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Update guidance.py

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updated comments only to clarify versions
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Katzlab 2025-06-18 08:37:19 -04:00 committed by GitHub
parent c767bd9a0a
commit c891188eec
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1 changed files with 2 additions and 2 deletions
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PTL2/Scripts/guidance.py
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@ -101,10 +101,10 @@ def run(params):
else:
mafft_alg = 'auto'
#For Guidance v2.1. COMMENT OUT THE FOLLOWING LINE IF USING v2.0.2
#For Guidance v2.1 (2025 version) 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. UNCOMMENT THE FOLLOWING LINE IF USING v2.0.2
#For Guidance v2.0.2 (origin version in PhyloTol6). 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')
#For UMass Unity users, use the following line and comment about the others: