diff --git a/PTL2/Scripts/guidance.py b/PTL2/Scripts/guidance.py index 27c21e8..72be893 100644 --- a/PTL2/Scripts/guidance.py +++ b/PTL2/Scripts/guidance.py @@ -101,13 +101,13 @@ def run(params): else: mafft_alg = 'auto' - #For Guidance v2.1 (2025 version) COMMENT OUT THE FOLLOWING LINE IF USING v2.0.2 + #For Guidance v2.1 (2025 version) on the grid ... 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 (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: + #For UMass Unity users, use the following line and comment out the others: #os.system('python3 /work/pi_lkatz_smith_edu/Guidance/guidance_Linux/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 Smith College Grid users, use the following line and comment about the others: