Fix ins/dups where splice region is preserved

Author: b0d0nne11

src/hgvs/assemblymapper.py

@@ -171,7 +171,27 @@ def n_to_c(self, var_n):
         return self._maybe_normalize(var_out)
 
     def c_to_p(self, var_c):
-        var_out = super(AssemblyMapper, self).c_to_p(var_c)
+        var_out = super(AssemblyMapper, self)._c_to_p(var_c)
+
+        if (
+            var_c.posedit.edit.type in ['ins', 'dup']
+            and var_c.type in "cnr"
+            and var_c.posedit.pos is not None
+            and (var_c.posedit.pos.start.offset != 0 or var_c.posedit.pos.end.offset != 0)
+            and var_out.posedit is None
+        ):
+            if self._fetch_AlignmentMapper(tx_ac=var_c.ac).strand == 1:
+                normalizer = hgvs.normalizer.Normalizer(
+                    self._norm.hdp, alt_aln_method=self.alt_aln_method, validate=False, shuffle_direction=5
+                )
+            else:
+                normalizer = hgvs.normalizer.Normalizer(
+                    self._norm.hdp, alt_aln_method=self.alt_aln_method, validate=False, shuffle_direction=3
+                )
+            var_g = normalizer.normalize(self.c_to_g(var_c))
+            var_c = self.g_to_c(var_g, var_c.ac)
+            var_out = super(AssemblyMapper, self)._c_to_p(var_c)
+
         return self._maybe_normalize(var_out)
 
     def relevant_transcripts(self, var_g):

src/hgvs/variantmapper.py

@@ -429,6 +429,21 @@ def c_to_p(self, var_c, pro_ac=None):
 
         """
 
+        var_p = self._c_to_p(var_c, pro_ac=None)
+
+        if (
+            var_c.posedit.edit.type in ['ins', 'dup']
+            and var_c.type in "cnr"
+            and var_c.posedit.pos is not None
+            and (var_c.posedit.pos.start.offset != 0 or var_c.posedit.pos.end.offset != 0)
+            and var_p.posedit is None
+        ):
+            raise HGVSUnsupportedOperationError('c_to_p not supported on VariantMapper for this var_c, try AssemblyMapper')
+
+        return var_p
+
+
+    def _c_to_p(self, var_c, pro_ac=None):
         if not (var_c.type == "c"):
             raise HGVSInvalidVariantError("Expected a cDNA (c.) variant; got " + str(var_c))
         if self._validator:

tests/data/cache-py3.hdp

@@ -58,6 +58,5 @@ ID00056	NC_000010.10:g.89693009delG	NM_000314.4:c.492+1delG	NP_000305.3:p.?
 ID00057	NC_000010.10:g.89711873A>C	NM_000314.4:c.493-2A>C	NP_000305.3:p.?
 ID00058	NC_000010.10:g.89717676G>A	NM_000314.4:c.701G>A	NP_000305.3:p.(Arg234Gln)
 ID00059	NC_000010.10:g.89717777G>A	NM_000314.4:c.801+1G>A	NP_000305.3:p.?
-ID00060	NC_000010.10:g.89720648dupT	NM_000314.4:c.802-3dupT	NP_000305.3:p.?
 ID00061	NC_000005.9:g.131705667G>T	NM_003060.3:c.3G>T	NP_003051.1:p.Met1?
 ID00062	NC_000005.9:g.131706014G>A	NM_003060.3:c.350G>A	NP_003051.1:p.(Trp117*)

tests/data/gcp/real.tsv

@@ -55,6 +55,9 @@ def get_tx_seq(self, ac):
     def get_seq(self, ac, start_i=None, end_i=None):
         return self.get_tx_seq(ac)[start_i:end_i]
 
+    def get_pro_ac_for_tx_ac(self, ac):
+        return 'MOCK'
+
     #
     # internal methods
     #

tests/support/mock_input_source.py

@@ -201,6 +201,16 @@ def test_c_to_p_with_stop_gain(self):
         self.assertEqual(str(var_p), hgvs_p)
 
 
+    def test_map_of_ins_splice_region_preserved(self):
+        hgvs_c = "NM_004119.2:c.1837+21_1837+22insCGAGAGAATATGAATATGATCTCAAATGGGAGTTTCCAAGAGAAAATTTAGAGTTTGGTAAGAATGGAATGTGCCAAA"
+        hgvs_p = "NP_004110.2:p.(Lys614_Val615insAsnGlyMetCysGlnThrArgGluTyrGluTyrAspLeuLysTrpGluPheProArgGluAsnLeuGluPheGlyLys)"
+
+        var_c = self.hp.parse_hgvs_variant(hgvs_c)
+        var_p = self.am.c_to_p(var_c)
+
+        self.assertEqual(str(var_p), hgvs_p)
+
+
 class Test_RefReplacement(unittest.TestCase):
     test_cases = [
         # These casese attempt to test reference update in four dimensions: