fixes #258, #330, #342: ensure that start and end datums are compatible

hgvs/location.py

@@ -115,6 +115,11 @@ def is_uncertain(self):
         """return True if the position is marked uncertain or undefined"""
         return self.uncertain or self.base is None or self.offset is None
 
+    @property
+    def is_intronic(self):
+        """returns True if the variant is intronic (if the offset is None or non-zero)"""
+        return (self.offset is None or self.offset != 0)
+
     def __sub__(lhs, rhs):
         assert type(lhs) == type(rhs), "Cannot substract coordinates of different representations"
         if lhs.datum != rhs.datum:

tests/test_bugs.py

@@ -39,6 +39,19 @@ def test_285_partial_palindrome_inversion(self):
         self.assertEqual(str(vn), "NM_000088.3:c.590_599inv")
 
 
+    def test_293_parser_attribute_assignment_error(self):
+        # https://bitbucket.org/biocommons/hgvs/issues/293/        
+        var = self.hp.parse_hgvs_variant('NG_029146.1:g.6494delG')
+        self.vn.normalize(var)  # per issue, should raise error
+
+    def test_314_parsing_identity_variant(self):
+        v = self.hp.parse_hgvs_variant("NM_206933.2:c.6317=")
+        self.assertEqual(str(v), "NM_206933.2:c.6317=")
+
+        v = self.hp.parse_hgvs_variant("NM_206933.2:c.6317C=")
+        self.assertEqual(str(v), "NM_206933.2:c.6317C=")
+
+
     def test_324_error_normalizing_simple_inversion(self):
         v = self.hp.parse_hgvs_variant("NM_000535.5:c.1673_1674inv")
         vn = self.vn.normalize(v)
@@ -89,10 +102,3 @@ def test_346_reject_partial_alignments(self):
                                                    alt_ac="NC_000010.10",
                                                    alt_aln_method="splign")
 
-    def test_314_parsing_identity_variant(self):
-        v = self.hp.parse_hgvs_variant("NM_206933.2:c.6317=")
-        self.assertEqual(str(v), "NM_206933.2:c.6317=")
-
-        v = self.hp.parse_hgvs_variant("NM_206933.2:c.6317C=")
-        self.assertEqual(str(v), "NM_206933.2:c.6317C=")
-

tests/test_hgvs_location.py

@@ -35,14 +35,17 @@ def test_success(self):
         self.assertEqual(cdsp.base, 5)
         self.assertEqual(cdsp.offset, 0)
         self.assertEqual(str(cdsp), "5")
+        self.assertFalse(cdsp.is_intronic)
 
         #r.5+6
         cdsp.offset = 6
         self.assertEqual(str(cdsp), "5+6")
+        self.assertTrue(cdsp.is_intronic)
 
         #r.5+?
         cdsp.offset = None
         self.assertEqual(str(cdsp), "5+?")
+        self.assertTrue(cdsp.is_intronic)
 
         #r.(5+?)
         cdsp.uncertain = True