4'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp) as index_fh:
index_content = index_fh.read()
self.assertTrue('observed_otus' in index_content)
self.assertTrue('shannon' in index_content)
metric_fp = os.path.join(output_dir, 'shannon-pet.jsonp')
with open(metric_fp) as metric_fh:
self.assertTrue('summer' not in metric_fh.read())
def test_alpha_rarefaction_with_phylogeny_and_metadata(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
p = skbio.TreeNode.read(io.StringIO(
'((O1:0.25, O2:0.50):0.25, O3:0.75)root;'))
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut']},
index=['S1', 'S2', 'S3']))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, phylogeny=p,
metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue('observed_otus' in open(index_fp).read())
self.assertTrue('shannon' in open(index_fp).read())
self.assertTrue('faith_pd' in open(index_fp).read())
def test_alpha_rarefaction_with_phylogeny_and_metadata(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
p = self._to_newick(skbio.TreeNode.read(io.StringIO(
'((O1:0.25, O2:0.50):0.25, O3:0.75)root;')))
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, phylogeny=p,
metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp) as index_fh:
index_content = index_fh.read()
self.assertTrue('observed_features' in index_content)
self.assertTrue('shannon' in index_content)
self.assertTrue('faith_pd' in index_content)
def test_alpha_rarefaction_with_empty_column_in_metadata(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut', 'summer'],
'foo': [np.nan, np.nan, np.nan, 'bar']},
index=['S1', 'S2', 'S3', 'S4']))
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, max_depth=200, metadata=md)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
with open(index_fp, 'r') as fh:
contents = fh.read()
self.assertTrue('observed_otus' in contents)
self.assertTrue('shannon' in contents)
self.assertTrue('did not contain any values:' in contents)
metric_fp = os.path.join(output_dir, 'shannon-pet.jsonp')
self.assertTrue('summer' not in open(metric_fp).read())
self.assertFalse(
os.path.exists(os.path.join(output_dir, 'shannon-foo.jsonp')))
def test_invalid_invocations(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id')))
empty_table = biom.Table(np.array([]), [], [])
bad_metadata = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'summer']},
index=pd.Index(['S1', 'S2', 'S4'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
with self.assertRaisesRegex(ValueError, 'must be greater'):
alpha_rarefaction(output_dir, t, min_depth=200, max_depth=1,
metadata=md)
with self.assertRaisesRegex(ValueError, 'phylogeny was not'):
alpha_rarefaction(output_dir, t, max_depth=200,
metadata=md, metrics=set(['faith_pd']))
with self.assertRaisesRegex(ValueError, 'Unknown metric: pole'):
alpha_rarefaction(output_dir, t, max_depth=200,
metadata=md, metrics=set(['pole-position']))
with self.assertRaisesRegex(ValueError, 'max_depth'):
alpha_rarefaction(output_dir, t, max_depth=1000)
with self.assertRaisesRegex(ValueError, 'steps'):
alpha_rarefaction(output_dir, t, max_depth=2)
with self.assertRaisesRegex(ValueError, 'empty'):
alpha_rarefaction(output_dir, empty_table, max_depth=200)
with self.assertRaisesRegex(ValueError, 'not present.*S3'):
alpha_rarefaction(output_dir, t, metadata=bad_metadata,
max_depth=200)
with self.assertRaisesRegex(ValueError, 'empty set'):
alpha_rarefaction(output_dir, t, max_depth=200,
metadata=md, metrics=set())
def test_invalid_invocations(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut']},
index=['S1', 'S2', 'S3']))
empty_table = biom.Table(np.array([]), [], [])
bad_metadata = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'summer']},
index=['S1', 'S2', 'S4']))
with tempfile.TemporaryDirectory() as output_dir:
with self.assertRaisesRegex(ValueError, 'must be greater'):
alpha_rarefaction(output_dir, t, min_depth=200, max_depth=1,
metadata=md)
with self.assertRaisesRegex(ValueError, 'phylogeny was not'):
alpha_rarefaction(output_dir, t, max_depth=200,
metadata=md, metrics=set(['faith_pd']))
with self.assertRaisesRegex(ValueError, 'Unknown metric: pole'):
alpha_rarefaction(output_dir, t, max_depth=200,
metadata=md, metrics=set(['pole-position']))
with self.assertRaisesRegex(ValueError, 'max_depth'):
alpha_rarefaction(output_dir, t, max_depth=1000)
with self.assertRaisesRegex(ValueError, 'steps'):
alpha_rarefaction(output_dir, t, max_depth=2)
with self.assertRaisesRegex(ValueError, 'empty'):
alpha_rarefaction(output_dir, empty_table, max_depth=200)
with self.assertRaisesRegex(ValueError, 'Missing'):
alpha_rarefaction(output_dir, t, metadata=bad_metadata,
max_depth=200)
with self.assertRaisesRegex(ValueError, 'empty set'):
alpha_rarefaction(output_dir, t, max_depth=200,
metadata=md, metrics=set())
def test_alpha_rarefaction_with_metric_set(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'],
['S1', 'S2', 'S3'])
metrics = set(['observed_otus', 'shannon', 'pielou_e'])
with tempfile.TemporaryDirectory() as output_dir:
alpha_rarefaction(output_dir, t, metrics=metrics,
max_depth=200)
index_fp = os.path.join(output_dir, 'index.html')
self.assertTrue(os.path.exists(index_fp))
self.assertTrue('observed_otus' in open(index_fp).read())
self.assertTrue('shannon' in open(index_fp).read())
self.assertTrue('pielou_e' in open(index_fp).read())
def test_invalid_invocations(self):
t = biom.Table(np.array([[100, 111, 113], [111, 111, 112]]),
['O1', 'O2'], ['S1', 'S2', 'S3'])
md = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'peanut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id')))
empty_table = biom.Table(np.array([]), [], [])
bad_metadata = qiime2.Metadata(
pd.DataFrame({'pet': ['russ', 'milo', 'summer']},
index=pd.Index(['S1', 'S2', 'S4'], name='id')))
with tempfile.TemporaryDirectory() as output_dir:
with self.assertRaisesRegex(ValueError, 'must be greater'):
alpha_rarefaction(output_dir,
t,
min_depth=200,
max_depth=1,
metadata=md)
with self.assertRaisesRegex(ValueError, 'phylogeny was not'):
alpha_rarefaction(output_dir,
t,
max_depth=200,
metadata=md,
metrics=set(['faith_pd']))
with self.assertRaisesRegex(TypeError, 'pole.*incompatible'):
alpha_rarefaction(output_dir,
t,
max_depth=200,
metadata=md,
metrics=set(['pole-position']))
with self.assertRaisesRegex(ValueError, 'max_depth'):
alpha_rarefaction(output_dir, t, max_depth=1000)
with self.assertRaisesRegex(ValueError, 'steps'):
alpha_rarefaction(output_dir, t, max_depth=2)
with self.assertRaisesRegex(ValueError, 'empty'):
alpha_rarefaction(output_dir, empty_table, max_depth=200)
with self.assertRaisesRegex(ValueError, 'not present.*S3'):
alpha_rarefaction(output_dir,
t,
metadata=bad_metadata,
max_depth=200)
with self.assertRaisesRegex(ValueError, 'empty set'):
alpha_rarefaction(output_dir,
t,
max_depth=200,
metadata=md,
metrics=set())