From 1d7d8b9e916d5bb1850d2373b54e8cab8b62c582 Mon Sep 17 00:00:00 2001 From: "Godwin N. Ani" Date: Tue, 6 May 2025 11:07:30 -0400 Subject: [PATCH] Update guidance.py --- PTL2/Scripts/guidance.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/PTL2/Scripts/guidance.py b/PTL2/Scripts/guidance.py index 043dd2f..4107dc7 100644 --- a/PTL2/Scripts/guidance.py +++ b/PTL2/Scripts/guidance.py @@ -97,11 +97,8 @@ def run(params): mafft_alg = 'auto' #Running Guidance (one per OG per iteration) - #for katzlab/Smith College HPC (Grid): - os.system('/guidance/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') - #Example: - #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') - + os.system('/guidance/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') + #Checking for a sequence score file; if not available, Guidance failed. if os.path.isfile(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names'): #All sequences below score cutoff