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Delete PTL1/Transcriptomes/Scripts/7_FinalizeName.py
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Auden Cote-L'Heureux
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#!/usr/bin/env python3.5
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##__Updated__: 31_08_2017
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##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
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##__Usage__: python 6_FilterPartials.py --help
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##################################################################################################
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## This script is intended to rename the outputs of the FilterPartials script ##
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## to a given 10-character that is used in the Katz lab Phylogenomic Tree building methods ##
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## ##
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## Prior to r`ning this script, ensure the following: ##
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## ##
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## 1. You have assembled your transcriptome and COPIED the 'assembly' file ##
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## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ##
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## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ##
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## 3. Removed SSU/LSU sequences from your Fasta File ##
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## 4. Classified your sequences as Strongly Prokaryotic/Eukaryotic or Undetermined ##
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## 5. Classified the Non-Strongly Prokaryotic sequences into OGs ##
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## 6. You either know (or have inferred) the genetic code of the organism ##
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## 7. You have translated the sequences and checked for the data in the RemovePartials folder ##
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## 8. Partial sequences have been removed from the transcriptomic data sets ##
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## ##
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## COMMAND Example Below ##
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## Extra Notes at Bottom of Script ##
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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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## Next Script(s) to Run: ##
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## NONE! You're FINISHED! :D ##
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## ##
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##################################################################################################
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import argparse, os, sys
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from argparse import RawTextHelpFormatter,SUPPRESS
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#----------------------- Solely to Make Print Statements Colorful -----------------------#
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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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###--------------------- 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 is intended to '+color.RED+'Rename '+color.END\
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+color.BOLD+'the core set of '+color.PURPLE+'ORFS\n'+color.END+color.BOLD+'with a valid '\
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+color.RED+'10-character code'+color.END+color.BOLD+' for use in the KatzLab\nPhylogenomic Pipeline'\
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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+' One of the Fasta files that is to be renamed\n'+color.END)
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required_arg_group.add_argument('--name','-n', action='store',
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help=color.BOLD+color.GREEN+' A valid 10-Character code for updating the data\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('-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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print ('\n')
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sys.exit()
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args.all_output_folder = '/'.join(args.input_file.split('/')[:-2])
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if '.allOGCleanresults' in args.input_TSV:
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args.out_XML = args.name+'_XX_'+args.input_TSV.split('/')[-1].replace('.allOGCleanresults.','.AA.ORF.')\
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.replace('.tsv','.fasta')+'_1e-10keepall_BlastOutall.oneHit'
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else:
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args.out_XML = args.name+'_XX_'+args.input_TSV.split('/')[-1].replace('_allOGCleanresults.','_AA.ORF.')\
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.replace('.tsv','.fasta')+'_1e-10keepall_BlastOutall.oneHit'
