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Update guidance.py

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Godwin Ani 2025-03-04 13:37:16 -05:00 committed by GitHub
parent ed3d53c108
commit 7b03c52d21
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1 changed files with 18 additions and 1 deletions
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PTL2/Scripts/guidance.py
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@ -95,7 +95,24 @@ def run(params):
#remove this block later (GA) #remove this block later (GA)
#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') #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: #Example:
subprocess.run('/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')
cmd = [
'/guidance/guidance.v2.02/www/Guidance/guidance.pl',
'--seqFile', f'{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', f'\\--{mafft_alg} --maxiterate 1000 --thread {params.guidance_threads} --bl 62 --anysymbol'
]
log_file_path = f'{params.output}/Output/Intermediate/Guidance/Output/{file[:10]}/log.txt'
# Ensure the log directory exists
os.makedirs(os.path.dirname(log_file_path), exist_ok=True)
with open(log_file_path, 'w') as log_file:
subprocess.run(cmd, stdout=log_file, stderr=subprocess.PIPE, check=True)subprocess.run('/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')
#Checking for a sequence score file; if not available, Guidance failed. #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'): if os.path.isfile(tax_guidance_outdir + '/MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names'):