Lint

Author: bpblanken

v03_pipeline/lib/annotations/shared_test.py

@@ -12,7 +12,11 @@
 class SharedAnnotationsTest(unittest.TestCase):
     @patch('v03_pipeline.lib.vep.validate_vep_config_reference_genome')
     @patch('v03_pipeline.lib.vep.hl.vep')
-    def test_sorted_transcript_consequences(self, mock_vep: Mock, mock_validate: Mock) -> None:
+    def test_sorted_transcript_consequences(
+        self,
+        mock_vep: Mock,
+        mock_validate: Mock,
+    ) -> None:
         ht = hl.Table.parallelize(
             [
                 {

v03_pipeline/lib/vep.py

@@ -2,12 +2,14 @@
 
 from v03_pipeline.lib.model import DatasetType, ReferenceGenome
 
+
 def validate_vep_config_reference_genome(reference_genome, config: str) -> None:
-    with open(config, 'r') as f:
-        if reference_genome.value not in myfile.read():
+    with open(config) as f:
+        if reference_genome.value not in f.read():
             msg = f'Vep config does not match supplied reference genome {reference_genome.value}'
             raise ValueError(msg)
 
+
 def run_vep(
     ht: hl.Table,
     dataset_type: DatasetType,