Merge pull request #371 from monarch-initiative/370-add-check-for-ref…

…-and-alt-alleles-for-variants-recorded-in-a-phenopacket

370 add check for ref and alt alleles for variants recorded in a phenopacket

src/pheval/prepare/prepare_corpus.py

@@ -57,6 +57,11 @@ def prepare_corpus(
                     f"Removed {phenopacket_path.name} from the corpus due to missing variant fields."
                 )
                 continue
+            elif phenopacket_util.check_variant_alleles():
+                info_log.warning(
+                    f"Removed {phenopacket_path.name} from the corpus due to identical "
+                    "reference and alternate allele fields."
+                )
         if gene_analysis:
             if phenopacket_util.check_incomplete_gene_record():
                 info_log.warning(

src/pheval/utils/phenopacket_utils.py

@@ -503,6 +503,19 @@ def check_incomplete_variant_record(self) -> bool:
                 return True
         return False
 
+    def check_variant_alleles(self) -> bool:
+        """
+        Check if any variant record in the phenopacket has identical reference and alternate alleles.
+
+        Returns:
+            bool: True if the reference and alternate alleles are identical, False otherwise.
+        """
+        variants = self.diagnosed_variants()
+        for variant in variants:
+            if variant.ref == variant.alt:
+                return True
+        return False
+
     def check_incomplete_gene_record(self) -> bool:
         """
         Check if any gene record in the phenopacket has incomplete information.

tests/test_phenopacket_utils.py

@@ -1,4 +1,5 @@
 import unittest
+from copy import deepcopy
 from pathlib import Path
 
 from phenopackets import (
@@ -606,6 +607,16 @@ def test_check_incomplete_disease_record(self):
     def test_check_incomplete_disease_record_missing_records(self):
         self.assertTrue(self.structural_variant_phenopacket.check_incomplete_disease_record())
 
+    def test_check_variant_alleles(self):
+        self.assertFalse(self.phenopacket.check_variant_alleles())
+
+    def test_check_variant_alleles_duplicate(self):
+        phenopacket_copy = deepcopy(self.phenopacket)
+        phenopacket_copy.phenopacket_contents.interpretations[0].diagnosis.genomic_interpretations[
+            0
+        ].variant_interpretation.variation_descriptor.vcf_record.alt = "C"
+        self.assertTrue(phenopacket_copy.check_variant_alleles())
+
 
 class TestPhenopacketRebuilder(unittest.TestCase):
     @classmethod