feat: add reading frame to assayed fusions (#163)

cancervariants · Jul 17, 2024 · 14eb1fe · 14eb1fe
1 parent 630a2af
commit 14eb1fe
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Showing 7 changed files with 15 additions and 13 deletions.
diff --git a/src/fusor/examples/bcr_abl1.json b/src/fusor/examples/bcr_abl1.json
@@ -75,7 +75,7 @@
       }
     }
   ],
-  "r_frame_preserved": true,
+  "reading_frame_preserved": true,
   "critical_functional_domains": [
     {
       "type": "FunctionalDomain",

diff --git a/src/fusor/examples/bcr_abl1_expanded.json b/src/fusor/examples/bcr_abl1_expanded.json
@@ -110,7 +110,7 @@
       "element_genomic_end": null
     }
   ],
-  "r_frame_preserved": true,
+  "reading_frame_preserved": true,
   "critical_functional_domains": [
     {
       "type": "FunctionalDomain",

diff --git a/src/fusor/fusor.py b/src/fusor/fusor.py
@@ -129,7 +129,6 @@ def fusion(self, fusion_type: FusionType | None = None, **kwargs) -> Fusion:
             categorical_attributes = any(
                 [
                     "critical_functional_domains" in kwargs,
-                    "r_frame_preserved" in kwargs,
                     self._contains_element_type(
                         kwargs, StructuralElementType.MULTIPLE_POSSIBLE_GENES_ELEMENT
                     ),
@@ -165,23 +164,22 @@ def categorical_fusion(
         structural_elements: CategoricalFusionElements,
         regulatory_element: RegulatoryElement | None = None,
         critical_functional_domains: list[FunctionalDomain] | None = None,
-        r_frame_preserved: bool | None = None,
+        reading_frame_preserved: bool | None = None,
     ) -> CategoricalFusion:
         """Construct a categorical fusion object
-
         :param structural_elements: elements constituting the fusion
         :param regulatory_element: affected regulatory element
         :param critical_functional_domains: lost or preserved functional domains
-        :param r_frame_preserved: ``True`` if reading frame is preserved. ``False``
-            otherwise
+        :param reading_frame_preserved: ``True`` if reading frame is preserved.
+            ``False`` otherwise
         :return: CategoricalFusion if construction successful
         :raise: FUSORParametersException if given incorrect fusion properties
         """
         try:
             fusion = CategoricalFusion(
                 structural_elements=structural_elements,
                 critical_functional_domains=critical_functional_domains,
-                r_frame_preserved=r_frame_preserved,
+                reading_frame_preserved=reading_frame_preserved,
                 regulatory_element=regulatory_element,
             )
         except ValidationError as e:
@@ -194,12 +192,15 @@ def assayed_fusion(
         causative_event: CausativeEvent | None = None,
         assay: Assay | None = None,
         regulatory_element: RegulatoryElement | None = None,
+        reading_frame_preserved: bool | None = None,
     ) -> AssayedFusion:
         """Construct an assayed fusion object
         :param structural_elements: elements constituting the fusion
         :param causative_event: event causing the fusion
         :param assay: how knowledge of the fusion was obtained
         :param regulatory_element: affected regulatory elements
+        :param reading_frame_preserved: ``True`` if reading frame is preserved.
+            ``False`` otherwise
         :return: Tuple containing optional AssayedFusion if construction successful,
             and any relevant validation warnings
         """
@@ -209,6 +210,7 @@ def assayed_fusion(
                 regulatory_element=regulatory_element,
                 causative_event=causative_event,
                 assay=assay,
+                reading_frame_preserved=reading_frame_preserved,
             )
         except ValidationError as e:
             raise FUSORParametersException(str(e)) from e

diff --git a/src/fusor/models.py b/src/fusor/models.py
@@ -444,6 +444,7 @@ class AbstractFusion(BaseModel, ABC):
     """Define Fusion class"""
 
     type: FusionType
+    reading_frame_preserved: StrictBool | None = None
     regulatory_element: RegulatoryElement | None = None
     structural_elements: list[BaseStructuralElement]
 
@@ -714,15 +715,14 @@ class CategoricalFusion(AbstractFusion):
     """
 
     type: Literal[FUSORTypes.CATEGORICAL_FUSION] = FUSORTypes.CATEGORICAL_FUSION
-    r_frame_preserved: StrictBool | None = None
     critical_functional_domains: list[FunctionalDomain] | None = None
     structural_elements: CategoricalFusionElements
 
     model_config = ConfigDict(
         json_schema_extra={
             "example": {
                 "type": "CategoricalFusion",
-                "r_frame_preserved": True,
+                "reading_frame_preserved": True,
                 "critical_functional_domains": [
                     {
                         "type": "FunctionalDomain",

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -563,7 +563,7 @@ def fusion_example():
     """Create test fixture for a fake fusion without additional property expansion."""
     return {
         "type": "CategoricalFusion",
-        "r_frame_preserved": True,
+        "reading_frame_preserved": True,
         "critical_functional_domains": [
             {
                 "type": "FunctionalDomain",

diff --git a/tests/test_fusor.py b/tests/test_fusor.py
@@ -331,7 +331,7 @@ def fusion_ensg_sequence_id(templated_sequence_element_ensg):
             templated_sequence_element_ensg,
             {"type": "MultiplePossibleGenesElement"},
         ],
-        "r_frame_preserved": True,
+        "reading_frame_preserved": True,
         "regulatory_element": None,
     }
     return CategoricalFusion(**params)

diff --git a/tests/test_models.py b/tests/test_models.py
@@ -690,7 +690,7 @@ def test_fusion(
     """Test that Fusion object initializes correctly"""
     # test valid object
     fusion = CategoricalFusion(
-        r_frame_preserved=True,
+        reading_frame_preserved=True,
         critical_functional_domains=[functional_domains[0]],
         structural_elements=[transcript_segments[1], transcript_segments[2]],
         regulatory_element=regulatory_elements[0],