# Last updated Sept 2017 # Author: Xyrus Maurer-Alcala # Translates CDSs sequences using the provided genetic code (as read from the gcode_output.tsv # file output by script 2, and filled in by the user if they did not pass genetic code # assignments to the --genetic_code argument to wrapper.py. The genetic code tables can be found # at the top of the script. In-frame stop codons are replaced with a * (the process is much simpler # here than in the transcriptomes pipeline). This script is intended to be run using the script # wrapper.py as part of the PhyloToL 6 Part 1 pipeline. #Dependencies import argparse, os, sys from argparse import RawTextHelpFormatter,SUPPRESS from Bio import SeqIO from Bio.Seq import Seq from Bio.Data.CodonTable import CodonTable #-------------------------- Set-up Codon Tables (Genetic Codes) --------------------------# blepharisma_table = CodonTable(forward_table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, start_codons = [ 'ATG'], stop_codons = ['TAA','TAG']) condylostoma_table = CodonTable(forward_table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Q', 'TAG': 'Q', 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, start_codons = [ 'ATG'], stop_codons = ['']) c_uncinata_table = CodonTable(forward_table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAG': 'Q', 'TGT': 'C', 'TGC': 'C', 'TGA': 'Q', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, start_codons = [ 'ATG'], stop_codons = ['TAA']) euplotes_table = CodonTable(forward_table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGA': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, start_codons = [ 'ATG'], stop_codons = ['TAA','TAG']) myrionecta_table = CodonTable(forward_table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Y', 'TAG': 'Y', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, start_codons = [ 'ATG'], stop_codons = ['TGA']) no_stop_table = CodonTable(forward_table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'X', 'TAG': 'X', 'TGT': 'C', 'TGC': 'C', 'TGA': 'X', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, start_codons = [ 'ATG'], stop_codons = ['']) peritrich_table = CodonTable(forward_table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'E', 'TAG': 'E', 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, start_codons = [ 'ATG'], stop_codons = ['TGA']) tag_table = CodonTable(forward_table={ 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Q', 'TGT': 'C', 'TGC': 'C', 'TGA': 'Q', 'TGG': 'W', 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, start_codons = [ 'ATG'], stop_codons = ['TAG']) #----------------------------- Colors For Print Statements ------------------------------# class color: PURPLE = '\033[95m' CYAN = '\033[96m' DARKCYAN = '\033[36m' ORANGE = '\033[38;5;214m' BLUE = '\033[94m' GREEN = '\033[92m' YELLOW = '\033[93m' RED = '\033[91m' BOLD = '\033[1m' UNDERLINE = '\033[4m' END = '\033[0m' #------------------------------- Main Functions of Script --------------------------------# ########################################################################################### ###------------------------- Checks the Command Line Arguments -------------------------### ########################################################################################### def check_args(): parser = argparse.ArgumentParser(description= color.BOLD + '\n\nThis script will '+color.RED+'Translate '+color.END+color.BOLD+'a '\ 'given Fasta file of CDS\nsequences using a given'+color.PURPLE+' Genetic Code.'+color.END+\ color.BOLD+usage_msg(), usage=SUPPRESS, formatter_class=RawTextHelpFormatter) required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END) required_arg_group.add_argument('--input_file','-in', action='store', help=color.BOLD+color.GREEN+' Fasta file with CDSs\n'+color.END) optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END) optional_arg_group.add_argument('--genetic_code','-g', action='store', default='universal', help=color.BOLD+color.GREEN+' Genetic code to use for translation\n (default = '\ '"universal")\n'+color.END) optional_arg_group.add_argument('--list_codes','-codes', action='store_true', help=color.BOLD+color.GREEN+' Lists supported genetic codes\n'+color.END) optional_arg_group.add_argument('-author', action='store_true', help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END) if len(sys.argv[1:]) == 0: print (parser.description) print ('\n') sys.exit() args = parser.parse_args() quit_eval = return_more_info(args) if quit_eval > 0: sys.exit() args.folder = '../'+args.input_file.split('/')[1] args.out_name = args.input_file.split('.Prepped')[0]+'.'+args.genetic_code.title()+'.AA.fasta' args.new_ntd_name = args.input_file.split('.Prepped')[0]+'.'