handle empty alignment error

cfe-lab · Jun 24, 2023 · bc695b9 · bc695b9
1 parent 401cd47
commit bc695b9
Showing 1 changed file with 4 additions and 1 deletion.
diff --git a/intact/intact.py b/intact/intact.py
@@ -666,7 +666,10 @@ def get_indel_impact(alignment):
 
         got_nucleotides = sequence.seq[best_match.start:best_match.start + len(got_protein) * 3]
         exp_nucleotides = reference[e.start:e.end].upper()
-        orf_alignment = aligner.align(exp_nucleotides, got_nucleotides)[0]
+        if got_nucleotides:
+            orf_alignment = aligner.align(exp_nucleotides, got_nucleotides)[0]
+        else:
+            orf_alignment = (exp_nucleotides, "-" * len(exp_nucleotides))
 
         deletions = (len(exp_protein) - len(got_protein)) * 3
         insertions = (len(got_protein) - len(exp_protein)) * 3