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228 lines
11 KiB
Python
228 lines
11 KiB
Python
# Last updated Sept 2023
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# Author: Auden Cote-L'Heureux
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# This script is a WRAPPER for the EukPhylo Part 1 GENOMES pipeline. Users should
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# use this script to run the pipeline, rather than running any of the sub-scripts (number 1a through 5b)
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# independently. To run an individual step in the pipeline, use --script X where X is the number (1 through 5).
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# To run multiple sets (usually all of them), use --first script 1 --last_script 5, or whichever first
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# and last scripts are desired. Run "python wrapper.py --help" for details on how to run this script. Before
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# running this script ensure that the databases are correctly located and named, and that input CDS are named
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# in the format Op_me_Hsap_GenBankCDS.fasta, where Op_me_Hsap can be replaced with any 10-digit sample
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# identifier.
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import os, sys, re
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import argparse
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import CheckSetup
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def get_args():
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parser = argparse.ArgumentParser(
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prog = 'EukPhylo Part 1 for GenBank Genomes',
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description = "Updated January 19th, 2023 by Auden Cote-L'Heureux. Link to GitHub: https://github.com/Katzlab/EukPhylo"
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)
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parser.add_argument('-s', '--script', default = -1, type = int, choices = { 1, 2, 3, 4, 5 }, help = 'Script to run if you are only running one script')
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parser.add_argument('-1', '--first_script', default = -1, type = int, choices = { 1, 2, 3, 4 }, help = 'First script to run')
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parser.add_argument('-2', '--last_script', default = -1, type = int, choices = { 2, 3, 4, 5 }, help = 'First script to run')
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parser.add_argument('-c', '--cds', type = str, help = 'Path to a folder of nucleotide CDS. Each file name should start with a unique 10 digit code, and end in "_GenBankCDS.fasta", E.g. Op_me_hsap_GenBankCDS.fasta')
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parser.add_argument('-o', '--output', default = '../', type = str, help = 'An "Output" folder will be created at this directory to contain all output files. By default this folder will be created at the parent directory of the Scripts folder')
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parser.add_argument('-g', '--genetic_code', type = str, help = 'If all of your taxa use the same genetic code, you may enter it here (to be used in script 4). Otherwise, stop after script 3 and fill in "gcode_output.tsv" before running script 4')
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parser.add_argument('-d', '--databases', type = str, default = '../Databases', help = 'Path to databases folder (which should contain db_OG)')
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return parser.parse_args()
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def script_one(args, ten_digit_codes):
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CheckSetup.run(args)
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for file in os.listdir(args.cds):
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if file[10:] == '_GenBankCDS.fasta' and file[:10] in ten_digit_codes:
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os.system('python 1_RenameCDS.py -in ' + args.cds + '/' + file + ' -s GenBank -o ' + args.output + '/Output')
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def script_two(args):
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valid_codes = ['bleph','blepharisma','chilo','chilodonella','condy', 'condylostoma','none','eup','euplotes','peritrich','vorticella','ciliate','universal','taa','tag','tga','mesodinium']
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for folder in os.listdir(args.output + '/Output'):
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if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.Prepped.fasta'):
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os.system('python 2_GCodeEval.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.Prepped.fasta')
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gcode_info = []
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for folder in os.listdir(args.output + '/Output'):
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if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.Prepped.GeneticCode.txt'):
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with open(args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.Prepped.GeneticCode.txt') as f:
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gcode_temp = [folder]
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for line in f:
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line_sep = line.strip().split('\t')
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if line_sep[0] == 'TGA':
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gcode_temp.append(line_sep[1])
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elif line_sep[0] == 'TAG':
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gcode_temp.append(line_sep[1])
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elif line_sep[0] == 'TAA':
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gcode_temp.append(line_sep[1])
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gcode_info.append(gcode_temp)
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stop = False
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gcode_file = { }
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if args.genetic_code.endswith('.txt') or args.genetic_code.endswith('.tsv'):
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if os.path.isfile(args.genetic_code):
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for line in open(args.genetic_code):
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try:
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if line.split('\t')[1].strip().lower() in valid_codes:
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gcode_file.update({ line.split('\t')[0] : line.split('\t')[1].strip() })
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else:
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print('Genetic code ERROR -- ' + line.split('\t')[1].strip() + ' is not a valid genetic code. Please fill out the "gcode_output.tsv" file and continue with script 3.')
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except IndexError:
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print('\nGenetic code ERROR -- it looks like you tried to enter a .txt/.tsv file, but it is improperly formatted. Stopping after script 2; you may fill out the file gcode_output.tsv and continue with script 3.\n')
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stop = True
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else:
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print('\nGenetic code ERROR -- it looks like you tried to enter a .txt/.tsv file, but it could not be found. Stopping after script 2; you may fill out the file gcode_output.tsv and continue with script 3.\n')
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stop = True
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with open(args.output + '/Output/gcode_output.tsv', 'w') as g:
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g.writelines('10 Digit Code\tIn-frame TAG Density\tIn-frame TGA Density\tIn-frame TAA Density\tGenetic Code\n')
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for row in gcode_info:
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if args.genetic_code == None:
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g.writelines(row[0] + '\t' + row[1] + '\t' + row[2] + '\t' + row[3] + '\t\n')
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elif args.genetic_code.lower() in valid_codes:
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g.writelines(row[0] + '\t' + row[1] + '\t' + row[2] + '\t' + row[3] + '\t' + args.genetic_code + '\n')
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elif args.genetic_code.endswith('.txt') or args.genetic_code.endswith('.tsv'):
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try:
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g.writelines(row[0] + '\t' + row[1] + '\t' + row[2] + '\t' + row[3] + '\t' + gcode_file[row[0]] + '\n')
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except KeyError:
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g.writelines(row[0] + '\t' + row[1] + '\t' + row[2] + '\t' + row[3] + '\t\n')
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print('\nGenetic code ERROR -- it looks like you tried to enter a .txt/.tsv file, but a taxon is missing. Stopping after script 2; you may fill out the file gcode_output.tsv and continue with script 3.\n')
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stop = True
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else:
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stop = True
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if stop or args.genetic_code == None:
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print('\nStopping after script 2 because genetic code information is incomplete. Please fill out the file "gcode_output.tsv" and continue with script 3.\n')
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exit()
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def script_three(args):
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valid_codes = ['bleph','blepharisma','chilo','chilodonella','condy', 'condylostoma','none','eup','euplotes','peritrich','vorticella','ciliate','universal','taa','tag','tga','mesodinium']
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lines = [line.strip().split('\t') for line in open(args.output + '/Output/gcode_output.tsv', 'r')]
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with open(args.output + '/Output/gcode_output.tsv', 'r') as g:
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for folder in os.listdir(args.output + '/Output'):
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if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.Prepped.fasta'):
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for line in lines:
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if line[0] == folder and line[-1].lower() in valid_codes:
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os.system('python 3_GCodeTranslate.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.Prepped.fasta --genetic_code ' + line[-1])
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elif line[-1].lower() not in valid_codes and line[-1] != 'Genetic Code':
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print('\n' + line[-1] + ' is not a valid genetic code. Skipping taxon ' + folder + '.\n')
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def script_four(args):
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valid_codes = ['universal', 'blepharisma', 'chilodonella', 'condylostoma', 'euplotes', 'peritrich', 'vorticella', 'mesodinium', 'tag', 'tga', 'taa', 'none']
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gcode_by_folder = { line.strip().split('\t')[0] : line.strip().split('\t')[-1] for line in open(args.output + '/Output/gcode_output.tsv', 'r') }
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for folder in os.listdir(args.output + '/Output'):
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if os.path.isdir(args.output + '/Output/' + folder):
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gcode_formatted = gcode_by_folder[folder][0].upper() + gcode_by_folder[folder].lower()[1:]
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if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.' + gcode_formatted + '.AA.fasta'):
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os.system('python 4_CountOGsDiamond.py -in ' + args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.' + gcode_formatted + '.AA.fasta -t 30 --databases ' + args.databases + ' --evalue 1e-15')
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def script_five(args):
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gcode_by_folder = { line.strip().split('\t')[0] : line.strip().split('\t')[-1] for line in open(args.output + '/Output/gcode_output.tsv', 'r') }
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for folder in os.listdir(args.output + '/Output'):
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if os.path.isdir(args.output + '/Output/' + folder):
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gcode_formatted = gcode_by_folder[folder][0].upper() + gcode_by_folder[folder].lower()[1:]
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if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_GenBankCDS.Renamed.' + gcode_formatted + '.AA.fasta'):
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step5_cmd = 'python 5a_FinalizeName.py -in ' + args.output + '/Output/' + folder + '/DiamondOG/' + folder + '_GenBankCDS.Renamed.' + gcode_formatted + '.AA.fasta -n ' + folder
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os.system(step5_cmd)
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os.mkdir(args.output + '/Output/Intermediate')
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for file in os.listdir(args.output + '/Output'):
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if file != 'ReadyToGo' and file != 'Intermediate':
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os.system('mv ' + args.output + '/Output/' + file + ' ' + args.output + '/Output/Intermediate')
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os.system('python 5b_SummaryStats.py -i ' + args.output + '/Output -d ' + args.databases)
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if __name__ == "__main__":
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args = get_args()
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if (args.first_script == 1 or args.script == 1) and not os.path.isdir(args.cds):
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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')
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exit()
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ten_digit_codes = []
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if args.first_script == 1 or args.script == 1:
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for file in os.listdir(args.cds):
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if file[10:] == '_GenBankCDS.fasta' and '.DS_Store' not in file:
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ten_digit_codes.append(file[:10])
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else:
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if not os.path.isdir(args.output + '/Output'):
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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')
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exit()
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if(len(ten_digit_codes) > len(list(dict.fromkeys(ten_digit_codes)))):
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print('\nDuplicate 10-digit codes are not allowed. Aborting.\n')
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exit()
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for code in ten_digit_codes:
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for c, char in enumerate(code):
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if (c != 2 and c != 5 and char not in 'qwertyuiopasdfghjklzxcvbnmQWERTYUIOPASDFGHJKLZXCVBNM1234567890') or ((c == 2 or c == 5) and char != '_'):
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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')
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exit()
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if os.path.isdir(args.output + '/Output') and (args.first_script == 1 or args.script == 1):
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print('\nAn "Output" folder already exists at the given path. Please delete or rename this folder and try again.\n')
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exit()
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elif os.path.isdir(args.output + '/Output/Intermediate'):
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print('\nIt looks like this run is already complete. Try deleting/renaming the Output folder and try again.\n')
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exit()
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elif not os.path.isdir(args.output + '/Output'):
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os.mkdir(args.output + '/Output')
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scripts = [0, script_one, script_two, script_three, script_four, script_five]
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if args.script == -1:
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if args.first_script < args.last_script:
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for i in range(1 + args.last_script - args.first_script):
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print('\nRunning script ' + str(i + args.first_script) + '...\n')
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if i + args.first_script == 1:
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scripts[i + args.first_script](args, ten_digit_codes)
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else:
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scripts[i + args.first_script](args)
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else:
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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')
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exit()
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else:
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if args.script == 1:
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scripts[args.script](args, ten_digit_codes)
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else:
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scripts[args.script](args)
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