Merge branch 'main' into mite_fix

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2018-2020, Alan F Rubin and Daniel Esposito
+Copyright (c) 2018-2021, Alan F Rubin and Daniel Esposito
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

docs/conf.py

@@ -19,7 +19,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "MAVE-HGVS"
-copyright = "2018-2020, Alan F Rubin and Daniel Esposito"
+copyright = "2018-2021, Alan F Rubin and Daniel Esposito"
 author = "Alan F Rubin and Daniel Esposito"
 
 

mavehgvs/variant.py

@@ -184,7 +184,7 @@ def sort_key(x):
             else:  # pragma: no cover
                 raise ValueError("invalid variant count")
 
-        if targetseq is not None:
+        if targetseq is not None and not self.is_target_identical():
             for vtype, pos, seq in self.variant_tuples():
                 if vtype == "sub":
                     if self._prefix == "p":

tests/test_variant.py

@@ -624,6 +624,23 @@ def test_create_multivariant(self):
 
 
 class TestTargetSequenceValidation(unittest.TestCase):
+    def test_target_identity(self):
+        variant_tuples = [
+            ("ACGT", "g.="),
+            ("ACGT", "m.="),
+            ("ACGT", "o.="),
+            ("ACGT", "c.="),
+            ("ACGT", "n.="),
+            ("ACGU", "r.="),
+            ("RCQY", "p.="),
+            ("RCQY", "p.(=)"),
+        ]
+
+        for target, s in variant_tuples:
+            with self.subTest(target=target, s=s):
+                v = Variant(s, targetseq=target)
+                self.assertEqual(s, str(v))
+
     def test_matching_dna_substitution(self):
         variant_tuples = [
             ("ACGT", "c.1A>T"),