Rewrite dup as ins and try both shuffle directions

Author: b0d0nne11

src/hgvs/assemblymapper.py

@@ -13,6 +13,9 @@
     HGVSUnsupportedOperationError,
 )
 from hgvs.variantmapper import VariantMapper
+from hgvs.posedit import PosEdit
+from hgvs.edit import NARefAlt
+from hgvs.location import SimplePosition, Interval
 
 _logger = logging.getLogger(__name__)
 
@@ -180,17 +183,18 @@ def c_to_p(self, var_c):
             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 = self.c_to_g(var_c)
+            strand = self._fetch_AlignmentMapper(tx_ac=var_c.ac).strand
+
+            for shuffle_direction in [3, 5]:
+                shifted_var_g = self._far_shift(var_g, shuffle_direction, strand)
+                shifted_var_c = super(AssemblyMapper, self).g_to_c(
+                    shifted_var_g, var_c.ac, alt_aln_method=self.alt_aln_method
                 )
-            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)
+                var_out = super(AssemblyMapper, self)._c_to_p(shifted_var_c)
+
+                if var_out.posedit is not None:
+                    break
 
         return self._maybe_normalize(var_out)
 
@@ -287,6 +291,34 @@ def _maybe_normalize(self, var):
                 # fall through to return unnormalized variant
         return var
 
+    def _far_shift(self, var_g, shuffle_direction, strand):
+        """Attempt to shift a variant all the way left or right. Rewrite
+        duplications as insertions so that the change is shifted as far as
+        possible."""
+        normalizer = hgvs.normalizer.Normalizer(
+            self._norm.hdp, alt_aln_method=self.alt_aln_method, validate=False, shuffle_direction=shuffle_direction
+        )
+        shifted_var_g = normalizer.normalize(var_g)
+        if shifted_var_g.posedit.edit.type == 'dup':
+            self._replace_reference(shifted_var_g)
+            if (strand == 1 and shuffle_direction == 3) or (strand == -1 and shuffle_direction == 5):
+                shifted_var_g.posedit = PosEdit(
+                    pos=Interval(
+                        start=SimplePosition(base=shifted_var_g.posedit.pos.start.base-1),
+                        end=SimplePosition(base=shifted_var_g.posedit.pos.start.base),
+                    ),
+                    edit=NARefAlt(ref=None, alt=shifted_var_g.posedit.edit.ref)
+                )
+            else:
+                shifted_var_g.posedit = PosEdit(
+                    pos=Interval(
+                        start=SimplePosition(base=shifted_var_g.posedit.pos.end.base),
+                        end=SimplePosition(base=shifted_var_g.posedit.pos.end.base+1),
+                    ),
+                    edit=NARefAlt(ref=None, alt=shifted_var_g.posedit.edit.ref)
+                )
+        return shifted_var_g
+
 
 # <LICENSE>
 # Copyright 2018 HGVS Contributors (https://github.com/biocommons/hgvs)

tests/data/cache-py3.hdp

@@ -210,6 +210,47 @@ def test_map_of_ins_splice_region_preserved(self):
 
         self.assertEqual(str(var_p), hgvs_p)
 
+    def test_map_of_dup_splice_region_preserved(self):
+        hgvs_c = "NM_004119.2:c.1835_1837+3dup"
+        hgvs_p = "NP_004110.2:p.(Gly613_Lys614insIleGly)"
+
+        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)
+
+        hgvs_c = "NM_005228.4:c.2284-5_2290dup"
+        hgvs_p = "NP_005219.2:p.(Ala763_Tyr764insPheGlnGluAla)"
+
+        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)
+
+        hgvs_c = "NM_004456.4:c.2196-1_2196dup"
+        hgvs_p = "NP_004447.2:p.(Tyr733AspfsTer8)"
+
+        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)
+
+        hgvs_c = "NM_024529.4:c.130_131+1dup"
+        hgvs_p = "NP_078805.3:p.(Gly44dup)"
+
+        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)
+
+        hgvs_c = "NM_016222.3:c.27+2_27+5dup"
+        hgvs_p = "NP_057306.2:p.(Arg10ValfsTer20)"
+
+        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 = [