From f4b7839ea9d10f0ecdba005847c3c492ccf02761 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Mon, 12 Jun 2023 13:31:06 -0400 Subject: [PATCH] Delete PTL1/Transcriptomes/Scripts directory --- .../Scripts/1a_ContigFiltStats.py | 267 ------ .../Scripts/1b_XSpeciesContaminationAgnes.py | 145 ---- PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py | 285 ------- PTL1/Transcriptomes/Scripts/2b_remove_Bact.py | 410 --------- .../Scripts/3_CountOGsDiamond.py | 354 -------- .../Scripts/4_InFrameStopFreq.py | 790 ------------------ .../Scripts/5_GCodeTranslate.py | 770 ----------------- .../Scripts/6_FilterPartials.py | 607 -------------- .../6b_update_cov_post_removepartials.py | 81 -- PTL1/Transcriptomes/Scripts/7_FinalizeName.py | 398 --------- PTL1/Transcriptomes/Scripts/wrapper.py | 215 ----- PTL1/Transcriptomes/Scripts/wrapper_submit.sh | 23 - 12 files changed, 4345 deletions(-) delete mode 100644 PTL1/Transcriptomes/Scripts/1a_ContigFiltStats.py delete mode 100644 PTL1/Transcriptomes/Scripts/1b_XSpeciesContaminationAgnes.py delete mode 100644 PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py delete mode 100644 PTL1/Transcriptomes/Scripts/2b_remove_Bact.py delete mode 100644 PTL1/Transcriptomes/Scripts/3_CountOGsDiamond.py delete mode 100644 PTL1/Transcriptomes/Scripts/4_InFrameStopFreq.py delete mode 100644 PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py delete mode 100644 PTL1/Transcriptomes/Scripts/6_FilterPartials.py delete mode 100644 PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py delete mode 100644 PTL1/Transcriptomes/Scripts/7_FinalizeName.py delete mode 100644 PTL1/Transcriptomes/Scripts/wrapper.py delete mode 100644 PTL1/Transcriptomes/Scripts/wrapper_submit.sh diff --git a/PTL1/Transcriptomes/Scripts/1a_ContigFiltStats.py b/PTL1/Transcriptomes/Scripts/1a_ContigFiltStats.py deleted file mode 100644 index 1c34ee5..0000000 --- a/PTL1/Transcriptomes/Scripts/1a_ContigFiltStats.py +++ /dev/null @@ -1,267 +0,0 @@ -#!/usr/bin/env python3.6 - -##__Updated__: 01_04_2023 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 1_ContigFiltStats.py -##__Options__: python 1_ContigFiltStats.py --help - -########################################################################################## -## This script is intended to remove small transcripts or small contigs below a given ## -## minimum size from a transcriptome assembly. ## -## ## -## Prior to running this script, ensure the following: ## -## 1. You have assembled your transcriptome and COPIED the 'assembly' file ## -## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ## -## ## -## COMMAND Example Below ## -## ## -## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ## -## ## -## Next Script(s) to Run: ## -## AutoBactVsEuk.py (removes SSU then Bact) or 2a_removeSSU.py then 2b_removeBact.py ## -## ## -########################################################################################## - - -import argparse, os, sys -from argparse import RawTextHelpFormatter,SUPPRESS -from Bio import SeqIO -from Bio.SeqUtils import GC - - -#----------------------------- Colors For Print Statements ------------------------------# - -class color: - PURPLE = '\033[95m' - CYAN = '\033[96m' - DARKCYAN = '\033[36m' - ORANGE = '\033[38;5;214m' - BLUE = '\033[94m' - GREEN = '\033[92m' - YELLOW = '\033[93m' - RED = '\033[91m' - BOLD = '\033[1m' - UNDERLINE = '\033[4m' - END = '\033[0m' - - -#------------------------------- Main Functions of Script --------------------------------# - -########################################################################################### -###--------------------- Parses and Checks Command-Line Arguments ----------------------### -########################################################################################### - -def check_args(): - - parser = argparse.ArgumentParser(description= - color.BOLD+'\nThis script will remove Contigs (and provide a summary of statistics)'\ - +'\nfrom your Assembly that are shorter than a given length.'+color.ORANGE+\ - '\n\nA good minimum length to start with is 200bp.'+color.END+color.BOLD+\ - '\n\nThe minimum length value should be adjusted for your data sets.