Update boundary conditions

biocommons · Dec 19, 2023 · 43b08ec · 43b08ec
1 parent 79998d8
commit 43b08ec
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Showing 5 changed files with 25 additions and 32 deletions.
diff --git a/src/hgvs/utils/altseqbuilder.py b/src/hgvs/utils/altseqbuilder.py
@@ -200,9 +200,12 @@ def _get_variant_region(self):
         elif self._var_c.posedit.edit.type == "ins" and self._var_c.posedit.pos.start.offset == 0 and self._var_c.posedit.pos.end.offset == 1:
             # ins at exon-intron boundary
             result = self.EXON
-        elif self._var_c.posedit.edit.type == "dup" and self._var_c.posedit.pos.start.offset <= -1 and self._var_c.posedit.pos.end.offset >= -1:
+        elif self._var_c.posedit.edit.type == "dup" and self._var_c.posedit.pos.end.offset == -1:
             # dup at intron-exon boundary
             result = self.EXON
+        elif self._var_c.posedit.edit.type == "dup" and self._var_c.posedit.pos.start.offset == 1:
+            # dup at exon-intron boundary
+            result = self.EXON
         elif self._var_c.posedit.pos.start.offset != 0 or self._var_c.posedit.pos.end.offset != 0:
             # leave out anything else intronic for now
             result = self.INTRON

diff --git a/tests/data/cache-py3.hdp b/tests/data/cache-py3.hdp
diff --git a/tests/test_hgvs_assemblymapper.py b/tests/test_hgvs_assemblymapper.py
@@ -201,14 +201,6 @@ def test_c_to_p_with_stop_gain(self):
         self.assertEqual(str(var_p), hgvs_p)
 
     def test_map_of_dup_intron_exon_boundary(self):
-        hgvs_c = "NM_004380.2:c.3251-1dup"
-        hgvs_p = "NP_004371.2:p.(Ile1084SerfsTer3)"
-
-        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.132-2_132-1dup"
         hgvs_p = "NP_078805.3:p.(Thr45GlyfsTer65)"
 
@@ -217,34 +209,35 @@ def test_map_of_dup_intron_exon_boundary(self):
 
         self.assertEqual(str(var_p), hgvs_p)
 
-        hgvs_c = "NM_004985.4:c.112-1_113dup"
-        hgvs_p = "NP_004976.2:p.(Glu37dup)"
+        hgvs_c = "NM_004985.4:c.112-8_112-1dup"
+        hgvs_p = "NP_004976.2:p.(Asp38LeufsTer10)"
 
         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_004380.2:c.3251dup"
-        hgvs_p = "NP_004371.2:p.(Phe1085LeufsTer2)"
+    def test_map_of_dup_intron_exon_boundary_rc(self):
+        hgvs_c = "NM_004380.2:c.3251-1dup"
+        hgvs_p = "NP_004371.2:p.(Ile1084SerfsTer3)"
 
         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)
 
     def test_map_of_dup_exon_intron_boundary(self):
-        hgvs_c = "NM_021140.3:c.619dup"
-        hgvs_p = "NP_066963.2:p.(Ile207AsnfsTer10)"
+        hgvs_c = "NM_024529.4:c.131+1_131+3dup"
+        hgvs_p = "NP_078805.3:p.(Gly44_Thr45insVal)"
 
         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)
 
-    def test_map_of_dup_intron_exon_boundary_rc(self):
-        hgvs_c = "NM_004985.4:c.112-1_112dup"
-        hgvs_p = "NP_004976.2:p.(Asp38GlyfsTer8)"
+    def test_map_of_dup_exon_intron_boundary_rc(self):
+        hgvs_c = "NM_004985.4:c.111+1_111+4dup"
+        hgvs_p = "NP_004976.2:p.(Asp38GlyfsTer11)"
 
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         var_p = self.am.c_to_p(var_c)

diff --git a/tests/test_hgvs_variantmapper.py b/tests/test_hgvs_variantmapper.py
@@ -131,34 +131,30 @@ def test_map_of_ins_exon_intron_boundary(self):
         self.assertEqual(str(var_p), "NP_004371.2:p.(Phe1085LeufsTer2)")
 
     def test_map_of_dup_intron_exon_boundary(self):
-        hgvs_c = "NM_004380.2:c.3251-1dup"
+        hgvs_c = "NM_024529.4:c.132-2_132-1dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         with self.assertRaises(HGVSError):
             var_p = self.vm.c_to_p(var_c)
 
-        hgvs_c = "NM_024529.4:c.132-2_132-1dup"
+        hgvs_c = "NM_004985.4:c.112-8_112-1dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         with self.assertRaises(HGVSError):
             var_p = self.vm.c_to_p(var_c)
 
-        hgvs_c = "NM_004985.4:c.112-1_113dup"
+    def test_map_of_dup_intron_exon_boundary_rc(self):
+        hgvs_c = "NM_004380.2:c.3251-1dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         with self.assertRaises(HGVSError):
             var_p = self.vm.c_to_p(var_c)
 
-        hgvs_c = "NM_004380.2:c.3251dup"
-        var_c = self.hp.parse_hgvs_variant(hgvs_c)
-        var_p = self.vm.c_to_p(var_c)
-        self.assertEqual(str(var_p), "NP_004371.2:p.(Phe1085LeufsTer2)")
-
     def test_map_of_dup_exon_intron_boundary(self):
-        hgvs_c = "NM_021140.3:c.619dup"
+        hgvs_c = "NM_024529.4:c.131+1_131+3dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
-        var_p = self.vm.c_to_p(var_c)
-        self.assertEqual(str(var_p), "NP_066963.2:p.(Ile207AsnfsTer10)")
+        with self.assertRaises(HGVSError):
+            var_p = self.vm.c_to_p(var_c)
 
-    def test_map_of_dup_intron_exon_boundary_rc(self):
-        hgvs_c = "NM_004985.4:c.112-1_112dup"
+    def test_map_of_dup_exon_intron_boundary_rc(self):
+        hgvs_c = "NM_004985.4:c.111+1_111+4dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         with self.assertRaises(HGVSError):
             var_p = self.vm.c_to_p(var_c)

diff --git a/tests/test_hgvs_variantmapper_cp_sanity.py b/tests/test_hgvs_variantmapper_cp_sanity.py
@@ -174,7 +174,8 @@ def test_dup_intron_exon_boundary(self):
     def test_dup_exon_intron_boundary(self):
         hgvsc = "NM_999999.1:c.39+1dup"
         hgvsp_expected = "MOCK:p.?"
-        self._run_conversion(hgvsc, hgvsp_expected)
+        with self.assertRaises(HGVSError):
+            self._run_conversion(hgvsc, hgvsp_expected)
 
     def test_five_prime_utr(self):
         hgvsc = "NM_999999.1:c.-2A>G"