From c0dfdb6248b130938b83d721a3cb26bfad731905 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Thu, 9 Jan 2025 12:11:10 -0500 Subject: [PATCH] Adding trimal cutoff as parameter --- PTL2/Scripts/guidance.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PTL2/Scripts/guidance.py b/PTL2/Scripts/guidance.py index 9b72c2b..ffb4a36 100644 --- a/PTL2/Scripts/guidance.py +++ b/PTL2/Scripts/guidance.py @@ -150,7 +150,7 @@ def run(params): os.system('mafft ' + tax_guidance_outdir + '/postGuidance_preTrimAl_unaligned.fasta > ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta') #Gap trimming - os.system('Scripts/trimal-trimAl/source/trimal -in ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta -out ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fasta -gapthreshold 0.05 -fasta') + os.system('Scripts/trimal-trimAl/source/trimal -in ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta -out ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fasta -gapthreshold ' + str(params.trimal_cutoff) + ' -fasta') #Copying over final aligments (pre and post gap trimming) into output folder. os.system('cp ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fasta ' + params.output + '/Output/Guidance/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fasta')