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args.file_prefix = args.input_file.split('/')[-1].split('_Filtered.Final')[0]
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if 'fasta' in args.file_prefix:
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args.file_prefix = args.name
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args.r2g_aa = args.all_output_folder + '/ReadyToGo/ReadyToGo_AA/'
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args.r2g_ntd = args.all_output_folder + '/ReadyToGo/ReadyToGo_NTD/'
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args.r2g_tsv = args.all_output_folder + '/ReadyToGo/ReadyToGo_TSV/'
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args.r2g_xml = args.all_output_folder + '/ReadyToGo/ReadyToGo_XML/'
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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 7_FinalizeName.py'\
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' --input_file ../ToRename/Op_me_Xxma_Filtered.Final.AA.ORF.fasta --name Op_me_Xxma'+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_args = 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_args += 1
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if args.input_file.endswith('AA.ORF.fasta'):
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args.input_NTD = args.input_file.replace('AA.ORF.fasta','NTD.ORF.fasta')
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args.input_AA = args.input_file
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# args.input_TSV = ('/').join(args.input_file.split('/')[:-1])+'/SpreadSheets/'+args.input_file.split('/')[-1].replace('AA.ORF.fasta','allOGCleanresults.tsv')
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args.input_TSV = args.input_file.replace('AA.ORF.fasta','allOGCleanresults.tsv')
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elif args.input_file.endswith('NTD.ORF.fasta'):
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args.input_NTD = args.input_file
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args.input_AA = args.input_file.replace('NTD.ORF.fasta','AA.ORF.fasta')
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# args.input_TSV = ('/').join(args.input_file.split('/')[:-1])+'/SpreadSheets/'+args.input_file.split('/')[-1].replace('NTD.ORF.fasta','allOGCleanresults.tsv')
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args.input_TSV = args.input_file.replace('AA.ORF.fasta','allOGCleanresults.tsv')
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print(args.input_TSV)
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if os.path.isfile(args.input_NTD) != True:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Nucleotide '\
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'Fasta file ('+color.DARKCYAN+args.input_NTD.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_args += 1
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if os.path.isfile(args.input_AA) != True:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Protein '\
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'Fasta file ('+color.DARKCYAN+args.input_AA.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_args += 1
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if os.path.isfile(args.input_TSV) != True:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided TSV '\
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' file ('+color.DARKCYAN+args.input_TSV.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_args += 1
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return valid_args
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###########################################################################################
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###-------------------- Double Checks Format for 10-Character Code ---------------------###
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###########################################################################################
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def check_code(args):
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check_name = args.name.split('_')
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if len(args.name) != 10:
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print (color.BOLD+'\n\nNew Species Prefix is not 10 characters long\n\n')
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print ('Three examples below:\n'+color.CYAN+'\n\tSr_ci_Cunc\n\n\tOp_me_Hsap\n\n\t'\
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'Am_ar_Ehis\n\n'+color.END)
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sys.exit()
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elif args.name.count('_') != 2:
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print (color.BOLD+'\n\nCheck the format of your Species Prefix!\n\n')
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print ('Three examples below:\n'+color.CYAN+'\n\tSr_ci_Cunc\n\n\tOp_me_Hsap\n\n\t'\
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'Am_ar_Ehis\n\n'+color.END)
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sys.exit()
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if len(check_name[0]) == 2 and len(check_name[1]) == 2 and len(check_name[2]) == 4:
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print (color.BOLD+"\n\nRenaming "+color.ORANGE+args.input_file.split('/')[-1]\
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.split('_Filtered')[0]+color.END+color.BOLD+"'s files with the following 10-character\n"\