+args.genetic_code.title()+'.NTD.fasta' return args ########################################################################################### ###------------------------------- Script Usage Message --------------------------------### ########################################################################################### def usage_msg(): return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 3g_GCodeTranslate.py'\ ' --input_file ../Stentor_coeruleus.WGS.CDS.Prep/Stentor_coeruleus.WGS.CDS.Prepped.fasta'\ ' --genetic_code Universal'+color.END) ########################################################################################## ###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------### ########################################################################################## def return_more_info(args): valid_arg = 0 supported_gcodes_names = ['bleph','blepharisma','chilo','chilodonella','condy',\ 'condylostoma','none','eup','euplotes','peritrich','vorticella','ciliate','universal',\ 'taa','tag','tga'] supported_gcodes_list = ['Blepharisma\t(TGA = W)','Chilodonella\t(TAG/TGA = Q)','Ciliate\t\t(TAR = Q)',\ 'Conylostoma\t(TAR = Q, TGA = W)','Euplotes\t(TGA = C)','Peritrich\t(TAR = E)','None\t\t(TGA/TAG/TAA = X)',\ 'Universal\t(TGA/TAG/TAA = STOP)','TAA\t\t(TAG/TGA = Q)', 'TAG\t\t(TRA = Q)', 'TGA\t\t(TAR = Q)'] author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\ ' maurerax@gmail.com\n\n'+color.END) if args.genetic_code != None and args.genetic_code.lower() not in supported_gcodes_names: print (color.BOLD+color.RED+'\nProvided genetic code is currently unsupported.\n\n'\ 'If you have a new genetic code, please contact the author (with some evidence).\n\n'\ 'Otherwise, use one of the currently supported genetic codes.\n'+color.END) print (color.BOLD+color.ORANGE+'\n'.join(supported_gcodes_list)+'\n\n'+color.END) print (author) valid_arg += 1 else: if args.list_codes == True: print (color.BOLD+color.RED+'\nThese are the currently supported genetic codes.\n'+color.END) print (color.BOLD+color.ORANGE+'\n'.join(supported_gcodes_list)+'\n\n'+color.END) valid_arg += 1 if args.author == True: print (author) valid_arg += 1 if args.input_file != None: if os.path.isfile(args.input_file) != False: if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])): print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) valid_arg += 1 else: print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) valid_arg += 1 return valid_arg ########################################################################################## ###------------------ Translates CDSs from the Provided Genetic Code ------------------### ########################################################################################## def translate_seqs(args): inFasta = [i for i in SeqIO.parse(args.input_file,'fasta')] print (color.BOLD+'\n\n\nTranslating: '+color.CYAN+args.input_file.split('/')[-1]+color.END+\ color.BOLD+'\nwith the '+color.GREEN+args.genetic_code.upper()+' Genetic Code\n'+color.END) if args.genetic_code.lower() == 'ciliate' or args.genetic_code.lower() == 'tga': translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=6)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta] if args.genetic_code.lower() == 'peritrich' or args.genetic_code.lower() == 'vorticella': translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=peritrich_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta] if args.genetic_code.lower() == 'tag': translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=tag_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta] if args.genetic_code.lower() == 'chilo' or args.genetic_code.lower() == 'chilodonella' or args.genetic_code.lower() == 'taa': translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=c_uncinata_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta] if args.genetic_code.lower() == 'bleph' or args.genetic_code.lower() == 'blepharisma': translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=blepharisma_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta] if args.genetic_code.lower() == 'eup' or args.genetic_code.lower() == 'euplotes': translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=euplotes_table)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta] if args.genetic_code.lower() == 'universal': translated_seqs = ['>'+seq_rec.description+'\n'+str(seq_rec.seq.translate(table=1)).rstrip('*').replace('*','X')+'\n' for seq_rec in inFasta] return translated_seqs ########################################################################################## ###---------------------------- Writes Out Translated CDSs ----------------------------### ########################################################################################## def write_out(args): translated_seqs = translate_seqs(args) ## Keep only ORFs greater than 10 amino acids long translated_seqs = [i for i in translated_seqs if len(i.split('\n')[1]) > 10] print (color.BOLD+'\nTranslated '+color.ORANGE+str(len(translated_seqs))+color.END\ +color.BOLD+' seqeunces using the '+color.GREEN+args.genetic_code.upper()+' Genetic Code\n\n'+color.END) with open(args.out_name,'w+') as w: w.write(''.join(translated_seqs)) ########################################################################################## ###--------------------- Cleans up the Folder and Moves Final Files -------------------### ########################################################################################## def clean_up(args): os.system('mv '+args.input_file+' '+args.new_ntd_name) ########################################################################################## ###----------------------------- Calls on Above Functions -----------------------------### ########################################################################################## def main(): args = check_args() write_out(args) clean_up(args) print (color.BOLD+'Next Script is: '+color.PURPLE+' 4g_CountOgsUsearch.py\n\n'+color.END) main()