\n'+color.END+usage_msg(), - usage=SUPPRESS,formatter_class=RawTextHelpFormatter) - - required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END) - - required_arg_group.add_argument('--input_file','-in', action='store', - help=color.BOLD+color.GREEN+" Fasta file of Protein/Nucleotide sequences\n"+color.END) - - required_arg_group.add_argument('--output_file','-out', - help=color.BOLD+color.GREEN+" Desired Output Name\n\n"+color.END) - - required_arg_group.add_argument('--minLen','-len', default=200, type=int, - help=color.BOLD+color.GREEN+" Minimum number of base pairs for contigs\n (default = 200)"+color.END) - - optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END) - - optional_arg_group.add_argument('--spades','-spades', action='store_true', - help=color.BOLD+color.GREEN+'rnaSPAdes transcriptome assembly\n'+color.END) - - optional_arg_group.add_argument('--genbank','-gb', action='store_true', - help=color.BOLD+color.GREEN+'Assembly from Genbank\n (Will include Accession Number in'\ - ' contig name)\n'+color.END) - - optional_arg_group.add_argument('-author', action='store_true', - help=color.BOLD+color.GREEN+' Print author contact information\n'+color.END) - - - if len(sys.argv[1:]) == 0: - print (parser.description) - print ('\n') - sys.exit() - - args = parser.parse_args() - - quit_eval = return_more_info(args) - if quit_eval > 0: - sys.exit() - - args = parser.parse_args() - - return args - - -########################################################################################### -###------------------------------- Script Usage Message --------------------------------### -########################################################################################### - -def usage_msg(): - return color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 1_ContigFiltStats.py'\ - ' --input_file ../Op_me_Xxma_rnaSPAdes_scaffolds_15_05.fasta --output_file '\ - 'Op_me_Xxma --minLen 200 --spades'+color.END - - -########################################################################################## -###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------### -########################################################################################## - -def return_more_info(args): - - valid_arg = 0 - - author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\ - ' maurerax@gmail.com\n\n'+color.END) - - if args.author == True: - print (author) - valid_arg += 1 - - if args.input_file != None: - if os.path.isfile(args.input_file) != False: - if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])): - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - else: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - - if args.output_file == None: - valid_arg += 1 - - return valid_arg - -########################################################################################### -###--------------------------- Does the Inital Folder Prep -----------------------------### -########################################################################################### - -def prep_folders(args): - Home_folder_name = args.output_file - - if os.path.isdir(args.output_file) != True: - os.system('mkdir ' + args.output_file) - - if os.path.isdir(args.output_file + '/OriginalFasta/') != True: - os.system('mkdir ' + args.output_file +'/OriginalFasta/') - - if os.path.isdir(args.output_file + '/SizeFiltered/') != True: - os.system('mkdir ' + args.output_file +'/SizeFiltered/') - - if os.path.isdir('/'.join(args.output_file.split('/')[:-1]) + '/XlaneBleeding/') != True: - os.system('mkdir ' + '/'.join(args.output_file.split('/')[:-1]) + '/XlaneBleeding/') - - -########################################################################################### -###---------- Renames the Contigs, Writes them out, and Calculates Basic Info ----------### -########################################################################################### - -def rename_Transcriptome(args): - - home_folder = args.output_file + '/SizeFiltered/' - - print (color.BOLD+'\n\nPrepping '+color.GREEN+args.input_file.split('/')[-1]+color.END) - - inFasta = [i for i in SeqIO.parse(args.input_file,'fasta') if len(i.seq) >= args.minLen] - inFasta.sort(key=lambda seq_rec: -len(seq_rec.seq)) - - renamed_seqs = [] - seq_code_dict = {} - - count = 1 - - seq_name_start = 'Contig' - - if args.genbank == True: - for seq_rec in inFasta: - seq_code_dict.setdefault(seq_rec.id,[]).append(seq_rec.id.split('_')[-1].split('.')