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Update guidance.py

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Godwin N. Ani 2025-07-17 14:47:39 -04:00 committed by GitHub
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PTL2/Scripts/guidance.py
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@ -183,7 +183,7 @@ 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') 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 #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 ' + str(params.trimal_cutoff) + ' -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] + '.70gapTrimmed.fasta -gapthreshold ' + str(params.trimal_cutoff) + ' -fasta')
#Copying over final aligments (pre and post gap trimming) into output folder. #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] + '.95gapTrimmed.fasta ' + params.output + '/Output/Guidance/' + file.split('.')[0].split('_preguidance')[0] + '.95gapTrimmed.fasta')