def test_balance_taxonomy(self):
index_fp = os.path.join(self.results, 'index.html')
balance_taxonomy(self.results, self.balances, self.tree,
self.taxonomy, balance_name='c')
self.assertTrue(os.path.exists(index_fp))
# test to make sure that the numerator file is there
num_fp = os.path.join(self.results, 'numerator.csv')
self.assertTrue(os.path.exists(num_fp))
# test to make sure that the denominator file is there
denom_fp = os.path.join(self.results, 'denominator.csv')
self.assertTrue(os.path.exists(denom_fp))
with open(index_fp, 'r') as fh:
html = fh.read()
self.assertIn('<h1>Balance Taxonomy</h1>', html)
self.assertIn('Numerator taxa', html)
self.assertIn('Denominator taxa', html)
# extract csv files and test for contents
exp = pd.DataFrame(
[['foo', 'barf', 'a', 'b', 'c', 'd', 'e'],
['foo', 'bark', 'f', 'g', 'h', 'i', 'j'],
['foo', 'bark', 'f', 'g', 'h', 'w', 'j']],
columns=['0', '1', '2', '3', '4', '5', '6'],
index=['x', 'y', 'z'])
res = pd.read_csv(num_fp, index_col=0)
pdt.assert_frame_equal(exp, res.sort_index())
exp = pd.DataFrame([['nom', 'tu', 'k', 'l', 'm', 't', 'o'],
['nom', 'tu', 'k', 'l', 'm', 'n', 'o']],
columns=['0', '1', '2', '3', '4', '5', '6'],
index=['q', 'k']).sort_index()
res = pd.read_csv(denom_fp, index_col=0)
pdt.assert_frame_equal(exp, res.sort_index())
def test_balance_taxonomy_categorical(self):
balance_taxonomy(self.results,
self.balances,
self.tree,
self.taxonomy,
balance_name='a',
metadata=self.categorical)
def test_balance_taxonomy_continuous(self):
balance_taxonomy(self.results,
self.balances,
self.tree,
self.taxonomy,
balance_name='a',
metadata=self.continuous)
def test_balance_taxonomy_tips(self):
index_fp = os.path.join(self.results, 'index.html')
balance_taxonomy(self.results,
self.balances,
self.tree,
self.taxonomy,
balance_name='a')
self.assertTrue(os.path.exists(index_fp))
# test to make sure that the numerator file is there
num_fp = os.path.join(self.results, 'numerator.csv')
self.assertTrue(os.path.exists(num_fp))
# test to make sure that the denominator file is there
denom_fp = os.path.join(self.results, 'denominator.csv')
self.assertTrue(os.path.exists(denom_fp))
exp = pd.DataFrame(['foo', 'bark', 'f', 'g', 'h', 'i', 'j'],
index=['0', '1', '2', '3', '4', '5', '6'],
columns=['y']).T
res = pd.read_csv(num_fp, index_col=0)
pdt.assert_frame_equal(exp, res)
res = pd.read_csv(denom_fp, index_col=0)
exp = pd.DataFrame(['foo', 'barf', 'a', 'b', 'c', 'd', 'e'],
index=['0', '1', '2', '3', '4', '5', '6'],
columns=['x']).T
pdt.assert_frame_equal(exp, res)
def test_balance_taxonomy_continuous(self):
index_fp = os.path.join(self.results, 'index.html')
balance_taxonomy(self.results,
self.table,
self.tree,
self.taxonomy,
balance_name='a',
metadata=self.continuous)
self.assertTrue(os.path.exists(index_fp))
# test to make sure that the numerator file is there
num_fp = os.path.join(self.results, 'numerator.csv')
self.assertTrue(os.path.exists(num_fp))
# test to make sure that the denominator file is there
denom_fp = os.path.join(self.results, 'denominator.csv')
self.assertTrue(os.path.exists(denom_fp))
box_fp = os.path.join(self.results, 'balance_metadata.pdf')
self.assertTrue(os.path.exists(box_fp))
prop_fp = os.path.join(self.results, 'proportion_plot.pdf')
self.assertTrue(os.path.exists(prop_fp))
box_fp = os.path.join(self.results, 'balance_metadata.pdf')
self.assertTrue(os.path.exists(box_fp))
with open(index_fp, 'r') as fh:
html = fh.read()
self.assertIn('<h1>Balance Taxonomy</h1>', html)
self.assertIn('Numerator taxa', html)
self.assertIn('Denominator taxa', html)
self.assertIn('Proportion', html)
def test_balance_taxonomy_full_numerical_categorical(self):
with self.assertRaisesRegex(ValueError, 'only numerical values'):
balance_taxonomy(self.results,
self.table,
self.tree,
self.taxonomy,
balance_name='a',
metadata=self.full_numerical_categorical)
def test_balance_taxonomy_categorical_error(self):
with self.assertRaises(ValueError):
balance_taxonomy(self.results,
self.table,
self.tree,
self.taxonomy,
balance_name='a',
metadata=self.categorical,
threshold=100.)
def test_balance_taxonomy_genus(self):
index_fp = os.path.join(self.results, 'index.html')
balance_taxonomy(self.results, self.balances, self.tree,
self.taxonomy, balance_name='c',
taxa_level=6)
self.assertTrue(os.path.exists(index_fp))
# test to make sure that the numerator file is there
num_fp = os.path.join(self.results, 'numerator.csv')
self.assertTrue(os.path.exists(num_fp))
# test to make sure that the denominator file is there
denom_fp = os.path.join(self.results, 'denominator.csv')
self.assertTrue(os.path.exists(denom_fp))
def test_balance_taxonomy_partial_numerical_categorical(self):
index_fp = os.path.join(self.results, 'index.html')
balance_taxonomy(self.results,
self.table,
self.tree,
self.taxonomy,
balance_name='a',
metadata=self.partial_numerical_categorical)
for file in [
'numerator.csv', 'denominator.csv', 'balance_metadata.pdf'
]:
self.assertTrue(os.path.exists(os.path.join(self.results, file)))
self.assertFalse(
os.path.exists(os.path.join(self.results, 'proportion_plot.pdf')))
with open(index_fp, 'r') as fh:
html = fh.read()
for exp in [
'<h1>Balance Taxonomy</h1>', 'Numerator taxa',
'Denominator taxa'
]:
self.assertIn(exp, html)
self.assertNotIn('Proportion', html)
