From 8dc9dd165362d8553be049d1e5bca7e651c46b32 Mon Sep 17 00:00:00 2001
From: Vitaliy Mysak <vmysak@bccfe.ca>
Date: Mon, 5 Jun 2023 16:30:41 -0700
Subject: [PATCH] do not run blast unless required

---
 intact/intact.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/intact/intact.py b/intact/intact.py
index fb47641..3344659 100644
--- a/intact/intact.py
+++ b/intact/intact.py
@@ -739,6 +739,12 @@ def iterate_sequences(input_file):
         for sequence in SeqIO.parse(in_handle, "fasta"):
             yield sequence
 
+
+def iterate_empty_lists():
+    while True:
+        yield []
+
+
 def intact( working_dir,
             input_file,
             subtype,
@@ -788,7 +794,7 @@ def intact( working_dir,
     rre_locus = [st.convert_from_hxb2_to_subtype(x, subtype) for x in hxb2_rre_locus]
 
     reference = st.subtype_sequence(subtype)
-    blast_it = blast_iterate(subtype, input_file)
+    blast_it = blast_iterate(subtype, input_file) if check_internal_inversion or check_nonhiv or check_scramble else iterate_empty_lists()
     blast_rows = []
 
     for sequence in iterate_sequences(input_file):