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"code: "+color.CYAN+args.name+color.END+'\n')
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else:
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print (color.BOLD+'\n\nCheck the format of your Species Prefix!\n\n')
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print ('Three examples below:\n'+color.CYAN+'\n\tSr_ci_Cunc\n\n\tOp_me_Hsap\n\n\t'\
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'Am_ar_Ehis\n\n'+color.END)
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sys.exit()
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##########################################################################################
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###------------------------- Creates Folders For Storing Data -------------------------###
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##########################################################################################
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def prep_folders(args):
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if os.path.isdir(args.all_output_folder + '/ReadyToGo/') != True:
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os.system('mkdir ' + args.all_output_folder + '/ReadyToGo')
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if os.path.isdir(args.r2g_ntd) != True:
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os.system('mkdir ' + args.r2g_ntd)
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if os.path.isdir(args.r2g_aa) != True:
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os.system('mkdir ' + args.r2g_aa)
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if os.path.isdir(args.r2g_tsv) != True:
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os.system('mkdir ' + args.r2g_tsv)
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if os.path.isdir(args.r2g_xml) != True:
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os.system('mkdir ' + args.r2g_xml)
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if os.path.isdir(args.all_output_folder + '/' + args.file_prefix + '/Renamed') != True:
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os.system('mkdir ' + args.all_output_folder + '/' + args.file_prefix + '/Renamed')
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###########################################################################################
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###----------- Renames the NTD and AA CDSs with the Given 10-Character Code ------------###
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###########################################################################################
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def rename_paralogs(args):
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home_folder = args.all_output_folder + '/' + args.file_prefix + '/Renamed/'
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print (color.BOLD+'\nRenaming Translated (Protein) '+color.PURPLE+'ORFs\n'+color.END)
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renamed_Final_Prots = open(args.input_AA).read().replace('>','>'+args.name+'_XX_')
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print (color.BOLD+'\nRenaming Nucleotide '+color.PURPLE+'ORFs\n'+color.END)
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renamed_Final_Nucs = open(args.input_NTD).read().replace('>','>'+args.name+'_XX_')
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print (color.BOLD+'\nUpdating CDS Names in the Spreadsheet'+color.END)
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if '\n\n' in open(args.input_TSV).read():
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renamed_Final_tsv = args.name+'_XX_'+open(args.input_TSV).read().rstrip('\n')\
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.replace('\n\n','\n'+args.name+'_XX_')
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else:
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renamed_Final_tsv = args.name+'_XX_'+open(args.input_TSV).read().rstrip('\n')\
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.replace('\n','\n'+args.name+'_XX_')
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with open(home_folder+args.name+'_XX_'+args.input_AA.split('/')[-1],'w+') as w:
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w.write(renamed_Final_Prots)
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with open(home_folder+args.name+'_XX_'+args.input_NTD.split('/')[-1],'w+') as x:
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x.write(renamed_Final_Nucs)
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with open(home_folder+args.name+'_XX_'+args.input_TSV.split('/')[-1],'w+') as y:
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y.write(renamed_Final_tsv)
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###########################################################################################
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###--------------------------------- Header/Tail Lines ---------------------------------###
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###########################################################################################
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def header_tail():
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header = '<?xml version="1.0"?>\n<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n'\
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'<BlastOutput>\n <BlastOutput_program>blastp</BlastOutput_program>\n <BlastOutput_version>BLASTP 2.2.29+</BlastOutput_version>\n'\
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' <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>\n'\
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' <BlastOutput_db>../OGBlastDB/renamed_aa_seqs_OrthoMCL-5_12653.fasta</BlastOutput_db>\n <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n'
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tail = '</BlastOutput_iterations>\n</BlastOutput>'
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return header, tail
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###########################################################################################
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###------------------------------- TSV to XML Conversion -------------------------------###
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###########################################################################################
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def convert_TSV_data(args):
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home_folder = args.all_output_folder + '/' + args.file_prefix + '/Renamed/'
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TSVforConvert = home_folder+args.name+'_XX_'+args.input_TSV.split('/')[-1]
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inTSV = [line.rstrip('\n') for line in open(TSVforConvert).readlines() if line != '\n']
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iterations = []
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for n in range(len(inTSV)):
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if n == 0:
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iterations.append(' <BlastOutput_query-def>'+inTSV[n].split('\t')[0]+'</BlastOutput_query-def>\n <BlastOutput_query-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</BlastOutput_query-len>\n'\
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' <BlastOutput_param>\n <Parameters>\n <Parameters_matrix>BLOSUM62</Parameters_matrix>\n <Parameters_expect>1e-10</Parameters_expect>\n'\
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' <Parameters_gap-open>11</Parameters_gap-open>\n <Parameters_gap-extend>1</Parameters_gap-extend>\n <Parameters_filter>F</Parameters_filter>\n'\
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' </Parameters>\n </BlastOutput_param>\n<BlastOutput_iterations>\n<Iteration>\n <Iteration_iter-num>1</Iteration_iter-num>\n <Iteration_query-ID>Query_1</Iteration_query-ID>\n'\
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' <Iteration_query-def>'+inTSV[n].split('\t')[0]+'</Iteration_query-def>\n <Iteration_query-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</Iteration_query-len>\n'\
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'<Iteration_hits>\n<Hit>\n <Hit_num>1</Hit_num>\n <Hit_id>Fake_Entry</Hit_id>\n <Hit_def>'+inTSV[n].split('\t')[1]+'</Hit_def>\n <Hit_accession>Fake_Accession</Hit_accession>\n'\
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' <Hit_len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</Hit_len>\n <Hit_hsps>\n <Hsp>\n <Hsp_num>1</Hsp_num>\n <Hsp_bit-score>1234</Hsp_bit-score>\n'\
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' <Hsp_score>'+inTSV[n].split('\t')[-1]+'</Hsp_score>\n <Hsp_evalue>'+inTSV[n].split('\t')[-2]+'</Hsp_evalue>\n <Hsp_query-from>'+inTSV[n].split('\t')[-4]+'</Hsp_query-from>\n'\
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' <Hsp_query-to>'+inTSV[n].split('\t')[-3]+'</Hsp_query-to>\n <Hsp_hit-from>'+inTSV[n].split('\t')[-4]+'</Hsp_hit-from>\n <Hsp_hit-to>'+inTSV[n].split('\t')[-3]+'</Hsp_hit-to>\n'\
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' <Hsp_query-frame>0</Hsp_query-frame>\n <Hsp_hit-frame>0</Hsp_hit-frame>\n <Hsp_identity>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_identity>\n'\
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' <Hsp_positive>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_positive>\n <Hsp_gaps>0</Hsp_gaps>\n <Hsp_align-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_align-len>\n'\
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' <Hsp_qseq></Hsp_qseq>\n <Hsp_hseq></Hsp_hseq>\n <Hsp_midline></Hsp_midline>\n </Hsp>\n </Hit_hsps>\n</Hit>\n'\
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'\n</Iteration_hits>\n <Iteration_stat>\n <Statistics>\n <Statistics_db-num>379660</Statistics_db-num>\n <Statistics_db-len>197499634</Statistics_db-len>\n'\
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' <Statistics_hsp-len>123</Statistics_hsp-len>\n <Statistics_eff-space>184705217500</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n'\
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' <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n </Statistics>\n </Iteration_stat>\n</Iteration>\n')
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else:
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iterations.append('<Iteration>\n <Iteration_iter-num>'+str(n+1)+'</Iteration_iter-num>\n <Iteration_query-ID>Query_'+str(n+1)+'</Iteration_query-ID>\n'\
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' <Iteration_query-def>'+inTSV[n].split('\t')[0]+'</Iteration_query-def>\n <Iteration_query-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</Iteration_query-len>\n'\
