issue SACGF/variantgrid_private#2027 - do HGVS trailing integer valid…

…ation (del50) for pyhgvs as well as biocommons

genes/hgvs/biocommons_hgvs/hgvs_converter_biocommons.py

@@ -135,11 +135,7 @@ def __init__(self, genome_build: GenomeBuild, local_resolution=True, clingen_res
     def _parser_hgvs(hgvs_string: str) -> SequenceVariant:
         """ All calls to parsing go through here """
 
-        if "ins" in hgvs_string:
-            if re.match(".*ins\d+$", hgvs_string):
-                raise HGVSException("Insertions require inserted sequence, not an integer length")
-            if re.match(".*ins$", hgvs_string):
-                raise HGVSException("Insertions require inserted sequence")
+        HGVSConverter._hgvs_string_validation(hgvs_string)
 
         # Biocommons HGVS doesn't accept integers on the end of indels - ie NM_001354689.1(RAF1):c.1_2dup3
         # We want to strip these and raise an error if the span is wrong

genes/hgvs/hgvs_converter.py

@@ -1,7 +1,8 @@
 import abc
+import re
 from enum import Enum
 
-from genes.hgvs import HGVSVariant
+from genes.hgvs import HGVSVariant, HGVSException
 from snpdb.models import GenomeBuild, VariantCoordinate
 
 
@@ -53,6 +54,18 @@ def __init__(self, genome_build: GenomeBuild, local_resolution=True, clingen_res
         self.local_resolution = local_resolution
         self.clingen_resolution = clingen_resolution
 
+    @staticmethod
+    def _hgvs_string_validation(hgvs_string: str):
+        """ raise exceptions on any errors """
+
+        if "ins" in hgvs_string:
+            if re.match(".*ins\d+$", hgvs_string):
+                raise HGVSException("Insertions require inserted sequence, not an integer length")
+            if re.match(".*ins$", hgvs_string):
+                raise HGVSException("Insertions require inserted sequence")
+
+
+
     @abc.abstractmethod
     def create_hgvs_variant(self, hgvs_string: str) -> HGVSVariant:
         pass

genes/hgvs/pyhgvs/hgvs_converter_pyhgvs.py

@@ -126,6 +126,8 @@ class PyHGVSConverter(HGVSConverter):
     @staticmethod
     def _hgvs_name(hgvs_string):
         """ Catches PyHGVS specific exceptions and converts to HGVSException """
+
+        HGVSConverter._hgvs_string_validation(hgvs_string)
         try:
             return HGVSName(hgvs_string)
         except pyhgvs.InvalidHGVSName as e:

genes/tests/test_hgvs.py

@@ -282,3 +282,21 @@ def _test_mitochondria_hgvs(self, hgvs_converter_type: HGVSConverterType):
 
         lib_hgvs_string = matcher.hgvs_converter.variant_coordinate_to_g_hgvs(vc)
         self.assertTrue("m." in str(lib_hgvs_string), "HGVS library conversion")
+
+    def test_biocommons_invalid_trailing_int(self):
+        return self._test_invalid_trailing_int(HGVSConverterType.BIOCOMMONS_HGVS)
+
+    def test_pyhgvs_invalid_trailing_int(self):
+        return self._test_invalid_trailing_int(HGVSConverterType.PYHGVS)
+
+    def _test_invalid_trailing_int(self, hgvs_converter_type: HGVSConverterType):
+        _bad_examples = [
+            "NM_000441.2(SLC26A4):c.1246_2341ins23",
+            "NM_003194.4(TBP):c.223_281delins50",
+        ]
+
+        matcher = HGVSMatcher(GenomeBuild.grch37(), hgvs_converter_type=hgvs_converter_type)
+        for hgvs_string in _bad_examples:
+            def get_vc():
+                return matcher.get_variant_coordinate(hgvs_string)
+            self.assertRaises(HGVSException, get_vc)