[0]+'_Contig_'+str(count)+'_Len'+str(len(seq_rec.seq))) - seq_code_dict.setdefault(seq_rec.id,[]).append(str(seq_rec.seq).upper()) - 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()) - count += 1 - elif args.spades == True: - for seq_rec in inFasta: - 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]))))) - seq_code_dict.setdefault(seq_rec.description,[]).append(seq_rec.description.split('_')[5]) - seq_code_dict.setdefault(seq_rec.description,[]).append(str(seq_rec.seq).upper()) - 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()) - count += 1 - else: - for seq_rec in inFasta: - seq_code_dict.setdefault(seq_rec.description,[]).append(seq_name_start+'_'+str(count)+'_Len'+str(len(seq_rec.seq))) - seq_code_dict.setdefault(seq_rec.description,[]).append(str(seq_rec.seq).upper()) - renamed_seqs.append('>'+seq_name_start+'_'+str(count)+'_Len'+str(len(seq_rec.seq))+'\n'+str(seq_rec.seq).upper()) - count += 1 - - print (color.BOLD+'\n\nThere are '+color.RED+str(len(renamed_seqs))+' contigs > '+str(args.minLen)\ - +color.END+color.BOLD+' in '+color.DARKCYAN+args.input_file.split('/')[-1]+color.END) - - with open(home_folder + args.output_file.split('/')[-1] + '.' + str(args.minLen)+'bp.fasta','w+') as w: - for seq in renamed_seqs: - w.write(seq+'\n') - - if args.spades != True: - with open(home_folder + args.output_file.split('/')[-1] + '.' + str(args.minLen) + 'bp.SeqCodes.tsv','w+') as w: - w.write('Original Name\tNew Name\tSeq Length\t Seq GC\n') - for k, v in seq_code_dict.items(): - w.write(k+'\t'+v[0]+'\t'+str(len(v[1]))+'\t'+str(GC(v[1]))+'\n') - else: - with open(home_folder + args.output_file.split('/')[-1] + '.' + str(args.minLen) + 'bp.SeqCodes.tsv','w+') as w: - w.write('Original Name\tNew Name\tSeq Length\tSeq GC\tSeq Coverage\n') - for k, v in seq_code_dict.items(): - w.write(k+'\t'+v[0]+'\t'+str(len(v[2]))+'\t'+str(GC(v[2]))+'\t'+str(v[1])+'\n') - - -########################################################################################### -###-------------------------- Cleans Up the PostAssembly Folder ------------------------### -########################################################################################### - -def clean_up(args): - - os.system('cp ' + args.input_file + ' ' + args.output_file + '/OriginalFasta/' + args.input_file.split('/')[-1].replace('.fasta', '.Original.fasta')) - - os.system('cp ' + args.output_file + '/SizeFiltered/' + args.output_file.split('/')[-1] + '.' + str(args.minLen)+'bp.fasta ' + '/'.join(args.output_file.split('/')[:-1]) + '/XlaneBleeding/') - - -########################################################################################### -###-------------------------------- Next Script Message --------------------------------### -########################################################################################### - -def next_script(args): - - print (color.BOLD+'\n\nLook for '+color.DARKCYAN+args.output_file+'.'+str(args.minLen)+\ - 'bp.fasta'+color.END+color.BOLD+'\n\n') - - print ('Next Script is: '+color.GREEN+'2_Auto_rRNA_BvE.py'+color.END\ - +color.BOLD+'\n(Alternatively'+color.GREEN+' 2a_remove_rRNA.py followed by 2b_remove_Bact.py'\ - +color.END+color.BOLD+')\n\n'+ color.END) - - -########################################################################################## -###--------------- Checks Command Line Arguments and Calls on Functions ---------------### -########################################################################################## - -def main(): - - args = check_args() - - prep_folders(args) - - temp = rename_Transcriptome(args) - - clean_up(args) - - next_script(args) - -main() - diff --git a/PTL1/Transcriptomes/Scripts/1b_XSpeciesContaminationAgnes.py b/PTL1/Transcriptomes/Scripts/1b_XSpeciesContaminationAgnes.py deleted file mode 100644 index c3ff819..0000000 --- a/PTL1/Transcriptomes/Scripts/1b_XSpeciesContaminationAgnes.py +++ /dev/null @@ -1,145 +0,0 @@ -#!