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IMP: adds underscore prefix to helper method inside filter seqs tests #297

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merged 2 commits into from
Dec 12, 2023
Merged

IMP: adds underscore prefix to helper method inside filter seqs tests #297

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bb8fe1f
added minor changes to filter sequences tests
hagenjp Dec 12, 2023
ca7b427
Merge branch 'qiime2:dev' into dev
hagenjp Dec 12, 2023
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24 changes: 12 additions & 12 deletions q2_feature_table/tests/filter/test_filter_sequences.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,8 +31,8 @@ def setUp(self):
md_full.index.name = 'FeatureID'
self.md_full = qiime2.Metadata(md_full)

def filter_and_assertEqual(self, exp, md=None, exclude_ids=False,
where=None):
def _filter_and_assertEqual(self, exp, md=None, exclude_ids=False,
where=None):
if md is None:
md = self.md_full
obs = filter_seqs(self.seqs, metadata=md,
Expand All @@ -41,13 +41,13 @@ def filter_and_assertEqual(self, exp, md=None, exclude_ids=False,

def test_id_based_filtering(self):
# filter none
self.filter_and_assertEqual(self.seqs,
md=qiime2.Metadata(self.df_lite))
self._filter_and_assertEqual(self.seqs,
md=qiime2.Metadata(self.df_lite))

# filter one
md = qiime2.Metadata(self.df_lite.drop(['O1']))
exp = pd.Series(['GCTA', 'CCCC', 'TGTT'], index=['O2', 'O3', 'O4'])
self.filter_and_assertEqual(exp, md=md)
self._filter_and_assertEqual(exp, md=md)

# filter all
md = qiime2.Metadata(pd.DataFrame({},
Expand All @@ -58,12 +58,12 @@ def test_id_based_filtering(self):
# exclude none
md = qiime2.Metadata(pd.DataFrame({},
index=pd.Index(['foo'], name='id')))
self.filter_and_assertEqual(self.seqs, md=md, exclude_ids=True)
self._filter_and_assertEqual(self.seqs, md=md, exclude_ids=True)

# exclude one
md = qiime2.Metadata(self.df_lite.drop(['O1', 'O2', 'O3']))
exp = pd.Series(['ACGT', 'GCTA', 'CCCC'], index=['O1', 'O2', 'O3'])
self.filter_and_assertEqual(exp, md=md, exclude_ids=True)
self._filter_and_assertEqual(exp, md=md, exclude_ids=True)

# exclude all
md = qiime2.Metadata(self.df_lite)
Expand All @@ -74,17 +74,17 @@ def test_id_based_filtering_with_extra_ids(self):
md = qiime2.Metadata(pd.DataFrame([],
index=pd.Index(['O1', 'O3', 'foo'], name='id')))
exp = pd.Series(['ACGT', 'CCCC'], index=['O1', 'O3'])
self.filter_and_assertEqual(exp, md=md)
self._filter_and_assertEqual(exp, md=md)

def test_where_param(self):
# filter none
where = "stuff='foo' OR stuff='bar' OR stuff='baz'"
self.filter_and_assertEqual(self.seqs, where=where)
self._filter_and_assertEqual(self.seqs, where=where)

# filter one
where = "stuff='foo' OR stuff='bar'"
exp = pd.Series(['ACGT', 'GCTA', 'TGTT'], index=['O1', 'O2', 'O4'])
self.filter_and_assertEqual(exp, where=where)
self._filter_and_assertEqual(exp, where=where)

# filter all
where = "stuff='boo'"
Expand All @@ -93,12 +93,12 @@ def test_where_param(self):

# exclude none
where = 'CAST(some_numbers AS INTEGER) < 0'
self.filter_and_assertEqual(self.seqs, exclude_ids=True, where=where)
self._filter_and_assertEqual(self.seqs, exclude_ids=True, where=where)

# exclude one
where = 'CAST(some_numbers AS INTEGER) > 3'
exp = pd.Series(['ACGT', 'GCTA', 'CCCC'], index=['O1', 'O2', 'O3'])
self.filter_and_assertEqual(exp, exclude_ids=True, where=where)
self._filter_and_assertEqual(exp, exclude_ids=True, where=where)

# exclude all
where = 'CAST(some_numbers AS INTEGER) BETWEEN 0 AND 5'
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