Implement variant search by HGVS expression

civicpy/civic.py

@@ -1166,10 +1166,25 @@ def search_variants_by_name(name):
     """
     return search_variants_by_attribute('name', name)
 
+def search_variants_by_hgvs(hgvs):
+    """
+    Search the cache for variants matching the queried HGVS expression
+
+    :param String name: HGVS expression to query
+
+    :return: Returns a list of variant hashes matching the HGVS expression
+    """
+    return search_variants_by_list_field('hgvs_expressions', hgvs)
+
 def search_variants_by_attribute(attribute, value):
     variants = get_all_variants()
     return [v for v in variants if getattr(v, attribute) == value]
 
+def search_variants_by_list_field(field, value):
+    variants = get_all_variants()
+    matched_variants = []
+    return [v for v in variants if value in getattr(v, field)]
+
 def search_variants_by_coordinates(coordinate_query, search_mode='any'):
     """
     Search the cache for variants matching provided coordinates using the corresponding search mode.

civicpy/tests/test_civic.py

@@ -122,6 +122,11 @@ def test_get_by_caid(self, v600e):
         assert len(variants) == 1
         assert variants[0] == v600e
 
+    def test_get_by_hgvs(self, v600e):
+        variants = civic.search_variants_by_hgvs("ENST00000288602.6:c.1799T>A")
+        assert len(variants) == 1
+        assert variants[0] == v600e
+
     def test_sanitize_coordinate_bases(self):
         variant1 = civic.get_variant_by_id(2696)
         variant2 = civic.get_variant_by_id(558)