/usr/bin/python3 - -__author__ = 'Jean-David Grattepanche' -__version__ = 'ACL fixed sequence naming issue Feb 23, 2022' -__email__ = 'jeandavid.grattepanche@gmail.com' - - - -import sys -import os -import re -import time -import string -import os.path -from Bio import SeqIO -from sys import argv -listtaxa=[] -toosim = 0.99 -seqcoverage = 0.7 - -def merge_files(folder, minlen): - mergefile = open('/'.join(folder.split('/')[:-1]) + '/forclustering.fasta','w+') - print("MERGE following files") - for taxafile in os.listdir(folder): - if taxafile[0] != ".": - listtaxa.append(taxafile.split('.' + str(minlen) + 'bp')[0]) - - for line2 in SeqIO.parse(folder+'/'+taxafile, 'fasta'): - if int(len(str(line2.seq))) >= int(minlen): - mergefile.write('>'+taxafile.split('.' + str(minlen) + 'bp')[0] + '_' + line2.description + '\n' + str(line2.seq) + '\n') - else: - print(line2, " is too short") - mergefile.close() - - sort_cluster(folder, listtaxa, minlen) - - -def sort_cluster(folder, listtaxa, minlen): - if not os.path.exists('/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/'): - os.makedirs('/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/') - - fastalist = []; fastadict= {} - - print('CREATE a dictionnary of sequences') - for record in SeqIO.parse(open('/'.join(folder.split('/')[:-1]) + '/forclustering.fasta','r'),'fasta'): - IDL = record.description, int(record.description.split('_Cov')[1].replace('\n','')) - fastalist.append(IDL) - fastadict[record.description] = record.seq - - print("CLUSTER sequences that overlap at least 70%") - os.system('vsearch --cluster_fast ' + '/'.join(folder.split('/')[:-1]) + '/forclustering.fasta --strand both --query_cov '+str(seqcoverage)+' --id '+str(toosim) +' --uc ' + '/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/results_forclustering.uc --threads 60' ) - - input2 = open('/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/results_forclustering.uc','r') - out2 = open('/'.join(folder.split('/')[:-1]) + '/fastatokeep.fas','w+') - out3 = open('/'.join(folder.split('/')[:-1]) + '/fastatoremoved.fas','w+') - out4 = open('/'.join(folder.split('/')[:-1]) + '/fastatoremoved.uc','w+') - print("CREATE a dictionary with clustering results") - clustdict= {}; clustlist = []; allseq = []; clustline = {}; list= []; i=0; j=0 - for row2 in input2: - if row2.split('\t')[0] == 'C' and int(row2.split('\t')[2]) < 2: # keep all unique sequences - out2.write('>'+row2.split('\t')[8] + '\n' + str(fastadict[row2.split('\t')[8]])+ '\n') - if row2.split('\t')[0] == 'C' and int(row2.split('\t')[2]) > 1: # create another dictionary -# print("create dico: ", row2.split('\t')[8]) - clustdict.setdefault(row2.split('\t')[8], [row2.split('\t')[8]]) - clustlist.append(row2.split('\t')[8]) - - for row3 in open('/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/results_forclustering.uc','r'): - if row3.split('\t')[0] == 'H': -# print("add dico: ", row3.split('\t')[9], row3.split('\t')[8]) - clustdict[row3.split('\t')[9].replace('\n','')].append(row3.split('\t')[8].replace('\n','')) - clustline[row3.split('\t')[8].replace('\n','')] = row3.replace('\n','') - clustline[row3.split('\t')[9].replace('\n','')] = row3.replace('\n','') - - - print("PARSE the clusters: keep seed sequences (highest coverage) for each cluster") - for clust in clustlist: - list = sorted(clustdict[clust], reverse = True, key=lambda x: int(x.split('_Cov')[1])) - master = list[0] - Covmaster = int(list[0].split('_Cov')[1]) - master8dig = ('_').join(list[0].split('_')[0:3])[:-2] - for seq in list: - clustered = seq.replace('\n','') - Covclustered = int(clustered.split('_Cov')[1]) - clustered8dig = ('_').join(clustered.split('_')[0:3])[:-2] -# print(master8dig, Covmaster, '//', clustered8dig, Covclustered) - if float(Covmaster/Covclustered) < 10: - out2.write('>'+clustered + '\n' + str(fastadict[clustered])+ '\n') - i +=1 - elif master8dig == clustered8dig: - out2.write('>'+clustered + '\n' + str(fastadict[clustered])+ '\n') - i +=1 - elif Covclustered >= 50: - out2.write('>'+clustered + '\n' + str(fastadict[clustered])+ '\n') - i +=1 - else: - j +=1 - out4 = open('/'.join(folder.split('/')[:-1]) + '/fastatoremoved.uc','a') - out3.write('>'+clustered + '\n' + str(fastadict[clustered])+ '\n') - print(clustline[clustered],'\t' , master ) - out4.write(clustline[clustered]+ '\t' + master + '\n') - out4.close() - print('there are ', str(i),' sequences kept and ',str(j),' sequences removed') - - out2.close() - out3.close() - - splittaxa(folder, listtaxa, minlen) - -def splittaxa(folder, listtaxa, minlen): - for taxa in listtaxa: - tax_sf_path = '/'.join(folder.split('/')[:-1]) + '/' + taxa + '/SizeFiltered/' - os.system('mv ' + tax_sf_path + taxa + '.' + str(minlen) + 'bp.fasta' + ' ' + tax_sf_path + taxa + '.' + str(minlen) + 'bp.preXPlate.fasta') - - with open(tax_sf_path + taxa + '.' + str(minlen) + 'bp.fasta','w') as o: - for kept in SeqIO.parse('/'.join(folder.split('/')[:-1]) + '/fastatokeep.fas','fasta'): - if taxa in kept.description: - o.write('>' + kept.description.replace(taxa + '_', '') + '\n' + str(kept.seq) + '\n') - - os.system('mv ' + '/'.join(folder.split('/')[:-1]) + '/fastatokeep.fas ' + '/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/') - os.system('mv ' + '/'.join(folder.split('/')[:-1]) + '/fastatoremoved.fas ' + '/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/') - os.system('mv ' + '/'.join(folder.split('/')[:-1]) + '/fastatoremoved.uc ' + '/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/') - os.system('mv ' + '/'.join(folder.split('/')[:-1]) + '/forclustering.fasta ' + '/'.join(folder.split('/')[:-1]) + '/clusteringresults_vsearch/') - -def main(): - - script, folder, minlen = argv - merge_files(folder, minlen) - -main() - - - - - - - - - - - - - - - - diff --git a/PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py b/PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py deleted file mode 100644 index d9c7719..0000000 --- a/PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py +++ /dev/null @@ -1,285 +0,0 @@ -#!/usr/bin/env python3.5 - -##__Updated__: 18_08_2017 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 2a_remove_rDNA.py --help - -########################################################################################## -## This script is intended to identify and isolate SSU/LSU sequences ## -## Prior to running this script, ensure the following: ## -## ## -## 1. You have assembled your transcriptome and COPIED the 'assembly' file ## -## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ## -## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ## -## 3. Have the Databases set up correctly (e.g. with BLAST or Diamond) and in their ## -## respective folders! See the manual if you need help ## -## ## -## COMMAND Example Below ## -## ## -## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ## -## ## -## Next Script(s) to Run: ## -## 2b_removeBact.py ## -## ## -########################################################################################## - - -import argparse, os, sys -from argparse import RawTextHelpFormatter,SUPPRESS -from Bio import SeqIO - - -#------------------------------ Colors For Print Statements ------------------------------# - -class color: - PURPLE = '\033[95m' - CYAN = '\033[96m' - DARKCYAN = '\033[36m' - ORANGE = '\033[38;5;214m' - BLUE = '\033[94m' - GREEN = '\033[92m' - YELLOW = '\033[93m' - RED = '\033[91m' - BOLD = '\033[1m' - UNDERLINE = '\033[4m' - END = '\033[0m' - - -#------------------------------- Main Functions of Script --------------------------------# - -########################################################################################### -###--------------------- Parses and Checks Command-Line Arguments ----------------------### -########################################################################################### - -def check_args(): - - parser = argparse.ArgumentParser(description= - color.BOLD+'\nThis script will remove '+color.RED+'rDNA contigs (both SSU and LSU)'+color.END\ - +color.BOLD+'\nfrom your Assembly using a set of '+color.RED+'SSU/LSU rDNAs '+color.END\ - +color.BOLD+'from diverse\n'+color.ORANGE+'Eukaryotes, Bacteria and Archaea'+color.END\ - +color.BOLD+'.'+color.END+usage_msg(), usage=SUPPRESS,formatter_class=RawTextHelpFormatter) - - required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END) - - required_arg_group.add_argument('--input_file','-in', action='store', - help=color.BOLD+color.GREEN+"Fasta file of Nucleotide sequences"+color.END) - required_arg_group.add_argument('--databases','-d', action='store', - help=color.BOLD+color.GREEN+"Path to databases"+color.END) - - optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END) - optional_arg_group.add_argument('--threads','-t', default='2', - help=color.BOLD+color.GREEN+' Number of threads to use for BLAST\n (default = 2)\n'+color.END) - optional_arg_group.add_argument('-author', action='store_true', - help=color.BOLD+color.GREEN+' Print author contact information\n'+color.END) - - if len(sys.argv[1:]) == 0: - print (parser.description) - print ('\n') - sys.exit() - - args = parser.parse_args() - - quit_eval = return_more_info(args) - if quit_eval > 0: - sys.exit() - - return args - - -########################################################################################### -###------------------------------- Script Usage Message --------------------------------### -########################################################################################### - -def usage_msg(): - 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 - - -########################################################################################## -###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------### -########################################################################################## - -def return_more_info(args): - - valid_arg = 0 - - author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\ - ' maurerax@gmail.com\n\n'+color.END) - - if args.author == True: - print (author) - valid_arg += 1 - - if args.input_file != None: - if os.path.isfile(args.input_file) != False: - if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])): - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - elif args.input_file.endswith('bp.fasta') != True: - print (color.BOLD + '\n\nCheck that you are giving an appropriately Named/Processed'\ - 'Fasta file(s) to this script\n\nNOTE that this script CURRENTLY expects your'\ - ' Fasta files to contain '+color.RED+ '"rna"'+color.END+color.BOLD+' in \nthe Fasta File'\ - ' Name and must end with ' + color.RED + '"bp.fasta"\n\n' + color.END) - valid_arg += 1 - else: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - - if os.path.isdir(args.databases + '/db_BvsE') != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\ - +color.ORANGE+'db_BvsE Folder!\n\n'+color.END+color.BOLD+'Ensure that this folder '\ - 'can be found in the main '+color.ORANGE+'Databases Folder'+color.END+color.BOLD\ - +'\n\nThen try once again.') - valid_arg += 1 - elif os.path.isfile(args.databases + '/db_BvsE/SSULSUdb.nhr') != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\ - 'BLAST+ formatted '+color.ORANGE+'SSU-LSU databases!\n\n'+color.END+color.BOLD+\ - 'Ensure that they can be found in the '+color.ORANGE+'db_BvsE folder'+color.END+\ - color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\ - color.END+color.BOLD+'\n\nThen try once again.') - valid_arg += 1 - - return valid_arg - - -########################################################################################### -###--------------------------- Does the Inital Folder Prep -----------------------------### -########################################################################################### - -def prep_folders(args): - code = args.input_file.split('/')[-1][:10] - rRNA_folder = args.input_file.split('SizeFiltered')[0] + '/rRNA_Removal/' - - if os.path.isdir(rRNA_folder) != True: - os.system('mkdir '+rRNA_folder) - - return code, rRNA_folder - - -########################################################################################### -###---------------------- Uses BLAST to identify SSU/LSU Sequences ---------------------### -########################################################################################### - -def remove_rDNA(args, rRNA_folder): - - blast_output = rRNA_folder + args.input_file.split('/')[-1].split('.200bp.fasta')[0]+'_allSSULSUresults.tsv' - - BLASTN_cmd = 'blastn -query ' + args.input_file + ' -evalue 1e-10 -max_target_seqs 1 -outfmt'\ - ' 6 -db ' + args.databases + '/db_BvsE/SSULSUdb -num_threads 2 -out ' + blast_output - - print (color.BOLD+'\n\nBLASTing '+color.DARKCYAN+args.input_file.split('/')[-1]+color.END\ - +color.BOLD+ ' against the rDNA database\n\n' + color.END) - - os.system(BLASTN_cmd) - - rDNA_Hits = list(set([i.split('\t')[0] for i in open(blast_output).readlines()])) - - print (color.BOLD+'Binning Sequences from '+color.DARKCYAN+args.input_file.split('/')[-1]\ - +color.END+color.BOLD+'\nas rDNA OR Potentially Protein-Coding\n\n'+color.END) - - no_SSULSU = 0 - with_SSULSU = 0 - - inFasta = [seq_rec for seq_rec in SeqIO.parse(args.input_file,'fasta')] - - with open(rRNA_folder + args.input_file.split('/')[-1].split('.200bp.fasta')[0]+'_rRNAseqs.fasta','w+') as HasSSU: - for seq_rec in inFasta: - if seq_rec.description in rDNA_Hits: - HasSSU.write('>'+seq_rec.description+'\n'+str(seq_rec.seq)+'\n') - with_SSULSU += 1 - - with open(rRNA_folder + args.input_file.split('/')[-1].split('.200bp.fasta')[0] + '_NorRNAseqs.fasta','w+') as NoSSU: - for seq_rec in inFasta: - if seq_rec.description not in rDNA_Hits: - NoSSU.write('>'+seq_rec.description+'\n'+str(seq_rec.seq)+'\n') - no_SSULSU += 1 - - return str(with_SSULSU), str(no_SSULSU) - - -########################################################################################### -###--------------------------- Updates Log of SSU/LSU Removal --------------------------### -########################################################################################### - -def update_log(args, with_SSU, no_SSU): - - if os.path.isdir('../PostAssembly_Logs/') != True: - os.system('mkdir ../PostAssembly_Logs/') - - print (color.BOLD+'There are '+color.RED+with_SSU+' rRNA contigs'+color.END+color.BOLD\ - +' and '+color.PURPLE+no_SSU+' Putative Protein-coding contigs'+color.END+color.BOLD\ - +'\nin '+color.DARKCYAN+args.input_file.split('/')[1]+'\n' + color.END) - - with open('../PostAssembly_Logs/'+args.input_file.split('/')[1].split('.fas')[0]+'.Log.txt','a') as LogFile: - LogFile.write('rDNA Contigs\t'+with_SSU+'\tn/a\tn/a\n') - LogFile.write('Non-rDNA Contigs\t'+no_SSU+'\tn/a\tn/a\n') - - -########################################################################################### -###-------------------------------- Next Script Message --------------------------------### -########################################################################################### - -def next_script(args): - - print (color.BOLD+'\nLook for '+color.ORANGE+args.input_file.split('/')[1].split('_rna')[0]\ - + '_NorRNAseqs.fasta'+color.END+color.BOLD+'\nin the '+args.input_file.split('/')[1].split('_rna')[0]\ - +' Folder\n\n' + color.END) - print (color.BOLD + 'Next Script is: ' + color.GREEN + '2b_remove_Bact.py\n\n'+ color.END) - - -########################################################################################### -###-------------------------- Cleans Up the PostAssembly Folder ------------------------### -########################################################################################### - -def clean_up(args): - - home_folder = args.input_file.split('SizeFiltered')[0] - - os.system('cp ' + home_folder + 'rRNA_Removal/*NorRNA*.fasta ' + home_folder) - -########################################################################################## -###--------------- Checks Command Line Arguments and Calls on Functions ---------------### -########################################################################################## - -def main(): - - args = check_args() - - code, rRNA_folder = prep_folders(args) - - with_SSULSU, no_SSULSU = remove_rDNA(args, rRNA_folder) - - #update_log(args, with_SSULSU, no_SSULSU) - - clean_up(args) - - next_script(args) - -main() - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/PTL1/Transcriptomes/Scripts/2b_remove_Bact.py b/PTL1/Transcriptomes/Scripts/2b_remove_Bact.py deleted file mode 100644 index a67ee47..0000000 --- a/PTL1/Transcriptomes/Scripts/2b_remove_Bact.py +++ /dev/null @@ -1,410 +0,0 @@ -#!