From 16a96f137ed163dd8b5e9c1bb22fa65fd71c1a9c Mon Sep 17 00:00:00 2001
From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com>
Date: Fri, 18 Apr 2025 08:48:42 -0400
Subject: [PATCH] Update guidance_path param

---
 PTL2/Scripts/guidance.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PTL2/Scripts/guidance.py b/PTL2/Scripts/guidance.py
index 2bc0147..e5e8500 100644
--- a/PTL2/Scripts/guidance.py
+++ b/PTL2/Scripts/guidance.py
@@ -96,10 +96,10 @@ def run(params):
 				else:
 					mafft_alg = 'auto'
 
-				#For Guidance v2.1
+				#For Guidance v2.1. COMMENT OUT THE FOLLOWING LINE IF USING v2.0.2
 				os.system('python ' + params.guidance_path + '/script/guidance_main.py --seqFile ' + guidance_input + '/' + file + ' --msaProgram MAFFT --seqType aa --outDir ' + tax_guidance_outdir + ' --seqCutoff ' + str(params.seq_cutoff) + ' --colCutoff ' + str(params.col_cutoff) + " --outOrder as_input --bootstraps 10 --MSA_Param '\\--" + mafft_alg + " --maxiterate 1000 --thread " + str(params.guidance_threads) + " --bl 62 --anysymbol' > " + params.output + '/Output/Intermediate/Guidance/Output/' + file[:10] + '/log.txt')
 
-				#For Guidance v2.0.2
+				#For Guidance v2.0.2. UNCOMMENT THE FOLLOWING LINE IF USING v2.0.2
 				#os.system('Scripts/guidance.v2.02/www/Guidance/guidance.pl --seqFile ' + guidance_input + '/' + file + ' --msaProgram MAFFT --seqType aa --outDir ' + tax_guidance_outdir + ' --seqCutoff ' + str(params.seq_cutoff) + ' --colCutoff ' + str(params.col_cutoff) + " --outOrder as_input --bootstraps 10 --MSA_Param '\\--" + mafft_alg + " --maxiterate 1000 --thread " + str(params.guidance_threads) + " --bl 62 --anysymbol' > " + params.output + '/Output/Intermediate/Guidance/Output/' + file[:10] + '/log.txt')
 
 				#Checking for a sequence score file; if not available, Guidance failed.