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Adding keep_iter parameter

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Godwin Ani 2024-03-22 15:05:54 -04:00 committed by GitHub
parent f40873b6b0
commit 80ad29e6d5
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1 changed files with 18 additions and 2 deletions
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20
PTL2/Scripts/guidance.py
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@ -98,8 +98,24 @@ def run(params):
guidance_removed_file.write(line)
#Copying over the old file with the new results
os.system('cp ' + tax_guidance_outdir + '/Seqs.Orig.fas.FIXED.Without_low_SP_Seq.With_Names ' + guidance_input + '/' + file)
#Cleaning up the intermediate files for the iteration.
os.system('rm -r ' + tax_guidance_outdir + '/*')
#Handling intermediate files for each iteration.
if params.keep_iter:
if i +1 < params.guidance_iters:
os.makedirs(params.output + '/Output/Intermediate/Guidance/Iterations/', exist_ok = True)
os.makedirs(params.output + '/Output/Intermediate/Guidance/Iterations/' + str(i+1)+'/', exist_ok = True)
os.makedirs(params.output + '/Output/Intermediate/Guidance/Iterations/' + str(i+1) + '/' + file.split('.')[0].split('_preguidance')[0], exist_ok = True)
iteration_folder = params.output + '/Output/Intermediate/Guidance/Iterations/' + str(i +1) + '/' + file.split('.')[0].split('_preguidance')[0]
os.system('cp -r ' + tax_guidance_outdir + '/* ' + iteration_folder)
os.system('rm -r ' + tax_guidance_outdir + '/*')
if not params.keep_temp:
for gdir_file in os.listdir(iteration_folder):
if gdir_file not in ('MSA.MAFFT.Guidance2_res_pair_seq.scr_with_Names', 'MSA.MAFFT.aln.With_Names', 'MSA.MAFFT.Guidance2_res_pair_col.scr', 'log', 'postGuidance_preTrimAl_unaligned.fasta'):
os.system('rm -r ' + iteration_folder + '/' + gdir_file)
else:
if gdir_file == 'MSA.MAFFT.aln.With_Names':
os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file + '.aln')
else:
os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file)
else:
fail = True
break