Merge pull request #731 from jPleyte/730-single-letter-amino-acid-fix

#730 - Fix single letter amino acid bug

src/hgvs/edit.py

@@ -190,7 +190,7 @@ def format(self, conf=None):
         p_3_letter, p_term_asterisk, p_init_met = self._format_config_aa(conf)
 
         if self.init_met and p_init_met:
-            s = "Met1?"
+            s = "Met1?" if p_3_letter else "M1?"
         elif self.init_met and not p_init_met:
             s = "?"
         # subst and delins

tests/issues/test_730.py

@@ -0,0 +1,39 @@
+import os
+import unittest
+
+import pytest
+from support import CACHE
+
+import hgvs.assemblymapper
+import hgvs.dataproviders.uta
+
+
+@pytest.mark.issues
+class Test_Issues(unittest.TestCase):
+    """
+    HGVS-730 fixes an issue where AARefAlt.format() sometimes returned the three letter amino acid
+    when the single letter format was requested.
+    """
+
+    @classmethod
+    def setUpClass(self):
+        self.hdp = hgvs.dataproviders.uta.connect(
+            mode=os.environ.get("HGVS_CACHE_MODE", "run"), cache=CACHE
+        )
+        self.am37 = hgvs.assemblymapper.AssemblyMapper(
+            self.hdp, replace_reference=True, assembly_name="GRCh37", alt_aln_method="splign"
+        )
+        self.hp = hgvs.parser.Parser()
+
+    def test_730_format_startloss_as_configured(self):
+        """
+        Parse a start loss and make sure the one letter and three letter protein genotypes come back as expected.
+        """
+        var_g = self.hp.parse_hgvs_variant("NC_000016.9:g.89985662_89985667del")
+        var_c = self.am37.g_to_c(var_g, str("NM_002386.3"))
+        var_p = self.am37.c_to_p(var_c)
+        var_p_one_letter = var_p.format(conf={"p_3_letter": False})
+        var_p_three_letter = var_p.format(conf={"p_3_letter": True})
+
+        self.assertEqual(var_p_one_letter, "NP_002377.4:p.M1?")
+        self.assertEqual(var_p_three_letter, "NP_002377.4:p.Met1?")