From 72660b742ba78fe829fbf53799a4e9cba20d2723 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Mon, 30 Oct 2023 17:18:56 -0400 Subject: [PATCH] Adding CheckSetup.py to the Genomes --- PTL1/Genomes/Scripts/CheckSetup.py | 71 ++++++++++++++++++++++++++++++ PTL1/Genomes/Scripts/wrapper.py | 21 +++++---- 2 files changed, 83 insertions(+), 9 deletions(-) create mode 100644 PTL1/Genomes/Scripts/CheckSetup.py diff --git a/PTL1/Genomes/Scripts/CheckSetup.py b/PTL1/Genomes/Scripts/CheckSetup.py new file mode 100644 index 0000000..5343196 --- /dev/null +++ b/PTL1/Genomes/Scripts/CheckSetup.py @@ -0,0 +1,71 @@ +import os, sys, re +from Bio import SeqIO + + +def check_cds(params): + + if os.path.isdir(params.cds): + for file in os.listdir(params.cds): + if file[10:] != '_GenBankCDS.fasta' and 'DS_Store' not in file: + print('\nERROR: The file ' + file + ' in the give folder of assembled transcripts is incorrectly formatted. The files must start with a ten digit taxon identifier and then be named like Op_me_Hsap_GenBankCDS.fasta\n') + exit() + else: + print('\nERROR: CDS folder could not be found. Please ensure the given path is correct.\n') + exit() + + +def check_databases(params): + + if os.path.isdir(params.databases): + if os.path.isdir(params.databases + '/db_OG'): + fasta = [file for file in os.listdir(params.databases + '/db_OG') if file.endswith('.fasta')] + dmnd = [file for file in os.listdir(params.databases + '/db_OG') if file.endswith('.dmnd')] + + if len(fasta) == 0: + print('\nERROR: No Hook fasta file found in the Databases/db_OG folder\n') + exit() + elif len(fasta) > 1: + print('\nERROR: More than one Hook fasta file found in the Databases/db_OG folder. Please delete all except for the correct file.\n') + exit() + else: + for rec in SeqIO.parse(params.databases + '/db_OG/' + fasta[0], 'fasta'): + try: + og_number = re.split('OG.{1}_', rec.id)[-1][:6] + og_prefix = rec.id.split(og_number)[-2][-4:] + og = og_prefix + og_number + + if rec.id[-10:] != og: + print('\nError: The sequence name ' + rec.id + ' in the given Hook database fasta file is incorrectly formatted. Each sequence ID should start with a ten-digit taxon identifier and end with a ten-digit gene family identifier (which must start with OGX_, with "X" being any digit. E.g. Op_me_Hsap_0_OG6_110767)\n') + exit() + except IndexError: + print('\nError: The sequence name ' + rec.id + ' in the given Hook database fasta file is incorrectly formatted. Each sequence ID should start with a ten-digit taxon identifier and end with a ten-digit gene family identifier (which must start with OGX_, with "X" being any digit. E.g. Op_me_Hsap_0_OG6_110767)\n') + exit() + if len(dmnd) == 0: + print('\nERROR: No Hook Diamond database (.dmnd) file found in the Databases/db_OG folder.\n') + exit() + elif len(dmnd) > 1: + print('\nERROR: No Hook Diamond database (.dmnd) file found in the Databases/db_OG folder. Please delete all except for the correct file.\n') + exit() + else: + print('\nERROR: The db_OG folder could not be found in the databases folder.\n') + exit() + else: + print('\nERROR: Databases folder could not be found. Please ensure the given path is correct.\n') + exit() + + +def run(params): + + print('\nChecking the input files and scripts setup...\n') + + check_cds(params) + + check_databases(params) + + print('\nAll checks passed!\n') + + + + + + diff --git a/PTL1/Genomes/Scripts/wrapper.py b/PTL1/Genomes/Scripts/wrapper.py index cba0969..2beacc0 100644 --- a/PTL1/Genomes/Scripts/wrapper.py +++ b/PTL1/Genomes/Scripts/wrapper.py @@ -1,5 +1,6 @@ import os, sys, re import argparse +import CheckSetup def get_args(): @@ -22,6 +23,8 @@ def get_args(): def script_one(args, ten_digit_codes): + CheckSetup.run(args) + for file in os.listdir(args.cds): if file[10:] == '_GenBankCDS.fasta' and file[:10] in ten_digit_codes: os.system('python 1_RenameCDS.py -in ' + args.cds + '/' + file + ' -s GenBank -o ' + args.output + '/Output') @@ -125,7 +128,7 @@ def script_five(args): if os.path.isdir(args.output + '/Output/' + folder): gcode_formatted = gcode_by_folder[folder][0].upper() + gcode_by_folder[folder].lower()[1:] if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.Renamed.' + gcode_formatted + '.AA.fasta'): - step5_cmd = 'python 5_FinalizeName.py -in ' + args.output + '/Output/' + folder + '/DiamondOG/' + folder + '_GenBankCDS.Renamed.' + gcode_formatted + '.AA.fasta -n ' + folder + step5_cmd = 'python 5a_FinalizeName.py -in ' + args.output + '/Output/' + folder + '/DiamondOG/' + folder + '_GenBankCDS.Renamed.' + gcode_formatted + '.AA.fasta -n ' + folder os.system(step5_cmd) os.mkdir(args.output + '/Output/Intermediate') @@ -134,7 +137,7 @@ def script_five(args): if file != 'ReadyToGo' and file != 'Intermediate': os.system('mv ' + args.output + '/Output/' + file + ' ' + args.output + '/Output/Intermediate') - os.system('python 6_SummaryStats.py -i ' + args.output + '/Output -d ' + args.databases) + os.system('python 5b_SummaryStats.py -i ' + args.output + '/Output -d ' + args.databases) if __name__ == "__main__": @@ -143,7 +146,7 @@ if __name__ == "__main__": if (args.first_script == 1 or args.script == 1) and not os.path.isdir(args.cds): print('\nIf starting at the first script, a valid path to a folder of nucleotide CDS files (which must end in .fasta) should be input using the --cds argument') - quit() + exit() ten_digit_codes = [] if args.first_script == 1 or args.script == 1: @@ -153,24 +156,24 @@ if __name__ == "__main__": else: if not os.path.isdir(args.output + '/Output'): print('\nA folder called "Output" is not found at the given output path. Enter the correct path for --output or start from script 1.\n') - quit() + exit() if(len(ten_digit_codes) > len(list(dict.fromkeys(ten_digit_codes)))): print('\nDuplicate 10-digit codes are not allowed. Aborting.\n') - quit() + exit() for code in ten_digit_codes: for c, char in enumerate(code): if (c != 2 and c != 5 and char not in 'qwertyuiopasdfghjklzxcvbnmQWERTYUIOPASDFGHJKLZXCVBNM1234567890') or ((c == 2 or c == 5) and char != '_'): print('\n' + code + ' is an invalid 10-digit code sample identifier. It must of the format Op_me_hsap (Homo sapiens for example). Please ask for help if this does not make sense.\n') - quit() + exit() if os.path.isdir(args.output + '/Output') and (args.first_script == 1 or args.script == 1): print('\nAn "Output" folder already exists at the given path. Please delete or rename this folder and try again.\n') - quit() + exit() elif os.path.isdir(args.output + '/Output/Intermediate'): print('\nIt looks like this run is already complete. Try deleting/renaming the Output folder and try again.\n') - quit() + exit() elif not os.path.isdir(args.output + '/Output'): os.mkdir(args.output + '/Output') @@ -186,7 +189,7 @@ if __name__ == "__main__": scripts[i + args.first_script](args) else: print('\nInvalid script combination: the first script must be less than the last script. If you want to use only once script, use the --script argument.\n') - quit() + exit() else: if args.script == 1: scripts[args.script](args, ten_digit_codes)