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New Script 4 with added Hook-relative length filter
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Auden Cote-L'Heureux
GitHub
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338
PTL1/Genomes/Scripts/4_CountOGsDiamond.py
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338
PTL1/Genomes/Scripts/4_CountOGsDiamond.py
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#!/usr/bin/env python3.5
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##__Updated__: 19_09_2017
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##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
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##__Usage__: python 3g_GCodeTranslate.py --help
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##############################################################################
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## ##
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## This scrip will categorize TRANSLATED CDSs into Homologous Gene Families ##
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## ##
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## Questions about Gene Family Binning/Source? SEE NOTES at Bottom! ##
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## ##
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## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
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## ##
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##############################################################################
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import argparse, os, re, sys
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from argparse import RawTextHelpFormatter, SUPPRESS
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from distutils import spawn
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from Bio import SeqIO
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from statistics import mean
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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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#------------------------------ UPDATE DIAMOND PATH BELOW! -------------------------------#
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def check_diamond_path():
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### IF Diamond is IN YOUR PATH then no updating is needed...
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diamond_path = ''
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if diamond_path == '':
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diamond_path = spawn.find_executable("diamond")
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#diamond_path = /path/to/diamond
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else:
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pass
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if diamond_path == None:
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print (color.BOLD + '\n\nPlease open this script and check that you have included'\
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+ ' the PATH to the' + color.BLUE + ' "diamond" '+ color.END + color.BOLD\
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+ 'executable.\n\n' + color.END)
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print (color.BOLD + color.BLUE + 'LOOK FOR:\n\n' + color.RED\
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+'#------------------------------ UPDATE DIAMOND PATH BELOW! -------------------------------#'\
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+ color.BLUE + '\n\nThis is somewhere around lines 55 - 80...\n\n' + color.END)
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sys.exit()
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else:
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pass
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return diamond_path
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#------------------------------- Main Functions of Script --------------------------------#
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###########################################################################################
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###--------------------- Parses and Checks 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 will categorize Contigs into'+color.ORANGE+' "Homologous" '\
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+color.END+color.BOLD+'Gene Families (OGs)\nbased on '+color.RED+'OrthoMCL'+color.END\
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+color.BOLD+"'s Gene Family Grouping\n\n\nNotes on this script and "+color.GREEN+\
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'OrthoMCL Families'+color.END+color.BOLD+' can be found\nat the bottom of '+color.GREEN\
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+'THIS script (4_CountOGsDiamond.py)\n'+color.END+usage_msg(), usage=SUPPRESS,
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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 of Nucleotide sequences enriched \nwith'\
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' Eukaryotic protein coding transcripts'+color.END)
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required_arg_group.add_argument('--databases','-d', action='store',
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help=color.BOLD+color.GREEN+'Path to folder containing db_OG'+color.END)
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required_arg_group.add_argument('--evalue','-e', action='store',
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help=color.BOLD+color.GREEN+'Maximum OG assignment e-value'+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('--threads','-t', default='2',
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help=color.BOLD+color.GREEN+' Number of threads to use for BLAST\n (default = 2)\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.diamond = check_diamond_path()
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args.home_folder = '/'.join(args.input_file.split('/')[:-1]) + '/'
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args.tsv_out = args.home_folder + args.input_file.split('/')[-1].replace('CDS','CDS.Renamed').replace('.AA.fasta','_allOGCleanresults.tsv')
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args.aa_out = args.home_folder + args.input_file.split('/')[-1].replace('CDS','CDS.Renamed')
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args.ntd_out = args.home_folder + args.input_file.split('/')[-1].replace('CDS','CDS.Renamed').replace('AA','NTD')
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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 4_CountOGsDiamond.py'\
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' --input_file ../Stentor_coeruleus.WGS.CDS.Prep/Stentor_coeruleus.WGS.CDS.Universal.AA.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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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.author == True:
