fix: Add gene symbol check in translator methods (#214)

src/fusor/translator.py

@@ -141,6 +141,23 @@ def _get_gene_element(self, genes: str, caller: Caller) -> GeneElement:
         ge = self.fusor.gene_element(gene=gene)
         return ge[0] if ge[0] else self._get_gene_element_unnormalized(gene)
 
+    def _are_fusion_partners_different(
+        self, gene_5prime: str, gene_3prime: str
+    ) -> bool:
+        """Check if the normalized gene symbols for the two fusion partners
+        are different. If not, this event is not a fusion
+
+        :param gene_5prime: The 5' gene partner
+        :param gene_3prime: The 3' gene partner
+        :return ``True`` if the gene symbols are different, ``False`` if not
+        """
+        if gene_5prime != gene_3prime:
+            return True
+        _logger.error(
+            "The supplied fusion is not valid as the two fusion partners are the same"
+        )
+        return False
+
     def _get_genomic_ac(self, chrom: str, build: Assembly) -> str:
         """Return a RefSeq genomic accession given a chromosome and a reference build
 
@@ -190,6 +207,9 @@ async def from_jaffa(
         gene_5prime = gene_5prime_element.gene.label
         gene_3prime = gene_3prime_element.gene.label
 
+        if not self._are_fusion_partners_different(gene_5prime, gene_3prime):
+            return None
+
         tr_5prime = await self.fusor.transcript_segment_element(
             tx_to_genomic_coords=False,
             genomic_ac=self._get_genomic_ac(chrom1, rb),
@@ -244,6 +264,9 @@ async def from_star_fusion(
         gene_5prime = gene_5prime_element.gene.label
         gene_3prime = gene_3prime_element.gene.label
 
+        if not self._are_fusion_partners_different(gene_5prime, gene_3prime):
+            return None
+
         five_prime = left_breakpoint.split(":")
         three_prime = right_breakpoint.split(":")
 
@@ -296,6 +319,10 @@ async def from_fusion_catcher(
         gene_3prime_element = self._get_gene_element(
             three_prime_partner, Caller.FUSION_CATCHER
         )
+        if not self._are_fusion_partners_different(
+            gene_5prime_element.gene.label, gene_3prime_element.gene.label
+        ):
+            return None
 
         five_prime = five_prime_fusion_point.split(":")
         three_prime = three_prime_fusion_point.split(":")
@@ -335,6 +362,9 @@ async def from_fusion_map(
         gene_5prime = self._get_gene_element(gene1, "fusion_map").gene.label
         gene_3prime = self._get_gene_element(gene2, "fusion_map").gene.label
 
+        if not self._are_fusion_partners_different(gene_5prime, gene_3prime):
+            return None
+
         tr_5prime = await self.fusor.transcript_segment_element(
             tx_to_genomic_coords=False,
             genomic_ac=self._get_genomic_ac(
@@ -414,6 +444,9 @@ async def from_arriba(
         gene_5prime = gene_5prime_element.gene.label
         gene_3prime = gene_3prime_element.gene.label
 
+        if not self._are_fusion_partners_different(gene_5prime, gene_3prime):
+            return None
+
         strand1 = strand1.split("/")[1]  # Determine strand that is transcribed
         strand2 = strand2.split("/")[1]  # Determine strand that is transcribed
         if strand1 == "+":
@@ -509,6 +542,9 @@ async def from_cicero(
         gene_5prime = gene_5prime_element.gene.label
         gene_3prime = gene_3prime_element.gene.label
 
+        if not self._are_fusion_partners_different(gene_5prime, gene_3prime):
+            return None
+
         tr_5prime = await self.fusor.transcript_segment_element(
             tx_to_genomic_coords=False,
             genomic_ac=self._get_genomic_ac(chr_5prime, rb),
@@ -559,6 +595,9 @@ async def from_mapsplice(
         gene_5prime = gene_5prime_element.gene.label
         gene_3prime = gene_3prime_element.gene.label
 
+        if not self._are_fusion_partners_different(gene_5prime, gene_3prime):
+            return None
+
         tr_5prime = await self.fusor.transcript_segment_element(
             tx_to_genomic_coords=False,
             genomic_ac=self._get_genomic_ac(mapsplice_row[0].split("~")[0], rb),
@@ -606,6 +645,9 @@ async def from_enfusion(
         gene_5prime = gene_5prime_element.gene.label
         gene_3prime = gene_3prime_element.gene.label
 
+        if not self._are_fusion_partners_different(gene_5prime, gene_3prime):
+            return None
+
         tr_5prime = await self.fusor.transcript_segment_element(
             tx_to_genomic_coords=False,
             genomic_ac=self._get_genomic_ac(chr_5prime, rb),
@@ -660,6 +702,9 @@ async def from_genie(
         gene_5prime = gene_5prime_element.gene.label
         gene_3prime = gene_3prime_element.gene.label
 
+        if not self._are_fusion_partners_different(gene_5prime, gene_3prime):
+            return None
+
         tr_5prime = await self.fusor.transcript_segment_element(
             tx_to_genomic_coords=False,
             genomic_ac=self._get_genomic_ac(site1_chrom, rb),

tests/test_translators.py

@@ -115,6 +115,15 @@ def test_gene_element_arriba(translator_instance):
     assert gene.gene.label == "MIR3672"
 
 
+def test_valid_fusion_partners(translator_instance):
+    """Test that the fusion partners supplied to the translator are different"""
+    partners_check = translator_instance._are_fusion_partners_different("BCR", "ABL1")
+    assert partners_check
+
+    partners_check = translator_instance._are_fusion_partners_different("BCR", "BCR")
+    assert not partners_check
+
+
 @pytest.mark.asyncio()
 async def test_jaffa(
     fusion_data_example, fusion_data_example_nonexonic, translator_instance