def test_where_param(self):
# filter none
where = "stuff='foo' OR stuff='bar' OR stuff='baz'"
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)
# filter all
where = "stuff='boo'"
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
filter_seqs(self.seqs, metadata=self.md_full, where=where)
# exclude none
where = 'CAST(some_numbers AS INTEGER) < 0'
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)
# exclude all
where = 'CAST(some_numbers AS INTEGER) BETWEEN 0 AND 5'
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
filter_seqs(self.seqs, metadata=self.md_full, where=where,
exclude_ids=True)
def test_table_based_filtering_exclude_ids(self):
# filter all
table = Table(np.array([[0, 1, 3], [1, 1, 2], [42, 3, 0], [0, 0, 0]]),
['O1', 'O2', 'O3', 'O4'],
['S1', 'S2', 'S3'])
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
obs = filter_seqs(self.seqs, table=table, exclude_ids=True)
# filter all (extra ids in table is ok)
table = Table(np.array([[0, 1, 3], [1, 1, 2],
[42, 3, 0], [0, 0, 0], [1, 0, 0]]),
['O1', 'O2', 'O3', 'O4', 'O5'],
['S1', 'S2', 'S3'])
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
obs = filter_seqs(self.seqs, table=table, exclude_ids=True)
# filter three
table = Table(np.array([[1, 1, 2], [42, 3, 0], [0, 0, 0]]),
['O2', 'O3', 'O4'],
['S1', 'S2', 'S3'])
obs = filter_seqs(self.seqs, table=table, exclude_ids=True)
exp = pd.Series(['ACGT'], index=['O1'])
assert_series_equal(obs, exp)
# filter none
table = Table(np.array([[0, 1, 3], [1, 1, 2], [42, 3, 0], [0, 0, 0]]),
['O1-alt', 'O2-alt', 'O3-alt', 'O4-alt'],
['S1', 'S2', 'S3'])
obs = filter_seqs(self.seqs, table=table, exclude_ids=True)
assert_series_equal(obs, self.seqs)
def test_id_based_filtering(self):
# filter none
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)
# filter all
md = qiime2.Metadata(pd.DataFrame({},
index=pd.Index(['foo'], name='id')))
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
filter_seqs(self.seqs, metadata=md)
# exclude none
md = qiime2.Metadata(pd.DataFrame({},
index=pd.Index(['foo'], name='id')))
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)
# exclude all
md = qiime2.Metadata(self.df_lite)
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
filter_seqs(self.seqs, metadata=md, exclude_ids=True)
def test_where_param(self):
# filter none
where = "stuff='foo' OR stuff='bar' OR stuff='baz'"
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)
# filter all
where = "stuff='boo'"
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
filter_seqs(self.seqs, metadata=self.md_full, where=where)
# exclude none
where = 'CAST(some_numbers AS INTEGER) < 0'
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)
# exclude all
where = 'CAST(some_numbers AS INTEGER) BETWEEN 0 AND 5'
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
filter_seqs(self.seqs, metadata=self.md_full, where=where,
exclude_ids=True)
def test_id_based_filtering(self):
# filter none
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)
# filter all
md = qiime2.Metadata(pd.DataFrame({},
index=pd.Index(['foo'], name='id')))
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
filter_seqs(self.seqs, metadata=md)
# exclude none
md = qiime2.Metadata(pd.DataFrame({},
index=pd.Index(['foo'], name='id')))
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)
# exclude all
md = qiime2.Metadata(self.df_lite)
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
filter_seqs(self.seqs, metadata=md, exclude_ids=True)
def test_table_based_filtering_exclude_ids(self):
# filter all
table = Table(np.array([[0, 1, 3], [1, 1, 2], [42, 3, 0], [0, 0, 0]]),
['O1', 'O2', 'O3', 'O4'],
['S1', 'S2', 'S3'])
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
obs = filter_seqs(self.seqs, table=table, exclude_ids=True)
# filter all (extra ids in table is ok)
table = Table(np.array([[0, 1, 3], [1, 1, 2],
[42, 3, 0], [0, 0, 0], [1, 0, 0]]),
['O1', 'O2', 'O3', 'O4', 'O5'],
['S1', 'S2', 'S3'])
with self.assertRaisesRegex(ValueError, 'All.*filtered'):
obs = filter_seqs(self.seqs, table=table, exclude_ids=True)
# filter three
table = Table(np.array([[1, 1, 2], [42, 3, 0], [0, 0, 0]]),
['O2', 'O3', 'O4'],
['S1', 'S2', 'S3'])
obs = filter_seqs(self.seqs, table=table, exclude_ids=True)
exp = pd.Series(['ACGT'], index=['O1'])
assert_series_equal(obs, exp)
# filter none
table = Table(np.array([[0, 1, 3], [1, 1, 2], [42, 3, 0], [0, 0, 0]]),
['O1-alt', 'O2-alt', 'O3-alt', 'O4-alt'],
['S1', 'S2', 'S3'])
obs = filter_seqs(self.seqs, table=table, exclude_ids=True)
assert_series_equal(obs, self.seqs)
def test_table_and_metadata_filter(self):
table = Table(np.array([[1, 1, 2], [42, 3, 0], [0, 0, 0]]),
['O2', 'O3', 'O4'], ['S1', 'S2', 'S3'])
# in the future, there may be a use case for supporting both
# metadata/id based filtering and table-based filtering, but one
# isn't clear right now, so we're just not going to support it (and
# it could always be achieved with two calls to this method as a
# work-around)
with self.assertRaisesRegex(ValueError, 'mutually exclusive'):
filter_seqs(self.seqs, metadata=self.md_full, table=table)
def test_table_and_metadata_filter(self):
table = Table(np.array([[1, 1, 2], [42, 3, 0], [0, 0, 0]]),
['O2', 'O3', 'O4'],
['S1', 'S2', 'S3'])
# in the future, there may be a use case for supporting both
# metadata/id based filtering and table-based filtering, but one
# isn't clear right now, so we're just not going to support it (and
# it could always be achieved with two calls to this method as a
# work-around)
with self.assertRaisesRegex(ValueError, 'mutually exclusive'):
filter_seqs(self.seqs, metadata=self.md_full, table=table)
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,
exclude_ids=exclude_ids, where=where)
assert_series_equal(exp, obs)
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,
exclude_ids=exclude_ids, where=where)
assert_series_equal(exp, obs)
def test_no_filter(self):
with self.assertRaisesRegex(ValueError, 'either table or metadata.'):
filter_seqs(self.seqs)
def test_no_filter(self):
with self.assertRaisesRegex(ValueError, 'either table or metadata.'):
filter_seqs(self.seqs)
