From 06ba70c0f78dc118e0ac0a198da4c9d9de1c3e15 Mon Sep 17 00:00:00 2001 From: Godwin Ani Date: Tue, 19 Mar 2024 10:31:59 -0400 Subject: [PATCH] Update Iteration parameter --- Utilities/for_fastas/GuidanceWrapper_v2.1.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/Utilities/for_fastas/GuidanceWrapper_v2.1.py b/Utilities/for_fastas/GuidanceWrapper_v2.1.py index 73b77b4..cc6d498 100644 --- a/Utilities/for_fastas/GuidanceWrapper_v2.1.py +++ b/Utilities/for_fastas/GuidanceWrapper_v2.1.py @@ -1,7 +1,7 @@ -# Last updated Sept 2023 +# Last updated March 2023 by Godwin Ani # Authors: Auden Cote-L'Heureux and Mario Ceron-Romero -########### new code + #Dependencies import os, sys, re @@ -33,10 +33,8 @@ args = parser.parse_args() os.makedirs(args.output + '/Output/Intermediate/Guidance') os.mkdir(args.output + '/Output/Intermediate/Guidance/Input') os.mkdir(args.output + '/Output/Intermediate/Guidance/Output') -#new os.mkdir(args.output + '/Output/Guidance') os.mkdir(args.output + '/Output/NotGapTrimmed') -#new guidance_input = args.output + 'Output/Intermediate/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) #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) - #new #Handling intermediate files for each iteration. if args.keep_iter: 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') else: os.system('mv ' + iteration_folder + '/' + gdir_file + ' ' + iteration_folder + '/' + file.split('.')[0].split('_preguidance')[0] + '_' + gdir_file) - #new + else: