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Adibvafa · Oct 29, 2024 · 7c20ff1 · 7c20ff1
1 parent 1356ebb
commit 7c20ff1
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Showing 3 changed files with 28 additions and 37 deletions.
diff --git a/CodonTransformer/CodonData.py b/CodonTransformer/CodonData.py
@@ -176,26 +176,30 @@ def preprocess_protein_sequence(protein: str) -> str:
 
     # Handle ambiguous amino acids based on the specified behavior
     config = ProteinConfig()
-    ambiguous_aminoacid_map_override = config.get('ambiguous_aminoacid_map_override')
-    ambiguous_aminoacid_behavior = config.get('ambiguous_aminoacid_behavior')
+    ambiguous_aminoacid_map_override = config.get("ambiguous_aminoacid_map_override")
+    ambiguous_aminoacid_behavior = config.get("ambiguous_aminoacid_behavior")
     ambiguous_aminoacid_map = AMBIGUOUS_AMINOACID_MAP.copy()
-    
+
     for aminoacid, standard_aminoacids in ambiguous_aminoacid_map_override.items():
         ambiguous_aminoacid_map[aminoacid] = standard_aminoacids
 
-    if ambiguous_aminoacid_behavior == 'raise_error':
+    if ambiguous_aminoacid_behavior == "raise_error":
         if any(aminoacid in ambiguous_aminoacid_map for aminoacid in protein):
             raise ValueError("Ambiguous amino acids found in protein sequence.")
-    elif ambiguous_aminoacid_behavior == 'standardize_deterministic':
+    elif ambiguous_aminoacid_behavior == "standardize_deterministic":
         protein = "".join(
-            ambiguous_aminoacid_map.get(aminoacid, [aminoacid])[0] for aminoacid in protein
+            ambiguous_aminoacid_map.get(aminoacid, [aminoacid])[0]
+            for aminoacid in protein
         )
-    elif ambiguous_aminoacid_behavior == 'standardize_random':
+    elif ambiguous_aminoacid_behavior == "standardize_random":
         protein = "".join(
-            random.choice(ambiguous_aminoacid_map.get(aminoacid, [aminoacid])) for aminoacid in protein
+            random.choice(ambiguous_aminoacid_map.get(aminoacid, [aminoacid]))
+            for aminoacid in protein
         )
     else:
-        raise ValueError(f"Invalid ambiguous_aminoacid_behavior: {ambiguous_aminoacid_behavior}.")
+        raise ValueError(
+            f"Invalid ambiguous_aminoacid_behavior: {ambiguous_aminoacid_behavior}."
+        )
 
     # Check for sequence validity
     if any(aminoacid not in AMINO_ACIDS + STOP_SYMBOLS for aminoacid in protein):

diff --git a/tests/test_CodonData.py b/tests/test_CodonData.py
@@ -8,11 +8,12 @@
     build_amino2codon_skeleton,
     get_amino_acid_sequence,
     is_correct_seq,
-    read_fasta_file,
     preprocess_protein_sequence,
+    read_fasta_file,
 )
 from CodonTransformer.CodonUtils import ProteinConfig
 
+
 class TestCodonData(unittest.TestCase):
     def test_preprocess_protein_sequence(self):
         with ProteinConfig() as config:

diff --git a/tests/test_CodonUtils.py b/tests/test_CodonUtils.py
@@ -18,33 +18,23 @@
 class TestCodonUtils(unittest.TestCase):
     def test_config_manager(self):
         with ProteinConfig() as config:
-            config.set(
-                "ambiguous_aminoacid_behavior",
-                "standardize_deterministic"
-            )
+            config.set("ambiguous_aminoacid_behavior", "standardize_deterministic")
             self.assertEqual(
-                config.get("ambiguous_aminoacid_behavior"),
-                "standardize_deterministic"
-            )
-            config.set(
-                "ambiguous_aminoacid_map_override",
-                {"X": ["A", "G"]}
+                config.get("ambiguous_aminoacid_behavior"), "standardize_deterministic"
             )
+            config.set("ambiguous_aminoacid_map_override", {"X": ["A", "G"]})
             self.assertEqual(
-                config.get("ambiguous_aminoacid_map_override"),
-                {"X": ["A", "G"]}
+                config.get("ambiguous_aminoacid_map_override"), {"X": ["A", "G"]}
             )
-            config.update({
-                "ambiguous_aminoacid_behavior": "raise_error",
-                "ambiguous_aminoacid_map_override": {"X": ["A", "G"]},
-            })
-            self.assertEqual(
-                config.get("ambiguous_aminoacid_behavior"),
-                "raise_error"
+            config.update(
+                {
+                    "ambiguous_aminoacid_behavior": "raise_error",
+                    "ambiguous_aminoacid_map_override": {"X": ["A", "G"]},
+                }
             )
+            self.assertEqual(config.get("ambiguous_aminoacid_behavior"), "raise_error")
             self.assertEqual(
-                config.get("ambiguous_aminoacid_map_override"),
-                {"X": ["A", "G"]}
+                config.get("ambiguous_aminoacid_map_override"), {"X": ["A", "G"]}
             )
             try:
                 config.set("invalid_key", "invalid_value")
@@ -53,13 +43,9 @@ def test_config_manager(self):
                 pass
         with ProteinConfig() as config:
             self.assertEqual(
-                config.get("ambiguous_aminoacid_behavior"),
-                "standardize_random"
-            )
-            self.assertEqual(
-                config.get("ambiguous_aminoacid_map_override"),
-                {}
+                config.get("ambiguous_aminoacid_behavior"), "standardize_random"
             )
+            self.assertEqual(config.get("ambiguous_aminoacid_map_override"), {})
 
     def test_load_python_object_from_disk(self):
         test_obj = {"key1": "value1", "key2": 2}