change default behavior of ProteinConfig

Adibvafa · Sep 25, 2024 · 0fcba6a · 0fcba6a
1 parent e27fe4d
commit 0fcba6a
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/CodonTransformer/CodonUtils.py b/CodonTransformer/CodonUtils.py
@@ -667,7 +667,7 @@ def reset_config(self) -> None:
         Reset the configuration to the default values.
         """
         self._config = {
-            'ambiguous_aminoacid_behavior': 'raise_error',
+            'ambiguous_aminoacid_behavior': 'standardize_random',
             'ambiguous_aminoacid_map_override': {}
         }
 

diff --git a/tests/test_CodonData.py b/tests/test_CodonData.py
@@ -16,6 +16,7 @@
 class TestCodonData(unittest.TestCase):
     def test_preprocess_protein_sequence(self):
         with ProteinConfig() as config:
+            config.set("ambiguous_aminoacid_behavior", "raise_error")
             protein = "Z_"
             try:
                 preprocess_protein_sequence(protein)

diff --git a/tests/test_CodonUtils.py b/tests/test_CodonUtils.py
@@ -54,7 +54,7 @@ def test_config_manager(self):
         with ProteinConfig() as config:
             self.assertEqual(
                 config.get("ambiguous_aminoacid_behavior"),
-                "raise_error"
+                "standardize_random"
             )
             self.assertEqual(
                 config.get("ambiguous_aminoacid_map_override"),