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Delete PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py
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Auden Cote-L'Heureux
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#!/usr/bin/env python3.5
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##__Updated__: 18_08_2017
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##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
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##__Usage__: python 2a_remove_rDNA.py --help
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##########################################################################################
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## This script is intended to identify and isolate SSU/LSU sequences ##
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## Prior to running 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. Have the Databases set up correctly (e.g. with BLAST or Diamond) and in their ##
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## respective folders! See the manual if you need help ##
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## ##
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## COMMAND Example Below ##
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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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## 2b_removeBact.py ##
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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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from Bio import SeqIO
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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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###--------------------- 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+'\nThis script will remove '+color.RED+'rDNA contigs (both SSU and LSU)'+color.END\
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+color.BOLD+'\nfrom your Assembly using a set of '+color.RED+'SSU/LSU rDNAs '+color.END\
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+color.BOLD+'from diverse\n'+color.ORANGE+'Eukaryotes, Bacteria and Archaea'+color.END\
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+color.BOLD+'.'+color.END+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 of Nucleotide sequences"+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 databases"+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+' Print 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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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 2a_remove_rRNA.py --input_file ../Op_me_Xxma_rna.200bp.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('bp.fasta') != True:
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print (color.BOLD + '\n\nCheck that you are giving an appropriately Named/Processed'\
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'Fasta file(s) to this script\n\nNOTE that this script CURRENTLY expects your'\
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' Fasta files to contain '+color.RED+ '"rna"'+color.END+color.BOLD+' in \nthe Fasta File'\
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' Name and must end with ' + color.RED + '"bp.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_BvsE') != 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_BvsE 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.')
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valid_arg += 1
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elif os.path.isfile(args.databases + '/db_BvsE/SSULSUdb.nhr') != True:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
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'BLAST+ formatted '+color.ORANGE+'SSU-LSU databases!\n\n'+color.END+color.BOLD+\
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'Ensure that they can be found in the '+color.ORANGE+'db_BvsE 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.')
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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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code = args.input_file.split('/')[-1][:10]
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rRNA_folder = args.input_file.split('SizeFiltered')[0] + '/rRNA_Removal/'
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if os.path.isdir(rRNA_folder) != True:
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os.system('mkdir '+rRNA_folder)
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return code, rRNA_folder
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###########################################################################################
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###---------------------- Uses BLAST to identify SSU/LSU Sequences ---------------------###
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###########################################################################################
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def remove_rDNA(args, rRNA_folder):
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blast_output = rRNA_folder + args.input_file.split('/')[-1].split('.200bp.fasta')[0]+'_allSSULSUresults.tsv'
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BLASTN_cmd = 'blastn -query ' + args.input_file + ' -evalue 1e-10 -max_target_seqs 1 -outfmt'\
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' 6 -db ' + args.databases + '/db_BvsE/SSULSUdb -num_threads 2 -out ' + blast_output
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print (color.BOLD+'\n\nBLASTing '+color.DARKCYAN+args.input_file.split('/')[-1]+color.END\
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+color.BOLD+ ' against the rDNA database\n\n' + color.END)
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os.system(BLASTN_cmd)
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rDNA_Hits = list(set([i.split('\t')[0] for i in open(blast_output).readlines()]))
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print (color.BOLD+'Binning Sequences from '+color.DARKCYAN+args.input_file.split('/')[-1]\
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+color.END+color.BOLD+'\nas rDNA OR Potentially Protein-Coding\n\n'+color.END)
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no_SSULSU = 0
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with_SSULSU = 0
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inFasta = [seq_rec for seq_rec in SeqIO.parse(args.input_file,'fasta')]
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with open(rRNA_folder + args.input_file.split('/')[-1].split('.200bp.fasta')[0]+'_rRNAseqs.fasta','w+') as HasSSU:
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for seq_rec in inFasta:
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if seq_rec.description in rDNA_Hits:
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HasSSU.write('>'+seq_rec.description+'\n'+str(seq_rec.seq)+'\n')
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with_SSULSU += 1
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with open(rRNA_folder + args.input_file.split('/')[-1].split('.200bp.fasta')[0] + '_NorRNAseqs.fasta','w+') as NoSSU:
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for seq_rec in inFasta:
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if seq_rec.description not in rDNA_Hits:
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NoSSU.write('>'+seq_rec.description+'\n'+str(seq_rec.seq)+'\n')
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no_SSULSU += 1
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return str(with_SSULSU), str(no_SSULSU)
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###########################################################################################
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###--------------------------- Updates Log of SSU/LSU Removal --------------------------###
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###########################################################################################
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def update_log(args, with_SSU, no_SSU):
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if os.path.isdir('../PostAssembly_Logs/') != True:
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os.system('mkdir ../PostAssembly_Logs/')
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print (color.BOLD+'There are '+color.RED+with_SSU+' rRNA contigs'+color.END+color.BOLD\
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+' and '+color.PURPLE+no_SSU+' Putative Protein-coding contigs'+color.END+color.BOLD\
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+'\nin '+color.DARKCYAN+args.input_file.split('/')[1]+'\n' + color.END)
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with open('../PostAssembly_Logs/'+args.input_file.split('/')[1].split('.fas')[0]+'.Log.txt','a') as LogFile:
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LogFile.write('rDNA Contigs\t'+with_SSU+'\tn/a\tn/a\n')
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LogFile.write('Non-rDNA Contigs\t'+no_SSU+'\tn/a\tn/a\n')
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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+'\nLook for '+color.ORANGE+args.input_file.split('/')[1].split('_rna')[0]\
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+ '_NorRNAseqs.fasta'+color.END+color.BOLD+'\nin the '+args.input_file.split('/')[1].split('_rna')[0]\
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+' Folder\n\n' + color.END)
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print (color.BOLD + 'Next Script is: ' + color.GREEN + '2b_remove_Bact.py\n\n'+ color.END)
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###########################################################################################
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###-------------------------- Cleans Up the PostAssembly Folder ------------------------###
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###########################################################################################
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def clean_up(args):
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home_folder = args.input_file.split('SizeFiltered')[0]
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os.system('cp ' + home_folder + 'rRNA_Removal/*NorRNA*.fasta ' + home_folder)
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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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code, rRNA_folder = prep_folders(args)
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with_SSULSU, no_SSULSU = remove_rDNA(args, rRNA_folder)
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#update_log(args, with_SSULSU, no_SSULSU)
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clean_up(args)
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next_script(args)
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main()
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