From f8e578eaabf9e24321afad2a9f11b7c54dc2d021 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Wed, 27 Sep 2023 08:48:59 -0700
Subject: [PATCH] use aligned_sequence.slice where possible

---
 util/find_orf.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/util/find_orf.py b/util/find_orf.py
index 8f70279..d81a864 100644
--- a/util/find_orf.py
+++ b/util/find_orf.py
@@ -60,7 +60,7 @@ def find_candidate_positions(aligned_sequence, e):
                     name=e.name,
                     start=closest_start,
                     end=closest_end,
-                    nucleotides=str(aligned_sequence.this.seq[closest_start:(closest_end + 1)]),
+                    nucleotides=str(aligned_sequence.slice(closest_start, closest_end).this.seq),
                     aminoacids=got_aminoacids,
                     protein=got_protein,
                     deletion_tolerence=e.deletion_tolerence,