make RNA VAF as default instead of DNA VAF

TRON-Bioinformatics · Dec 16, 2022 · 1a0df50 · 1a0df50
1 parent 1f2ef34
commit 1a0df50
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Showing 2 changed files with 16 additions and 8 deletions.
diff --git a/neofox/published_features/expression.py b/neofox/published_features/expression.py
@@ -46,9 +46,9 @@ def _get_expression_annotation(
 
     def get_annotations(self, neoantigen: Neoantigen) -> List[Annotation]:
 
-        vaf = neoantigen.dna_variant_allele_frequency
+        vaf = neoantigen.rna_variant_allele_frequency
         if vaf is None or vaf == -1:
-            vaf = neoantigen.rna_variant_allele_frequency
+            vaf = neoantigen.dna_variant_allele_frequency
 
         return [
             AnnotationFactory.build_annotation(

diff --git a/neofox/tests/unit_tests/test_expression.py b/neofox/tests/unit_tests/test_expression.py
@@ -19,7 +19,7 @@
 
 from unittest import TestCase
 
-from neofox.model.factories import NOT_AVAILABLE_VALUE
+from neofox.model.factories import NOT_AVAILABLE_VALUE, NeoantigenFactory
 from neofox.model.neoantigen import Neoantigen
 from neofox.published_features.expression import Expression
 
@@ -30,20 +30,28 @@ def setUp(self) -> None:
         self.expression = Expression()
 
     def test_calculate_expression_mutation(self):
-        neoantigen = Neoantigen(rna_expression=12.0, dna_variant_allele_frequency=0.2)
+        neoantigen = NeoantigenFactory.build_neoantigen(
+            rna_expression=12.0, dna_variant_allele_frequency=0.2, patient_identifier="patient1",
+            mutated_xmer="DDDDD")
         result = self.expression.get_annotations(neoantigen=neoantigen)[0]
-        self.assertGreater(result.value, "0.0")
+        self.assertGreater(float(result.value), 0.0)
 
         # no reads for mut
-        neoantigen = Neoantigen(rna_expression=12.0, dna_variant_allele_frequency=0.0)
+        neoantigen = NeoantigenFactory.build_neoantigen(
+            rna_expression=12.0, dna_variant_allele_frequency=0.0, patient_identifier="patient1",
+            mutated_xmer="DDDDD")
         result = self.expression.get_annotations(neoantigen=neoantigen)[0]
         self.assertEqual(result.value, "0")
 
         # no reads for mut/wt
-        neoantigen = Neoantigen(rna_expression=12.0, dna_variant_allele_frequency=-1, rna_variant_allele_frequency=-1)
+        neoantigen = NeoantigenFactory.build_neoantigen(
+            rna_expression=12.0, dna_variant_allele_frequency=-1, rna_variant_allele_frequency=-1, patient_identifier="patient1",
+            mutated_xmer="DDDDD")
         result = self.expression.get_annotations(neoantigen=neoantigen)[0]
         self.assertEqual(result.value, NOT_AVAILABLE_VALUE)
 
-        neoantigen = Neoantigen(rna_expression=None, dna_variant_allele_frequency=-1, rna_variant_allele_frequency=-1)
+        neoantigen = NeoantigenFactory.build_neoantigen(
+            rna_expression=None, dna_variant_allele_frequency=-1, rna_variant_allele_frequency=-1,
+            patient_identifier="patient1", mutated_xmer="DDDDD")
         result = self.expression.get_annotations(neoantigen=neoantigen)[0]
         self.assertEqual(result.value, NOT_AVAILABLE_VALUE)