Merge pull request #65 from mutalyzer/synonymous-p-is

Fix bug in recognizing p.(=)

mutalyzer/util.py

@@ -439,14 +439,14 @@ def in_frame_description(s1, s2):
     @todo: More intelligently handle longest_common_prefix().
     @todo: Refactor this code (too many return statements).
     """
+    s1 = s1.rstrip('*')
+    s2 = s2.rstrip('*')
+
     if s1 == s2:
         # Nothing happened.
         return ('p.(=)', 0, 0, 0)
 
     s2_stop = '*' in s2
-    s1 = s1.rstrip('*')
-    s2 = s2.rstrip('*')
-
     lcp = len(longest_common_prefix(s1, s2))
     lcs = len(longest_common_suffix(s1[lcp:], s2[lcp:]))
     s1_end = len(s1) - lcs

tests/test_variantchecker.py

@@ -1349,3 +1349,11 @@ class TestVariantchecker(MutalyzerTest):
         """
         check_variant('NM_000193.2:c.1388_1389insC', self.output)
         assert 'NM_000193.2(SHH_i001):p.(*463Cysext*?)' in self.output.getOutput('protDescriptions')
+
+    @fix(cache('AB026906.1'))
+    def test_synonymous_p_is(self):
+        """
+        Synonymous mutation should yield a p.(=) description.
+        """
+        check_variant('AB026906.1:c.276C>T', self.output)
+        assert 'AB026906.1(SDHD_i001):p.(=)' in self.output.getOutput('protDescriptions')