def test_invalid_formula(self):
md = qiime2.Metadata(pd.DataFrame(
[[1, 'a'], [1, 'b'], [2, 'b']], columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3'], name='id')))
with self.assertRaisesRegex(ValueError, "not a column"):
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+fakecolumn')
def test_metadata_is_subset(self):
md = qiime2.Metadata(pd.DataFrame(
[[1, 'a'], [1, 'b'], [2, 'b']], columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'peanuts'], name='id')))
with self.assertRaisesRegex(ValueError, "Missing samples"):
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+number')
def test_metadata_is_superset(self):
md = qiime2.Metadata(pd.DataFrame(
[[1, 'a'], [1, 'b'], [2, 'b'], [2, 'a']],
columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3', 'F'], name='id')))
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+number')
def test_adonis_handles_single_quotes_in_metadata(self):
md = qiime2.Metadata(pd.DataFrame(
[[1, 'a\'s'], [1, 'b\'s'], [2, 'b\'s'], [2, 'a\'s']],
columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3', 'F'], name='id')))
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+number')
def test_metadata_index_rename(self):
md = qiime2.Metadata(
pd.DataFrame([[1, 'a'], [1, 'b'], [2, 'b'], [2, 'a']],
columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3', 'F'],
name='#SampleID')))
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+number')
def test_adonis_handles_single_quotes_in_metadata(self):
md = qiime2.Metadata(
pd.DataFrame([[1, 'a\'s'], [1, 'b\'s'], [2, 'b\'s'], [2, 'a\'s']],
columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3', 'F'],
name='id')))
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+number')
def test_invalid_formula(self):
md = qiime2.Metadata(
pd.DataFrame([[1, 'a'], [1, 'b'], [2, 'b']],
columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3'],
name='id')))
with self.assertRaisesRegex(ValueError, "not a column"):
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+fakecolumn')
def test_metadata_is_subset(self):
md = qiime2.Metadata(
pd.DataFrame([[1, 'a'], [1, 'b'], [2, 'b']],
columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'peanuts'],
name='id')))
with self.assertRaisesRegex(ValueError, "Missing samples"):
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+number')
def test_nans_in_unused_column(self):
md = qiime2.Metadata(
pd.DataFrame([[1, 'a'], [1, 'b'], [np.nan, 'b']],
columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3'],
name='id')))
with redirected_stdio(stderr=os.devnull):
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+letter')
def test_nans_in_formula_column(self):
md = qiime2.Metadata(
pd.DataFrame([[1, 'a'], [1, 'b'], [np.nan, 'b']],
columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3'],
name='id')))
with redirected_stdio(stderr=os.devnull):
with self.assertRaisesRegex(ValueError, "no NaN values.*`number`"):
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+number')
def test_execute_and_validate_output(self):
md = qiime2.Metadata(pd.DataFrame(
[[1, 'a'], [1, 'b'], [2, 'b']], columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3'], name='id')))
exp = pd.DataFrame(
[[1.0, 0.322916667, 0.322916667, 0.0, 0.534482759, 1.0],
[1.0, 0.281250000, 0.281250000, 0.0, 0.465517241, 1.0],
[0.0, -1.403048e-18, -np.Infinity, np.nan, -2.322286e-18, np.nan],
[2.0, 0.604166667, np.nan, np.nan, 1.0, np.nan]],
columns=['Df', 'SumsOfSqs', 'MeanSqs', 'F.Model', 'R2', 'Pr(>F)'],
index=['letter', 'number', 'Residuals', 'Total'])
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+number')
with open(os.path.join(temp_dir_name, 'adonis.tsv'), 'r') as fh:
res = pd.read_csv(fh, sep='\t')
pdt.assert_frame_equal(
res, exp, check_dtype=False, check_frame_type=False)
def test_execute_and_validate_output(self):
md = qiime2.Metadata(
pd.DataFrame([[1, 'a'], [1, 'b'], [2, 'b']],
columns=['number', 'letter'],
index=pd.Index(['sample1', 'sample2', 'sample3'],
name='id')))
exp = pd.DataFrame(
[[1.0, 0.322916667, 0.322916667, 0.0, 0.534482759, 1.0],
[1.0, 0.281250000, 0.281250000, 0.0, 0.465517241, 1.0],
[0.0, -1.403048e-18, -np.Infinity, np.nan, -2.322286e-18, np.nan],
[2.0, 0.604166667, np.nan, np.nan, 1.0, np.nan]],
columns=['Df', 'SumsOfSqs', 'MeanSqs', 'F.Model', 'R2', 'Pr(>F)'],
index=['letter', 'number', 'Residuals', 'Total'])
with tempfile.TemporaryDirectory() as temp_dir_name:
adonis(temp_dir_name, self.dm, md, 'letter+number')
with open(os.path.join(temp_dir_name, 'adonis.tsv'), 'r') as fh:
res = pd.read_csv(fh, sep='\t')
pdt.assert_frame_equal(res,
exp,
check_dtype=False,
check_frame_type=False)
