fix: handle cases where gene_context is not found

src/variation/gnomad_vcf_to_protein_variation.py

@@ -581,11 +581,18 @@ async def gnomad_vcf_to_protein(self, vcf_query: str) -> GnomadVcfToProteinServi
  except GnomadVcfToProteinError as e:
  warnings.append(str(e))
 
+ if p_data.gene and c_data.gene and p_data.gene != c_data.gene:
+ warnings.append(
+ f"Protein gene ({p_data.gene}) and cDNA gene ({c_data.gene}) mismatch"
+ )
+ gene = p_data.gene or c_data.gene
+ gene_context = self._get_gene_context(gene) if gene else None
+
  return GnomadVcfToProteinService(
  variation_query=vcf_query,
  variation=variation,
  vrs_ref_allele_seq=self._get_vrs_ref_allele_seq(variation.location, p_ac),
- gene_context=self._get_gene_context(p_data.gene),
+ gene_context=gene_context,
  warnings=warnings,
  service_meta_=ServiceMeta(
  version=__version__,

tests/test_gnomad_vcf_to_protein.py

@@ -388,6 +388,12 @@ async def test_delins(test_handler, delins_pos, delins_neg):
  assert resp.vrs_ref_allele_seq == "PRLLFPTNSSSHLVALQGQP"
  assert resp.gene_context
 
+ # CA16602420. Example where protein gene not found, but cDNA gene found
+ resp = await test_handler.gnomad_vcf_to_protein("7-140453136-AC-TT")
+ assert resp.variation
+ assert resp.gene_context
+ assert resp.warnings == []
+
 
 @pytest.mark.asyncio()
 async def test_invalid(test_handler):