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Delete PTL1/Transcriptomes/Scripts/1a_ContigFiltStats.py
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Auden Cote-L'Heureux
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#!/usr/bin/env python3.6
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##__Updated__: 01_04_2023
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##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
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##__Usage__: python 1_ContigFiltStats.py
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##__Options__: python 1_ContigFiltStats.py --help
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##########################################################################################
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## This script is intended to remove small transcripts or small contigs below a given ##
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## minimum size from a transcriptome assembly. ##
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## ##
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## Prior to running this script, ensure the following: ##
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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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## ##
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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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## AutoBactVsEuk.py (removes SSU then Bact) or 2a_removeSSU.py then 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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from Bio.SeqUtils import GC
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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 Contigs (and provide a summary of statistics)'\
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+'\nfrom your Assembly that are shorter than a given length.'+color.ORANGE+\
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'\n\nA good minimum length to start with is 200bp.'+color.END+color.BOLD+\
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'\n\nThe minimum length value should be adjusted for your data sets.\n'+color.END+usage_msg(),
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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 Protein/Nucleotide sequences\n"+color.END)
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required_arg_group.add_argument('--output_file','-out',
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help=color.BOLD+color.GREEN+" Desired Output Name\n\n"+color.END)
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required_arg_group.add_argument('--minLen','-min', default=200, type=int,
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help=color.BOLD+color.GREEN+" Minimum number of base pairs for contigs\n (default = 200)"+color.END)
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required_arg_group.add_argument('--maxLen','-max', default=15000, type=int,
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help=color.BOLD+color.GREEN+" Minimum number of base pairs for contigs\n (default = 15000)"+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('--spades','-spades', action='store_true',
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help=color.BOLD+color.GREEN+'rnaSPAdes transcriptome assembly\n'+color.END)
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optional_arg_group.add_argument('--genbank','-gb', action='store_true',
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help=color.BOLD+color.GREEN+'Assembly from Genbank\n (Will include Accession Number in'\
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' contig name)\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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args = parser.parse_args()
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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 1_ContigFiltStats.py'\
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' --input_file ../Op_me_Xxma_rnaSPAdes_scaffolds_15_05.fasta --output_file '\
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'Op_me_Xxma --minLen 200 --spades'+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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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 args.output_file == None:
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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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Home_folder_name = args.output_file
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if os.path.isdir(args.output_file) != True:
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os.system('mkdir ' + args.output_file)
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if os.path.isdir(args.output_file + '/OriginalFasta/') != True:
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os.system('mkdir ' + args.output_file +'/OriginalFasta/')
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if os.path.isdir(args.output_file + '/SizeFiltered/') != True:
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os.system('mkdir ' + args.output_file +'/SizeFiltered/')
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if os.path.isdir('/'.join(args.output_file.split('/')[:-1]) + '/XlaneBleeding/') != True:
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os.system('mkdir ' + '/'.join(args.output_file.split('/')[:-1]) + '/XlaneBleeding/')
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###########################################################################################
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###---------- Renames the Contigs, Writes them out, and Calculates Basic Info ----------###
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###########################################################################################
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def rename_Transcriptome(args):
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home_folder = args.output_file + '/SizeFiltered/'
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print (color.BOLD+'\n\nPrepping '+color.GREEN+args.input_file.split('/')[-1]+color.END)
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inFasta = [i for i in SeqIO.parse(args.input_file,'fasta') if len(i.seq) >= args.minLen and len(i.seq) <= args.maxLen]
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inFasta.sort(key=lambda seq_rec: -len(seq_rec.seq))
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renamed_seqs = []
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seq_code_dict = {}
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count = 1
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seq_name_start = 'Contig'
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if args.genbank == True:
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for seq_rec in inFasta:
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seq_code_dict.setdefault(seq_rec.id,[]).append(seq_rec.id.split('_')[-1].split('.')[0]+'_Contig_'+str(count)+'_Len'+str(len(seq_rec.seq)))
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seq_code_dict.setdefault(seq_rec.id,[]).append(str(seq_rec.seq).upper())
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renamed_seqs.append('>'+seq_rec.id.split('_')[-1].split('.')[0]+'_Contig_'+str(count)+'_Len'+str(len(seq_rec.seq))+'\n'+str(seq_rec.seq).upper())
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count += 1
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elif args.spades == True:
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for seq_rec in inFasta:
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seq_code_dict.setdefault(seq_rec.description,[]).append(seq_name_start+'_'+str(count)+'_Len'+str(len(seq_rec.seq))+'_Cov'+str(int(round(float(seq_rec.description.split('_')[-3])))))
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seq_code_dict.setdefault(seq_rec.description,[]).append(seq_rec.description.split('_')[5])
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seq_code_dict.setdefault(seq_rec.description,[]).append(str(seq_rec.seq).upper())
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renamed_seqs.append('>'+seq_name_start+'_'+str(count)+'_Len'+str(len(seq_rec.seq))+'_Cov'+str(int(round(float(seq_rec.description.split('_')[-3]))))+'\n'+str(seq_rec.seq).upper())
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count += 1
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else:
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for seq_rec in inFasta:
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seq_code_dict.setdefault(seq_rec.description,[]).append(seq_name_start+'_'+str(count)+'_Len'+str(len(seq_rec.seq)))
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seq_code_dict.setdefault(seq_rec.description,[]).append(str(seq_rec.seq).upper())
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renamed_seqs.append('>'+seq_name_start+'_'+str(count)+'_Len'+str(len(seq_rec.seq))+'\n'+str(seq_rec.seq).upper())
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count += 1
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print (color.BOLD+'\n\nThere are '+color.RED+str(len(renamed_seqs))+' contigs > '+str(args.minLen)\
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+color.END+color.BOLD+' in '+color.DARKCYAN+args.input_file.split('/')[-1]+color.END)
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with open(home_folder + args.output_file.split('/')[-1] + '.' + str(args.minLen)+'bp.fasta','w+') as w:
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for seq in renamed_seqs:
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w.write(seq+'\n')
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if args.spades != True:
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with open(home_folder + args.output_file.split('/')[-1] + '.' + str(args.minLen) + 'bp.SeqCodes.tsv','w+') as w:
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w.write('Original Name\tNew Name\tSeq Length\t Seq GC\n')
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for k, v in seq_code_dict.items():
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w.write(k+'\t'+v[0]+'\t'+str(len(v[1]))+'\t'+str(GC(v[1]))+'\n')
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else:
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with open(home_folder + args.output_file.split('/')[-1] + '.' + str(args.minLen) + 'bp.SeqCodes.tsv','w+') as w:
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w.write('Original Name\tNew Name\tSeq Length\tSeq GC\tSeq Coverage\n')
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for k, v in seq_code_dict.items():
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w.write(k+'\t'+v[0]+'\t'+str(len(v[2]))+'\t'+str(GC(v[2]))+'\t'+str(v[1])+'\n')
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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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os.system('cp ' + args.input_file + ' ' + args.output_file + '/OriginalFasta/' + args.input_file.split('/')[-1].replace('.fasta', '.Original.fasta'))
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os.system('cp ' + args.output_file + '/SizeFiltered/' + args.output_file.split('/')[-1] + '.' + str(args.minLen)+'bp.fasta ' + '/'.join(args.output_file.split('/')[:-1]) + '/XlaneBleeding/')
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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+'\n\nLook for '+color.DARKCYAN+args.output_file+'.'+str(args.minLen)+\
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'bp.fasta'+color.END+color.BOLD+'\n\n')
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print ('Next Script is: '+color.GREEN+'2_Auto_rRNA_BvE.py'+color.END\
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+color.BOLD+'\n(Alternatively'+color.GREEN+' 2a_remove_rRNA.py followed by 2b_remove_Bact.py'\
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+color.END+color.BOLD+')\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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prep_folders(args)
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temp = rename_Transcriptome(args)
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clean_up(args)
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next_script(args)
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main()
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