Add tests for dups spanning boundary

biocommons · Jan 23, 2024 · 8c9faf2 · 8c9faf2
1 parent c9be9db
commit 8c9faf2
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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
@@ -201,6 +201,14 @@ 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_024529.4:c.132-1_132dup"
+        hgvs_p = "NP_078805.3:p.?"
+
+        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)"
 
@@ -227,6 +235,14 @@ def test_map_of_dup_intron_exon_boundary_rc(self):
         self.assertEqual(str(var_p), hgvs_p)
 
     def test_map_of_dup_exon_intron_boundary(self):
+        hgvs_c = "NM_024529.4:c.130_131+1dup"
+        hgvs_p = "NP_078805.3:p.?"
+
+        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.131+1_131+3dup"
         hgvs_p = "NP_078805.3:p.(Thr45Ter)"
 

diff --git a/tests/test_hgvs_variantmapper.py b/tests/test_hgvs_variantmapper.py
@@ -131,6 +131,11 @@ 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_024529.4:c.132-1_132dup"
+        var_c = self.hp.parse_hgvs_variant(hgvs_c)
+        var_p = self.vm.c_to_p(var_c)
+        self.assertEqual(str(var_p), "NP_078805.3:p.?")
+
         hgvs_c = "NM_024529.4:c.132-2_132-1dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         with self.assertRaises(HGVSError):
@@ -148,6 +153,11 @@ def test_map_of_dup_intron_exon_boundary_rc(self):
             var_p = self.vm.c_to_p(var_c)
 
     def test_map_of_dup_exon_intron_boundary(self):
+        hgvs_c = "NM_024529.4:c.130_131+1dup"
+        var_c = self.hp.parse_hgvs_variant(hgvs_c)
+        var_p = self.vm.c_to_p(var_c)
+        self.assertEqual(str(var_p), "NP_078805.3:p.?")
+
         hgvs_c = "NM_024529.4:c.131+1_131+3dup"
         var_c = self.hp.parse_hgvs_variant(hgvs_c)
         with self.assertRaises(HGVSError):