From 030401e9b011a0bc2de4b5f9740a12a40e6f1955 Mon Sep 17 00:00:00 2001 From: "Adri K. Grow" <42044618+adriannagrow@users.noreply.github.com> Date: Fri, 14 Feb 2025 13:57:57 -0500 Subject: [PATCH] Update guidance.py --- PTL2/Scripts/guidance.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/PTL2/Scripts/guidance.py b/PTL2/Scripts/guidance.py index f3ef4f3..21b4609 100644 --- a/PTL2/Scripts/guidance.py +++ b/PTL2/Scripts/guidance.py @@ -91,7 +91,10 @@ def run(params): mafft_alg = 'auto' #Running Guidance (one per OG per iteration) - 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 katzlab/Smith College HPC (Grid): + os.system('python /gridapps/software/Guidance_mid/2.1b-foss-2023a/bin/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') + #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') #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'):