Merge branch 'develop' into 'master'

Release 1.0.2 - set expression to use RNA VAF by default instead of DNA VAF See merge request tron/addannot!226
TRON-Bioinformatics · Dec 16, 2022 · d5452a6 · d5452a6
2 parents a8d656a + 1a0df50
commit d5452a6
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Showing 3 changed files with 17 additions and 9 deletions.
diff --git a/neofox/__init__.py b/neofox/__init__.py
@@ -18,7 +18,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.#
 
 
-VERSION = "1.0.1"
+VERSION = "1.0.2"
 
 
 REFERENCE_FOLDER_ENV = "NEOFOX_REFERENCE_FOLDER"

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)