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250 lines
10 KiB
Python
250 lines
10 KiB
Python
# Last updated Sept 2017
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# Author: Xyrus Maurer-Alcala
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# This script is intended to aid in determining which genetic code to use in translating sequences
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# (done in script 3) by checking stop codons used at the end of the input CDS, as well as determining
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# if there is a significant number of in-frame stop codons (>5%). It outputs the results of this
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# stop-codon analysis into the gcode_output.tsv file, which the user can fill in with desired genetic
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# codes to use in translation. If genetic codes were input originally (using the --genetic_code argument in
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# wrapper.py), then no action is needed here. This script is intended to be run as part of the PhyloToL 6
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# Part 1 pipeline using the script wrapper.py.
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#Dependencies
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import argparse, os, sys
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from argparse import RawTextHelpFormatter,SUPPRESS
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from Bio import SeqIO
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from Bio.Seq import Seq
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#----------------------------- Colors For Print Statements ------------------------------#
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class color:
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PURPLE = '\033[95m'
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CYAN = '\033[96m'
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DARKCYAN = '\033[36m'
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ORANGE = '\033[38;5;214m'
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BLUE = '\033[94m'
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GREEN = '\033[92m'
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YELLOW = '\033[93m'
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RED = '\033[91m'
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BOLD = '\033[1m'
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UNDERLINE = '\033[4m'
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END = '\033[0m'
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#------------------------------- Main Functions of Script --------------------------------#
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###########################################################################################
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###------------------------- Checks the Command Line Arguments -------------------------###
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###########################################################################################
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def check_args():
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parser = argparse.ArgumentParser(description=
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color.BOLD + '\n\nThis script is intended to aid you with '+color.RED+'evaluating\n(or checking) '+\
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color.END+color.BOLD+'the putative '+color.PURPLE+'Genetic Code'+color.END+color.BOLD+\
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' for a given\nFasta file of annotated (and untranslated) CDSs.\n\nTo do so, this script'\
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' checks for stop codon usages,\n'+color.RED+'suggesting '+color.END+color.BOLD+'the use of'\
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+color.PURPLE+' published and well-known\nalternate genetic codes'+color.END+color.BOLD+\
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' that are supported by the\nnext script: '+color.END+color.BOLD+color.PURPLE+'3g_GCodeTranslate.py'\
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+usage_msg(), usage=SUPPRESS, formatter_class=RawTextHelpFormatter)
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required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END)
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required_arg_group.add_argument('--input_file','-in', action='store',
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help=color.BOLD+color.GREEN+' Fasta file with CDSs\n'+color.END)
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optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END)
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optional_arg_group.add_argument('--list_codes','-codes', action='store_true',
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help=color.BOLD+color.GREEN+' Lists supported genetic codes\n'+color.END)
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optional_arg_group.add_argument('-author', action='store_true',
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help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END)
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if len(sys.argv[1:]) == 0:
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print (parser.description)
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print ('\n')
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sys.exit()
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args = parser.parse_args()
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quit_eval = return_more_info(args)
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if quit_eval > 0:
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sys.exit()
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args.folder = '/'.join(args.input_file.split('/')[:-1])
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return args
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###########################################################################################
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###------------------------------- Script Usage Message --------------------------------###
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###########################################################################################
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def usage_msg():
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return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 2g_GCodeEval.py'\
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' --input_file ../Stentor_coeruleus.WGS.CDS.Prep/Stentor_coeruleus.WGS.CDS.Renamed.fasta'+color.END)
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##########################################################################################
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###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------###
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##########################################################################################
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def return_more_info(args):
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valid_arg = 0
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supported_gcodes = ['Blepharisma\t(TGA = W)','Chilodonella\t(TAG/TGA = Q)','Ciliate\t\t(TAR = Q)',\
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'Conylostoma\t(TAR = Q, TGA = W)','Euplotes\t(TGA = C)','Peritrich\t(TAR = E)','None\t\t(TGA/TAG/TAA = X)',\
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'Universal\t(TGA/TAG/TAA = STOP)','TAA\t\t(TAG/TGA = Q)', 'TAG\t\t(TRA = Q)', 'TGA\t\t(TAR = Q)']
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author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\
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' maurerax@gmail.com\n\n'+color.END)
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if args.list_codes == True:
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print (color.BOLD+color.RED+'\nThese are the currently supported genetic codes.\n'+color.END)
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print (color.BOLD+color.ORANGE+'\n'.join(supported_gcodes)+'\n\n'+color.END)
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valid_arg += 1
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if args.author == True:
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print (author)
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valid_arg += 1
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print(args.input_file.split('/')[-1], '/'.join(args.input_file.split('/')[:-1]))
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if args.input_file != None:
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if os.path.isfile(args.input_file) != False:
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if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])):
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\
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'('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
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' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
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valid_arg += 1
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else:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\
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'('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
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' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
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valid_arg += 1
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return valid_arg
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###########################################################################################
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###-------------------- Counts Several Metrics of Stop Codon Usage ---------------------###
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###########################################################################################
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def count_stops(args):
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print (color.BOLD+'\n\nScanning CDSs for In-Frame Stop Codons and Tracking\nFINAL '\
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'(Terminal) stop codon usage\n\n'+color.END)
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inFasta = [i for i in SeqIO.parse(args.input_file,'fasta')]
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seq_ends = [str(i.seq)[-3:].lower() for i in inFasta]
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inFrame_stops_raw = [str(i.seq[:-3].translate()).count('*') for i in inFasta]
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inFrame_stops_summary = [i for i in inFrame_stops_raw if i != 0]
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tga_end = seq_ends.count('tga')
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tag_end = seq_ends.count('tag')
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taa_end = seq_ends.count('taa')
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end_stop_freq = [tga_end, tag_end, taa_end]
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if max(end_stop_freq) > 0.95*sum(end_stop_freq):
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pos_to_keep = [i for i, j in enumerate(end_stop_freq) if j == max(end_stop_freq)][0]
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try:
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if pos_to_keep == 0:
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end_stop_freq = [end_stop_freq[0],0,0]
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elif pos_to_keep == 1:
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end_stop_freq = [0,end_stop_freq[1],0]
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elif pos_to_keep == 2:
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end_stop_freq = [0,0,end_stop_freq[2]]
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except:
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pass
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inFrame_stop_info = [len(inFrame_stops_summary), int(round(len(inFrame_stops_raw)*0.05)), sum(inFrame_stops_summary)]
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return end_stop_freq, inFrame_stop_info
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###########################################################################################
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###-------------------- Suggests Genetic Code Given Stop Codon Usage -------------------###
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###########################################################################################
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def suggest_code(args):
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stop_freq, inFrames = count_stops(args)
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genetic_code = ''
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if stop_freq.count(0) == 3:
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print (color.BOLD + color.RED + '\n\nNO Stop Codons Present in Data-set\n\n')
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genetic_code = 'None (UNDETERMINED -- NO STOP CODONS)'
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else:
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## DUMB way of checking if there are a significant (> 5%) number of CDSs with IN-FRAME stop codons
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if inFrames[0] < inFrames[1]:
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print (color.BOLD + '\n\nSuggested Genetic Code is: '+color.CYAN+' Universal (table = 1)'+color.END)
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genetic_code = 'Universal (table = 1)'
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else:
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if stop_freq[0] != 0 and stop_freq[1] != 0 and stop_freq[2] != 0:
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print (color.BOLD + '\n\nSuggested Genetic Code is: '+color.CYAN+' Condylostoma-Code'\
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' (No Dedicated Stops) OR None (all stops = "X")'+color.END)
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genetic_code = 'Condylostoma or None'
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if stop_freq[0] == 0 and stop_freq[1] == 0:
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print (color.BOLD + '\n\nSuggested Genetic Code is: '+color.CYAN+' Chilodonella-Code'\
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+' (Only Stop = TAA)'+color.END)
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genetic_code = 'Chilodonella or TAA'
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if stop_freq[0] == 0 and stop_freq[2] == 0:
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print (color.BOLD + '\n\nSuggested Genetic Code is: '+color.CYAN+' TAG-Code'\
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+' (Only Stop = TAG)'+color.END)
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genetic_code = 'TAG'
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if stop_freq[1] == 0 and stop_freq[2] == 0:
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print (color.BOLD + '\n\nSuggested Genetic Code is: '+color.CYAN+' Ciliate-Code'\
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+' (table = 6)'+color.END)
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genetic_code = 'Ciliate (table = 6)'
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if stop_freq[0] != 0 and stop_freq[1] != 0 and stop_freq[2] == 0:
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print (color.BOLD + '\n\nSuggested Genetic Code is: '+color.CYAN+' TGA/TAG are STOP'+color.END)
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genetic_code = 'TGA/TAG'
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if stop_freq[0] != 0 and stop_freq[1] == 0 and stop_freq[2] != 0:
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print (color.BOLD + '\n\nSuggested Genetic Code is: '+color.CYAN+' TGA/TAA are STOP'+color.END)
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genetic_code = 'TGA/TAA'
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if stop_freq[0] == 0 and stop_freq[1] != 0 and stop_freq[2] != 0:
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print (color.BOLD + '\n\nSuggested Genetic Code is: '+color.CYAN+' Blepharisma/Euplotes-Codes'\
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+color.END + color.BOLD+'\n--- NOTE: '+color.RED+' Stop-Codon Reassignments'\
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+' differ! (TGA = W or TGA = C)' + color.END)
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genetic_code = 'Blepharisma (TGA = W) or Euplotes (TGA = C)'
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return genetic_code, stop_freq
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###########################################################################################
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###---------------- Writes Out Currently Crummy Summary of Genetic Codes ---------------###
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###########################################################################################
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def summarize(args):
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suggestion, stop_freq = suggest_code(args)
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with open(args.input_file.split('.fa')[0]+'.GeneticCode.txt','w+') as w:
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w.write('Stop Codon\tFrequency\n')
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w.write('TGA\t'+str(stop_freq[0])+'\n')
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w.write('TAG\t'+str(stop_freq[1])+'\n')
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w.write('TAA\t'+str(stop_freq[2])+'\n\n')
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w.write('Suggestion For Genetic Code:\t'+suggestion+'\n\n')
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##########################################################################################
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###--------------- Checks Command Line Arguments and Calls on Functions ---------------###
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##########################################################################################
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def main():
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args = check_args()
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summarize(args)
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print (color.BOLD+'\nNext Script is: '+color.PURPLE+' 3g_GCodeTranslate.py\n\n'+color.END)
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main()
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