Merge pull request #539 from uclahs-cds/czhu-fix-call-noncoding

fix the additional nucleotide issue during translation

moPepGen/svgraph/TVGNode.py

@@ -484,7 +484,10 @@ def append_right(self, other:TVGNode) -> None:
 
     def translate(self) -> svgraph.PVGNode:
         """ translate to a PVGNode """
-        seq = self.seq.translate()
+        if not self.out_edges:
+            seq = self.seq[:len(self.seq) - len(self.seq) % 3].translate()
+        else:
+            seq = self.seq.translate()
 
         locations = []
         for loc in self.seq.locations:

moPepGen/util/brute_force_noncoding.py

@@ -76,7 +76,9 @@ def brute_force_noncoding(args:argparse.Namespace):
         for it in re.finditer('M', str(frame_seq.seq)):
             i = it.start()
             j = frame_seq.seq[i:].find('*')
-            if not j == -1:
+            if j == -1:
+                j = len(frame_seq.seq)
+            else:
                 j += i
             aa_seq = frame_seq[i:j]
             peptides = aa_seq.enzymatic_cleave(rule, exception)