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print (author)
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valid_arg += 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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elif args.input_file.endswith('AA.fasta') != True:
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print (color.BOLD+'\n\nInvalid Fasta File! Only Fasta Files that were processed'\
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' with '+color.GREEN+'3g_GCodeTranslate.py '+color.END+color.BOLD+'are valid\n\n'\
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'However, to bypass that issue, Fasta Files MUST end with '+color.CYAN+\
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'"AA.fasta"\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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if os.path.isdir(args.databases + '/db_OG') != True:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
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+color.ORANGE+'db_OG Folder!\n\n'+color.END+color.BOLD+'Ensure that this folder '\
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'can be found in the main '+color.ORANGE+'Databases Folder'+color.END+color.BOLD\
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+'\n\nThen try once again\n\n.'+color.END)
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valid_arg += 1
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ogdb_count = 0
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for file in os.listdir(args.databases + '/db_OG'):
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if file.endswith('.dmnd'):
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ogdb_count += 1
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if ogdb_count == 0:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
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'Diamond formatted '+color.ORANGE+'Gene Family databases!\n\n'+color.END+color.BOLD+\
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'Ensure that they can be found in the '+color.ORANGE+'db_OG folder'+color.END+\
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color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\
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color.END+color.BOLD+'\n\nThen try once again.\n\n'+color.END)
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valid_arg += 1
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elif ogdb_count > 1:
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print('\nMultiple OG databases found. Please only provide 1 database in the db_OG folder.\n')
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valid_arg += 1
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return valid_arg
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###########################################################################################
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###--------------------------- Does the Inital Folder Prep -----------------------------###
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###########################################################################################
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def prep_folders(args):
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OG_folder = '/'.join(args.input_file.split('/')[:-1])+'/DiamondOG/'
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if os.path.isdir(OG_folder) != True:
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os.system('mkdir '+OG_folder)
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###########################################################################################
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###--------------------- Runs Diamond on Split OrthoMCL Databases ----------------------###
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###########################################################################################
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def OG_ublast(args):
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db = [file for file in os.listdir(args.databases + '/db_OG') if file.endswith('.dmnd')][0]
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OG_diamond_cmd = args.diamond + ' blastp -q ' + args.input_file + ' -d ' + args.databases + '/db_OG/' + db + ' --evalue ' + args.evalue + ' --subject-cover 0.5 --threads ' + args.threads + ' --outfmt 6 -o ' + args.input_file.split('.fas')[0] + '_allOGresults'
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os.system(OG_diamond_cmd)
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###########################################################################################
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###--------------- Keeps the Single BEST Hit (HSP-score) Per Transcript ----------------###
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###########################################################################################
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def keep_best(args):
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print (color.BOLD+color.PURPLE+'\n\nProcessing OG-database results to keep only the BEST'\
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'\nmatch for each transcript\n\n'+color.END)
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inTSV = [i for i in open(args.input_file.split('.fas')[0]+'_allOGresults').read().split('\n') if i != '']
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inTSV.sort(key = lambda x: -float(x.split('\t')[-1]))
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keep = []
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for i in inTSV:
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if any(i.split('\t')[0] in j for j in keep) != True:
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keep.append(i)
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updated_lines = list(set([line.split('\t')[0]+'_'+'_'.join(line.split('\t')[1].split('_')[-2:])+\
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'\t'+'\t'.join(line.split('\t')[1:]) for line in keep]))
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with open(args.tsv_out, 'w+') as w:
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for i in updated_lines:
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w.write(i+'\n')
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###########################################################################################
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###-------- Copies and Updates Names of Transcripts With OG Hits to New Fasta ----------###
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###########################################################################################
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def update_fasta(args):
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print (color.BOLD+color.PURPLE+'Updating Sequence Names with their BEST OG hits\n\n'+color.END)
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hook_fasta = [file for file in os.listdir(args.databases + '/db_OG') if file.endswith('.fasta')][0]
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OGLenDB = {}
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for rec in SeqIO.parse(args.databases + '/db_OG/' + hook_fasta, 'fasta'):
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if rec.id[-10:] not in OGLenDB:
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OGLenDB.update({ rec.id[-10:] : [] })
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OGLenDB[rec.id[-10:]].append(len(str(rec.seq)))
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for og in OGLenDB:
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OGLenDB[og] = mean(OGLenDB[og])
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keep = [i for i in open(args.tsv_out).read().split('\n') if i != '']
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keep_dict = { }
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for line in keep:
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og_number = re.split('OG.{1}_', line.split('\t')[1])[1][:6]
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og_prefix = line.split('\t')[1].split(og_number)[0][-4:]
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og = og_prefix + og_number
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keep_dict.update({ re.split('_OG.{1}_', line.split('\t')[0])[0] : re.split('_OG.{1}_', line.split('\t')[0])[0] + '_' + og_prefix + line.split('\t')[1].split('_')[-1] })
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protFasta = [seq_rec for seq_rec in SeqIO.parse(args.input_file,'fasta')]
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ntdFasta = [seq_rec for seq_rec in SeqIO.parse(args.input_file.replace('.AA.','.NTD.'),'fasta')]
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updated_prot_name = { keep_dict[i.description] : str(i.seq).rstrip('*') for i in protFasta if i.description in keep_dict.keys() }
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updated_ntd_name = { keep_dict[i.description] : str(i.seq).rstrip('*') for i in ntdFasta if i.description in keep_dict.keys() }
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with open(args.aa_out,'w+') as w:
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for rec in updated_prot_name:
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og_number = re.split('OG.{1}_', rec)[1][:6]
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og_prefix = rec.split(og_number)[0][-4:]
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og = og_prefix + og_number
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if len(updated_prot_name[rec]) > 0.33*OGLenDB[og] and len(updated_prot_name[rec]) < 1.5*OGLenDB[og]:
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w.write('>' + rec + '\n' + updated_prot_name[rec] + '\n\n')
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with open(args.ntd_out,'w+') as x:
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for rec in updated_ntd_name:
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og_number = re.split('OG.{1}_', rec)[1][:6]
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og_prefix = rec.split(og_number)[0][-4:]
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og = og_prefix + og_number
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if len(updated_ntd_name[rec]) > OGLenDB[og] and len(updated_ntd_name[rec]) < 4.5*OGLenDB[og]:
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x.write('>' + rec + '\n' + updated_ntd_name[rec] + '\n\n')
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##########################################################################################
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###--------------------- Cleans up the Folder and Moves Final Files -------------------###
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##########################################################################################
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def clean_up(args):
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os.system('mv '+args.input_file.replace('.fasta','_allOGresults')+' '+args.home_folder+\
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'/DiamondOG')
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os.system('cp '+args.aa_out+' '+args.home_folder+'/DiamondOG/')
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os.system('cp '+args.ntd_out+' '+args.home_folder+'/DiamondOG/')
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os.system('cp '+args.tsv_out+' '+args.home_folder+'/DiamondOG/')
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##########################################################################################
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###----------------------------- Calls on Above Functions -----------------------------###
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##########################################################################################
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def main():
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args = check_args()
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prep_folders(args)
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OG_ublast(args)
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keep_best(args)
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update_fasta(args)
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clean_up(args)
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print (color.BOLD+'Next Script is: '+color.GREEN+'5g_FinalizeName.py\n\n'+color.END)
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main()
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#----------------------------------------- NOTES -----------------------------------------#
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#
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# This script uses a "BLAST"-based approach to identify ANCIENT homologous gene families.
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#
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# Gene family designations were taken from OrthoMCL.org and serve as the database for
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# this script's gene family assignments. These gene family assignments are NON-EXHAUSTIVE
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# and most Lineage-Specific families will be missed!
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#
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# If you have any questions contact Xyrus (author): maurerax@gmail.com
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