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Update Iteration parameter

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Godwin Ani 2024-03-19 10:31:59 -04:00 committed by GitHub
parent b91cf0fb63
commit 06ba70c0f7
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1 changed files with 3 additions and 6 deletions
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Utilities/for_fastas/GuidanceWrapper_v2.1.py
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@ -1,7 +1,7 @@
# Last updated Sept 2023 # Last updated March 2023 by Godwin Ani
# Authors: Auden Cote-L'Heureux and Mario Ceron-Romero # Authors: Auden Cote-L'Heureux and Mario Ceron-Romero
########### new code
#Dependencies #Dependencies
import os, sys, re import os, sys, re
@ -33,10 +33,8 @@ args = parser.parse_args()
os.makedirs(args.output + '/Output/Intermediate/Guidance') os.makedirs(args.output + '/Output/Intermediate/Guidance')
os.mkdir(args.output + '/Output/Intermediate/Guidance/Input') os.mkdir(args.output + '/Output/Intermediate/Guidance/Input')
os.mkdir(args.output + '/Output/Intermediate/Guidance/Output') os.mkdir(args.output + '/Output/Intermediate/Guidance/Output')
#new
os.mkdir(args.output + '/Output/Guidance') os.mkdir(args.output + '/Output/Guidance')
os.mkdir(args.output + '/Output/NotGapTrimmed') os.mkdir(args.output + '/Output/NotGapTrimmed')
#new
guidance_input = args.output + 'Output/Intermediate/Guidance/Input/' guidance_input = args.output + 'Output/Intermediate/Guidance/Input/'
os.system('cp -r ' + args.input + '/* ' + guidance_input) os.system('cp -r ' + args.input + '/* ' + guidance_input)
@ -92,7 +90,6 @@ for file in [f for f in os.listdir(guidance_input) if f.endswith('.fa') or f.end
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)
#new
#Handling intermediate files for each iteration. #Handling intermediate files for each iteration.
if args.keep_iter: if args.keep_iter:
if i +1 < args.iterations: if i +1 < args.iterations:
@ -111,7 +108,7 @@ for file in [f for f in os.listdir(guidance_input) if f.endswith('.fa') or f.end
os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file + '.aln') os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file + '.aln')
else: else:
os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file) os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file)
#new
else: else: