From 21e54ab7e447389cb838963b9d7766e555bc8cd5 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Mon, 1 Apr 2024 11:04:37 -0400 Subject: [PATCH] Reverting to previous version --- PTL2/Scripts/guidance.py | 20 ++------------------ 1 file changed, 2 insertions(+), 18 deletions(-) diff --git a/PTL2/Scripts/guidance.py b/PTL2/Scripts/guidance.py index 2275805..3d68db2 100644 --- a/PTL2/Scripts/guidance.py +++ b/PTL2/Scripts/guidance.py @@ -98,24 +98,8 @@ 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) - #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) + #Cleaning up the intermediate files for the iteration. + os.system('rm -r ' + tax_guidance_outdir + '/*') else: fail = True break