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'<Iteration_hits>\n<Hit>\n <Hit_num>1</Hit_num>\n <Hit_id>Fake_Entry</Hit_id>\n <Hit_def>'+inTSV[n].split('\t')[1]+'</Hit_def>\n <Hit_accession>Fake_Accession</Hit_accession>\n'\
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' <Hit_len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'</Hit_len>\n <Hit_hsps>\n <Hsp>\n <Hsp_num>1</Hsp_num>\n <Hsp_bit-score>1234</Hsp_bit-score>\n'\
|
||||
' <Hsp_score>'+inTSV[n].split('\t')[-1]+'</Hsp_score>\n <Hsp_evalue>'+inTSV[n].split('\t')[-2]+'</Hsp_evalue>\n <Hsp_query-from>'+inTSV[n].split('\t')[-4]+'</Hsp_query-from>\n'\
|
||||
' <Hsp_query-to>'+inTSV[n].split('\t')[-3]+'</Hsp_query-to>\n <Hsp_hit-from>'+inTSV[n].split('\t')[-4]+'</Hsp_hit-from>\n <Hsp_hit-to>'+inTSV[n].split('\t')[-3]+'</Hsp_hit-to>\n'\
|
||||
' <Hsp_query-frame>0</Hsp_query-frame>\n <Hsp_hit-frame>0</Hsp_hit-frame>\n <Hsp_identity>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_identity>\n'\
|
||||
' <Hsp_positive>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_positive>\n <Hsp_gaps>0</Hsp_gaps>\n <Hsp_align-len>'+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'</Hsp_align-len>\n'\
|
||||
' <Hsp_qseq></Hsp_qseq>\n <Hsp_hseq></Hsp_hseq>\n <Hsp_midline></Hsp_midline>\n </Hsp>\n </Hit_hsps>\n</Hit>\n'\
|
||||
'\n</Iteration_hits>\n <Iteration_stat>\n <Statistics>\n <Statistics_db-num>379660</Statistics_db-num>\n <Statistics_db-len>197499634</Statistics_db-len>\n'\
|
||||
' <Statistics_hsp-len>123</Statistics_hsp-len>\n <Statistics_eff-space>184705217500</Statistics_eff-space>\n <Statistics_kappa>0.041</Statistics_kappa>\n'\
|
||||
' <Statistics_lambda>0.267</Statistics_lambda>\n <Statistics_entropy>0.14</Statistics_entropy>\n </Statistics>\n </Iteration_stat>\n</Iteration>\n')
|
||||
|
||||
return iterations
|
||||
|
||||
|
||||
###########################################################################################
|
||||
###--------------------------- Writes Out the Fake XML File ----------------------------###
|
||||
###########################################################################################
|
||||
|
||||
def write_Fake_XML(args):
|
||||
|
||||
home_folder = args.all_output_folder + '/' + args.file_prefix + '/'
|
||||
|
||||
print (color.BOLD+'\n\nConverting '+color.ORANGE+args.input_file.split('/')[-1]+color.END\
|
||||
+color.BOLD+' to XML format\n'+color.END)
|
||||
|
||||
header, tail = header_tail()
|
||||
|
||||
iterations = convert_TSV_data(args)
|
||||
|
||||
with open(home_folder+args.out_XML,'w+') as w:
|
||||
w.write(header)
|
||||
w.write(''.join(iterations))
|
||||
w.write(tail)
|
||||
|
||||
##########################################################################################
|
||||
###-------------------- Cleans up the Folder and Moves Final Files --------------------###
|
||||
##########################################################################################
|
||||
def clean_up(args):
|
||||
|
||||
home_folder = args.all_output_folder + '/' + args.file_prefix + '/Renamed/'
|
||||
|
||||
os.system('cp ' + args.all_output_folder + '/' + args.file_prefix+'/'+args.out_XML+' '+args.r2g_xml)
|
||||
|
||||
os.system('cp '+home_folder+'*tsv '+args.r2g_tsv)
|
||||
|
||||
os.system('cp '+home_folder+'*_XX_*AA.ORF.fasta '+args.r2g_aa)
|
||||
os.system('cp '+home_folder+'*_XX_*NTD.ORF.fasta '+args.r2g_ntd)
|
||||
|
||||
os.system('cp '+home_folder+'*_XX_*tsv ' + args.all_output_folder + '/' + args.file_prefix)
|
||||
os.system('cp '+home_folder+'*_XX_*AA.ORF.fasta ' + args.all_output_folder + '/' + args.file_prefix)
|
||||
os.system('cp '+home_folder+'*_XX_*NTD.ORF.fasta ' + args.all_output_folder + '/' + args.file_prefix)
|
||||
|
||||
os.system('rm ' + args.all_output_folder + '/ToRename/*'+args.file_prefix+'*')
|
||||
|
||||
if os.path.isdir(args.all_output_folder + '/Finished/') != True:
|
||||
os.system('mkdir ' + args.all_output_folder + '/Finished')
|
||||
|
||||
os.system('mv ' + args.all_output_folder + '/' + args.file_prefix + ' ' + args.all_output_folder + '/Finished')
|
||||
|
||||
###########################################################################################
|
||||
###-------------------------------- Next Script Message --------------------------------###
|
||||
###########################################################################################
|
||||
|
||||
def next_script(args):
|
||||
|
||||
print (color.BOLD+'\nThere is no next script! The final '+color.ORANGE+args.out_XML\
|
||||
.split('_XX')[0]+color.END+color.BOLD+' files can be\nfound in the '+color.RED+\
|
||||
args.out_XML.split('_XX_')[-1].split('_Filtered')[0]+color.END+color.BOLD+' and '\
|
||||
+color.RED+'ReadyToGo folders'+color.END+color.BOLD+' and are ready\n'\
|
||||
'for the KatzLab Phylogenomic Tree-Building Steps!\n\n'+color.END)
|
||||
|
||||
##########################################################################################
|
||||
###--------------- Checks Command Line Arguments and Calls on Functions ---------------###
|
||||
##########################################################################################
|
||||
|
||||
def main():
|
||||
|
||||
args = check_args()
|
||||
|
||||
check_code(args)
|
||||
|
||||
prep_folders(args)
|
||||
|
||||
rename_paralogs(args)
|
||||
|
||||
write_Fake_XML(args)
|
||||
|
||||
clean_up(args)
|
||||
|
||||
next_script(args)
|
||||
|
||||
main()
|
||||
Loading…
x
Reference in New Issue
Block a user