fix index error

arpcard · Aug 28, 2018 · 7197e9c · 7197e9c
1 parent 947e082
commit 7197e9c
Showing 1 changed file with 7 additions and 5 deletions.
diff --git a/app/Base.py b/app/Base.py
@@ -276,6 +276,7 @@ def nudge_strict_to_perfect(self, strict):
                 orf_dna_sequence_ = ""
                 orf_end_ = ""
                 orf_start_ = ""
+                _partial_protein = ""
                 # Missing n-terminus or c-terminus
                 if len(query) < len(reference) and query in reference:
                     length_nucleotides = (len(reference) - len(strict[s]["match"]))*3
@@ -290,7 +291,7 @@ def nudge_strict_to_perfect(self, strict):
 
                     # check if partial_bases are multiples of 3
                     if len(partial_bases) % 3 == 0:
-                        # logger.info("Missing part: {}".format(partial_bases))
+                        logger.info("Missing part: [{}]".format(partial_bases))
                         if strict[s]["orf_strand"] == "-":
                             # update orf_end
                             strict[s]["orf_end_possible"] = orf_end_ + 1
@@ -306,11 +307,12 @@ def nudge_strict_to_perfect(self, strict):
                             partial_protein = str(Seq(partial_bases, generic_dna).translate(table=11))
                             # logger.info("Forward strand: {}".format(partial_protein))
 
-                        # logger.info("Translated protein: {}".format(partial_protein))
+                        logger.info("Translated protein: [{}]".format(partial_protein))
                         # update start codon to M for all other alternate start codons
-                        _partial_protein = partial_protein[0]
-                        if partial_protein[0] in ["L","M","I","V"]:
-                            _partial_protein = "M"+partial_protein[1:]
+                        if len(_partial_protein) > 0:
+                            _partial_protein = partial_protein[0]
+                            if partial_protein[0] in ["L","M","I","V"]:
+                                _partial_protein = "M"+partial_protein[1:]
 
                         combine = _partial_protein + strict[s]["match"]