diff --git a/scripts/generate_modifications_cache.py b/scripts/generate_modifications_cache.py index bbc0178..69140e8 100755 --- a/scripts/generate_modifications_cache.py +++ b/scripts/generate_modifications_cache.py @@ -8,7 +8,7 @@ from Bio.Data import SCOPData -VALID_RNA_CODES = set('ACGUT') +VALID_RNA_CODES = set("ACGUT") # a few values are adjusted manually to make sure we are as correct as possible # and to avoid inconsistency with AlphaFold @@ -106,7 +106,7 @@ def main(args): for k, v in modifications.items(): if comp_types[k] == "protein": - data["protein"][k] = v + data["protein"][k] = v if comp_types[k] == "rna": if v in VALID_RNA_CODES: data["rna"][k] = v diff --git a/tests/test_modifications.py b/tests/test_modifications.py index ff945ca..7e9270c 100644 --- a/tests/test_modifications.py +++ b/tests/test_modifications.py @@ -8,7 +8,9 @@ class TestModifications(unittest.TestCase): - modification_handler = ModificationHandler("tests/test_data/modifications_cache.json") + modification_handler = ModificationHandler( + "tests/test_data/modifications_cache.json" + ) # accept both A and U for selenocysteines # note that selenocysteines that are incorrectly encoded in SCOPData @@ -64,4 +66,3 @@ def test_biopython_coverage(self): if __name__ == "__main__": unittest.main() -