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Godwin Ani 2024-04-11 14:43:53 -04:00 committed by GitHub
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24
PTL2/Scripts/guidance.py
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@ -1,4 +1,4 @@
# Last updated Sept 2023 # Last updated Apr 2 2024
# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero # Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
# This script runs Guidance in an iterative fashion for more both MSA construction # This script runs Guidance in an iterative fashion for more both MSA construction
@ -98,7 +98,27 @@ def run(params):
guidance_removed_file.write(line) guidance_removed_file.write(line)
#Copying over the old file with the new results #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) 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.
#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)
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)
os.system('rm -r ' + tax_guidance_outdir + '/*') os.system('rm -r ' + tax_guidance_outdir + '/*')
else: else:
fail = True fail = True