From 873862adbcb7a0cc24a0f8fb769a94c68f6465b3 Mon Sep 17 00:00:00 2001 From: GiuliaRibeiro <41350697+GiuliaRibeiro@users.noreply.github.com> Date: Thu, 7 Aug 2025 09:53:42 -0400 Subject: [PATCH] Update guidance.py fixed 70gapTrimmed line --- PTL2/Scripts/guidance.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/PTL2/Scripts/guidance.py b/PTL2/Scripts/guidance.py index 78259bc..ececd77 100644 --- a/PTL2/Scripts/guidance.py +++ b/PTL2/Scripts/guidance.py @@ -186,7 +186,7 @@ def run(params): 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] + '.70gapTrimmed.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') + os.system('cp ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.70gapTrimmed.fasta ' + params.output + '/Output/Guidance/' + file.split('.')[0].split('_preguidance')[0] + '.70gapTrimmed.fasta') os.system('cp ' + tax_guidance_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta ' + params.output + '/Output/NotGapTrimmed/' + file.split('.')[0].split('_preguidance')[0] + '.postGuidance_preTrimAl_aligned.fasta') #Removing intermediate files if not --keep_temp @@ -225,5 +225,6 @@ def run(params): +