def test_with_exclude_ids_filter_all(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
with self.assertRaisesRegex(ValueError, "All samples.*filtered"):
filter_distance_matrix(dm, metadata, where=None, exclude_ids=True)
def test_without_where_all_filtered(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S4', 'S5', 'S6'])
with self.assertRaisesRegex(ValueError, 'All samples.*filtered'):
filter_distance_matrix(dm, metadata)
def test_without_where_all_filtered(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S4', 'S5', 'S6'])
with self.assertRaisesRegex(ValueError, 'All samples.*filtered'):
filter_distance_matrix(dm, metadata)
def test_with_exclude_ids_filter_all(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
with self.assertRaisesRegex(ValueError, "All samples.*filtered"):
filter_distance_matrix(dm, metadata, where=None, exclude_ids=True)
def test_with_where_no_filtering(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
filtered = filter_distance_matrix(
dm, metadata, where="SampleType='gut' OR SampleType='tongue'")
self.assertEqual(self._sorted(filtered), dm)
def test_without_where_some_filtered(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1'],
'SampleType': ['gut', 'tongue']},
index=pd.Index(['S1', 'S2'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
filtered = filter_distance_matrix(dm, metadata)
expected = skbio.DistanceMatrix([[0, 1], [1, 0]], ['S1', 'S2'])
self.assertEqual(self._sorted(filtered), expected)
def test_with_exclude_ids_filter_nothing(self):
df = pd.DataFrame({'Subject': ['subject-1'],
'SampleType': ['tongue']},
index=pd.Index(['S2000'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
filtered = filter_distance_matrix(dm, metadata,
where=None,
exclude_ids=True)
self.assertEqual(self._sorted(filtered), dm)
def test_with_where_no_filtering(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
filtered = filter_distance_matrix(
dm, metadata, where="SampleType='gut' OR SampleType='tongue'")
self.assertEqual(self._sorted(filtered), dm)
def test_without_where_some_filtered(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1'],
'SampleType': ['gut', 'tongue']},
index=pd.Index(['S1', 'S2'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
filtered = filter_distance_matrix(dm, metadata)
expected = skbio.DistanceMatrix([[0, 1], [1, 0]], ['S1', 'S2'])
self.assertEqual(self._sorted(filtered), expected)
def test_with_exclude_ids_filter_nothing(self):
df = pd.DataFrame({'Subject': ['subject-1'],
'SampleType': ['tongue']},
index=pd.Index(['S2000'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
filtered = filter_distance_matrix(dm, metadata,
where=None,
exclude_ids=True)
self.assertEqual(self._sorted(filtered), dm)
def test_without_where_no_filtering(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
filtered = filter_distance_matrix(dm, metadata)
# There is no guaranteed order to output. Sort by ID before comparing
# to expected.
self.assertEqual(self._sorted(filtered), dm)
def test_without_where_no_filtering(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
filtered = filter_distance_matrix(dm, metadata)
# There is no guaranteed order to output. Sort by ID before comparing
# to expected.
self.assertEqual(self._sorted(filtered), dm)
def test_with_where_some_filtered(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['gut', 'tongue', 'gut']},
index=['S1', 'S2', 'S3'])
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
filtered = filter_distance_matrix(dm, metadata,
where="Subject='subject-2'")
expected = skbio.DistanceMatrix([[0]], ['S3'])
self.assertEqual(filtered, expected)
def test_with_exclude_ids_where_filter_two(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['elbow', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
where = "SampleType='tongue' OR SampleType='gut'"
filtered = filter_distance_matrix(dm, metadata,
where,
exclude_ids=True)
expected = skbio.DistanceMatrix([[0]], ['S1'])
self.assertEqual(filtered, expected)
def test_with_exclude_ids_where_filter_two(self):
df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'],
'SampleType': ['elbow', 'tongue', 'gut']},
index=pd.Index(['S1', 'S2', 'S3'], name='id'))
metadata = qiime2.Metadata(df)
dm = skbio.DistanceMatrix([[0, 1, 2], [1, 0, 3], [2, 3, 0]],
['S1', 'S2', 'S3'])
where = "SampleType='tongue' OR SampleType='gut'"
filtered = filter_distance_matrix(dm, metadata,
where,
exclude_ids=True)
expected = skbio.DistanceMatrix([[0]], ['S1'])
self.assertEqual(filtered, expected)
