def test_saves_to_file_location_if_no_dst_supplied(self, patch):
p = enrich2.Enrich2(src=self.store, wt_sequence=self.wt, offset=0)
p.parse_input(self.enrich2.load_input_file())
expected_base_path = os.path.normpath(
os.path.join(self.data_dir, "enrich2", "test_store"))
for call_args in patch.call_args_list:
self.assertIn(expected_base_path, call_args[0][0])
def test_saves_to_output_directory(self, patch):
output = os.path.join(self.data_dir, "enrich2", "new")
p = enrich2.Enrich2(src=self.store,
dst=output,
wt_sequence=self.wt,
offset=0)
p.parse_input(p.load_input_file())
for call_args in patch.call_args_list:
self.assertIn(output, call_args[0][0])
def test_fails_when_no_variants(self):
output = os.path.join(self.data_dir, "enrich2", "new")
p = enrich2.Enrich2(src=self.store,
dst=output,
wt_sequence=self.wt,
offset=0)
with self.assertRaises(ValueError) as cm:
p.parse_input(p.load_input_file())
self.assertEqual(str(cm.exception),
"unable to find variants data in HDF5")
def setUp(self):
super().setUp()
self.wt = "GCTGAT"
self.path = os.path.join(self.data_dir, "enrich2", "enrich2.tsv")
self.enrich2 = enrich2.Enrich2(
self.path,
wt_sequence=self.wt,
offset=0,
one_based=True,
hgvs_column="sequence",
is_coding=False,
)
def setUp(self):
super().setUp()
self.wt = "GCTGAT"
self.path = os.path.join(self.data_dir, "enrich2", "test_store.h5")
self.store = pd.HDFStore(self.path, "w")
self.enrich2 = enrich2.Enrich2(self.path,
wt_sequence=self.wt,
offset=0,
one_based=True)
scores, shared, counts, *_ = self.mock_synonymous_frames()
self.store["/main/synonymous/scores/"] = scores
self.store["/main/synonymous/scores_shared/"] = shared
self.store["/main/synonymous/counts/"] = counts
self.files = [
os.path.normpath(
os.path.join(
self.data_dir,
"enrich2",
"test_store",
"mavedb_test_store_synonymous_counts_c1.csv",
)),
os.path.normpath(
os.path.join(
self.data_dir,
"enrich2",
"test_store",
"mavedb_test_store_synonymous_counts_c2.csv",
)),
os.path.normpath(
os.path.join(
self.data_dir,
"enrich2",
"test_store",
"mavedb_test_store_synonymous_scores_c1.csv",
)),
os.path.normpath(
os.path.join(
self.data_dir,
"enrich2",
"test_store",
"mavedb_test_store_synonymous_scores_c2.csv",
)),
]
self.store.close()
self.store = pd.HDFStore(self.path, mode="r")