From b2e381e01d6a715562594cb0657611929d59ff52 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Mon, 2 Oct 2023 11:12:44 -0400 Subject: [PATCH] Typo fix --- PTL1/Transcriptomes/Scripts/wrapper.py | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/PTL1/Transcriptomes/Scripts/wrapper.py b/PTL1/Transcriptomes/Scripts/wrapper.py index 16ebf6b..61c7a72 100644 --- a/PTL1/Transcriptomes/Scripts/wrapper.py +++ b/PTL1/Transcriptomes/Scripts/wrapper.py @@ -8,7 +8,7 @@ def get_args(): parser = argparse.ArgumentParser( prog = 'PhyloToL v6.0 Part 1 for Transcriptomes', - description = "Updated January 19th, 2023 by Auden Cote-L'Heureux. Link to GitHub: https://github.com/AudenCote/PhyloToL_v6.0" + description = "Updated September 29th, 2023 by Auden Cote-L'Heureux. Link to GitHub: https://github.com/AudenCote/PhyloToL_v6.0" ) parser.add_argument('-s', '--script', default = -1, type = int, choices = { 1, 2, 3, 4, 5, 6, 7 }, help = 'Script to run if you are only running one script') @@ -30,20 +30,20 @@ def get_args(): def script_one(args, ten_digit_codes): for file in os.listdir(args.assembled_transcripts): if file[10:] == '_assembledTranscripts.fasta' and file[:10] in ten_digit_codes: - os.system('python 1a_ContigFiltStats.py --input_file ' + args.assembled_transcripts + '/' + file + ' --output_file ' + args.output + '/Output/' + file[:10] + ' --minLen ' + str(args.minlen) + ' --maxLen ' + str(args.maxlen) + ' --spades') #SPADES ARGUMENT?? + os.system('python 1a_TranscriptLengthFilter.py --input_file ' + args.assembled_transcripts + '/' + file + ' --output_file ' + args.output + '/Output/' + file[:10] + ' --minLen ' + str(args.minlen) + ' --maxLen ' + str(args.maxlen) + ' --spades') #SPADES ARGUMENT?? if args.xplate_contam: - os.system('python 1b_XSpeciesContaminationAgnes.py ' + args.output + '/Output/XlaneBleeding ' + str(args.minlen) + ' ' + args.conspecific_names) + os.system('python 1b_CrossPlateContamination.py ' + args.output + '/Output/XlaneBleeding ' + str(args.minlen) + ' ' + args.conspecific_names) def script_two(args): for folder in os.listdir(args.output + '/Output/'): if os.path.isfile(args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta'): - os.system('python 2a_remove_rRNA.py --input_file ' + args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta --databases ' + args.databases) + os.system('python 2a_Identify_rRNA.py --input_file ' + args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta --databases ' + args.databases) fasta_withBact = args.output + '/Output/' + folder + '/' + folder + '_NorRNAseqs.fasta' - os.system('python 2b_remove_Bact.py --input_file ' + fasta_withBact + ' --databases ' + args.databases) + os.system('python 2b_Identify_Proks.py --input_file ' + fasta_withBact + ' --databases ' + args.databases) #NEED TO SORT OUT FILE NAMES ETC. BELOW HERE @@ -52,14 +52,14 @@ def script_three(args): for folder in os.listdir(args.output + '/Output'): if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.fasta'): - os.system('python 3_CountOGsDiamond.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.fasta --evalue 1e-15 --databases ' + args.databases) + os.system('python 3_AssignOGs.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.fasta --evalue 1e-15 --databases ' + args.databases) #running the fourth script def script_four(args): for folder in os.listdir(args.output + '/Output'): if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta'): - os.system('python 4_InFrameStopFreq.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --databases ' + args.databases) + os.system('python 4_InFrameStopCodonEstimator.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --databases ' + args.databases) #putting all of the gcode summaries produced by fourth script into a spreadsheet gcode_info = [] @@ -147,10 +147,7 @@ def script_six(args): for prefix in unique_prefixes: os.system('python 6_FilterPartials.py --file_prefix ' + args.output + '/Output/' + prefix + ' --hook_fasta ' + hook_fasta) - - for prefix in unique_prefixes: - os.system('python 6b_update_cov_post_removepartials.py ' + args.output + '/Output/' + prefix) - + def script_seven(args):