Make sure non-coding doesn't have 5' or 3' UTR offsets

counsyl · Sep 7, 2021 · 957d25c · 957d25c
1 parent a6e238e
commit 957d25c
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/pyhgvs/__init__.py b/pyhgvs/__init__.py
@@ -851,6 +851,11 @@ def parse_allele(self, allele):
 
         if kind in ("c", 'n'):
             self.parse_cdna(details)
+            if kind == 'n':  # Ensure no 3'UTR or 5'UTR coords in non-coding
+                if self.cdna_start.coord < 0:
+                    raise InvalidHGVSName(allele, 'allele', "Non-coding transcript cannot contain negative (5'UTR) coordinates")
+                if self.cdna_start.landmark == 'cdna_stop' or self.cdna_end and self.cdna_end.landmark == 'cdna_stop':
+                    raise InvalidHGVSName(allele, 'allele', "Non-coding transcript cannot contain '*' (3'UTR) coordinates")
         elif kind == "p":
             self.parse_protein(details)
         elif kind == "g":