code tidying

CountESS-Project · Apr 5, 2024 · 805a56b · 805a56b
1 parent c960dcf
commit 805a56b
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Showing 3 changed files with 4 additions and 6 deletions.
diff --git a/countess/plugins/variant.py b/countess/plugins/variant.py
@@ -4,7 +4,7 @@
 
 from countess import VERSION
 from countess.core.logger import Logger
-from countess.core.parameters import BooleanParam, ColumnChoiceParam, ColumnOrStringParam, ColumnOrNoneChoiceParam, IntegerParam, StringParam
+from countess.core.parameters import BooleanParam, ColumnChoiceParam, ColumnOrStringParam, IntegerParam, StringParam
 from countess.core.plugins import PandasTransformDictToDictPlugin
 from countess.utils.variant import find_variant_string
 

diff --git a/countess/utils/variant.py b/countess/utils/variant.py
@@ -390,7 +390,7 @@ def _ref(ref_offset):
 
         if opcode.tag == "delete":
             assert dest_pro == ""
-            if ref_pro[src_end] == '*':
+            if ref_pro[src_end] == "*":
                 # if the codon just after this deletion is a terminator,
                 # consider this an early termination.
                 yield f"{_ref(src_start)}Ter"

diff --git a/tests/plugins/test_variant.py b/tests/plugins/test_variant.py
@@ -6,10 +6,9 @@
 
 logger = MultiprocessLogger()
 
+
 def test_variant_ref_value():
-    input_df = pd.DataFrame(
-            [{"seq": "TGAAGTAGAGG"}, {"seq": "AGAAGTTGTGG"}, {"seq": "ATAAGAAGAGG"}]
-    )
+    input_df = pd.DataFrame([{"seq": "TGAAGTAGAGG"}, {"seq": "AGAAGTTGTGG"}, {"seq": "ATAAGAAGAGG"}])
     plugin = VariantPlugin()
     plugin.set_parameter("column", "seq")
     plugin.set_parameter("reference", "AGAAGTAGAGG")
@@ -26,7 +25,6 @@ def test_variant_ref_value():
     assert output[2]["out"] == "g.[2G>T;6T>A]"
 
 
-
 def test_variant_ref_column():
     input_df = pd.DataFrame(
         [{"ref": "TACACACAG", "seq": "TACAGACAG"}, {"ref": "ATGGTTGGTTC", "seq": "ATGGTTGGTGGTTCG"}]