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300 lines
12 KiB
Python
300 lines
12 KiB
Python
#!/usr/bin/env python3.5
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##__Updated__: 9_29_2023 by Auden Cote-L'Heureux
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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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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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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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print(args.input_file)
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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.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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###-------------------- Cleans up the Folder and Moves Final Files --------------------###
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##########################################################################################
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def clean_up(args):
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home_folder = args.all_output_folder + '/' + args.file_prefix + '/Renamed/'
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os.system('cp '+home_folder+'*tsv '+args.r2g_tsv)
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os.system('cp '+home_folder+'*_XX_*AA.ORF.fasta '+args.r2g_aa)
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os.system('cp '+home_folder+'*_XX_*NTD.ORF.fasta '+args.r2g_ntd)
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os.system('cp '+home_folder+'*_XX_*tsv ' + args.all_output_folder + '/' + args.file_prefix)
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os.system('cp '+home_folder+'*_XX_*AA.ORF.fasta ' + args.all_output_folder + '/' + args.file_prefix)
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os.system('cp '+home_folder+'*_XX_*NTD.ORF.fasta ' + args.all_output_folder + '/' + args.file_prefix)
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os.system('rm ' + args.all_output_folder + '/ToRename/*'+args.file_prefix+'*')
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if os.path.isdir(args.all_output_folder + '/Finished/') != True:
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os.system('mkdir ' + args.all_output_folder + '/Finished')
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os.system('mv ' + args.all_output_folder + '/' + args.file_prefix + ' ' + args.all_output_folder + '/Finished')
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###########################################################################################
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###-------------------------------- Next Script Message --------------------------------###
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###########################################################################################
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def next_script(args):
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print (color.BOLD+'\nThere is no next script!\n\n'+color.END)
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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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check_code(args)
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prep_folders(args)
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rename_paralogs(args)
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clean_up(args)
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next_script(args)
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main() |