/usr/bin/env python3.5 - -##__Updated__: 18_08_2017 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 2b_remove_Bact.py --help - -########################################################################################## -## This script is intended to identify and isolate SSU/LSU sequences ## -## Prior to running this script, ensure the following: ## -## ## -## 1. You have assembled your transcriptome and COPIED the 'assembly' file ## -## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ## -## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ## -## 3. Have the Databases set up correctly (e.g. with BLAST or Diamond) and in their ## -## respective folders! See the manual if you need help ## -## 4. Run removeSSU.py on your Fasta file ## -## ## -## COMMAND Example Below ## -## ## -## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ## -## ## -## Next Script(s) to Run: ## -## 3_CountOGsDiamond.py ## -## ## -########################################################################################## - - -import argparse, os, sys -from argparse import RawTextHelpFormatter,SUPPRESS -from distutils import spawn -from Bio import SeqIO - - -#------------------------------ Colors For Print Statements ------------------------------# -class color: - PURPLE = '\033[95m' - CYAN = '\033[96m' - DARKCYAN = '\033[36m' - ORANGE = '\033[38;5;214m' - BLUE = '\033[94m' - GREEN = '\033[92m' - YELLOW = '\033[93m' - RED = '\033[91m' - BOLD = '\033[1m' - UNDERLINE = '\033[4m' - END = '\033[0m' - - -#------------------------------- Main Functions of Script --------------------------------# - -########################################################################################### -###---------------------------- UPDATE DIAMOND PATH BELOW! -----------------------------### -########################################################################################### - ## IF Diamond is IN YOUR PATH then no updating is needed... - -def check_diamond_path(): - - diamond_path = '' - - if diamond_path == '': - diamond_path = spawn.find_executable("diamond") - #diamond_path = '/path/to/diamond' - else: - pass - - if diamond_path == None: - print (color.BOLD + '\n\nPlease open this script and check that you have included'\ - +' the PATH to the'+color.BLUE+' "Diamond" '+color.END+color.BOLD+'executable.\n\n'+color.END) - print (color.BOLD+color.BLUE+'LOOK FOR:\n\n'+color.RED\ - +'#------------------------------ UPDATE DIAMOND PATH BELOW! -------------------------------#'\ - +color.BLUE+'\n\nThis is somewhere around lines 50 - 80...\n\n'+color.END) - - sys.exit() - else: - pass - - return diamond_path - - -########################################################################################### -###--------------------- Parses and Checks Command-Line Arguments ----------------------### -########################################################################################### - -def check_args(): - - parser = argparse.ArgumentParser(description= - color.BOLD + '\nThis script will categorize Contigs as'+color.ORANGE+' STRONGLY '+color.END\ - +color.BOLD+color.RED+'Eukaryotic \nOR Prokaryotic'+color.END+color.BOLD+' using a set of Proteins'\ - ' from diverse\n'+color.ORANGE+'Eukaryotes, Bacteria and Archaea'+color.END\ - +color.BOLD+'.'+color.END+usage_msg(), usage=SUPPRESS,formatter_class=RawTextHelpFormatter) - - required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END) - - required_arg_group.add_argument('--input_file','-in', action='store', - help=color.BOLD+color.GREEN+'Fasta file of Nucleotide sequences (with rRNAs removed)'+color.END) - required_arg_group.add_argument('--databases','-d', action='store', - help=color.BOLD+color.GREEN+"Path to databases"+color.END) - - optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END) - optional_arg_group.add_argument('-author', action='store_true', - help=color.BOLD+color.GREEN+' Print author contact information\n'+color.END) - - if len(sys.argv[1:]) == 0: - print (parser.description) - print ('\n') - sys.exit() - - args = parser.parse_args() - - quit_eval = return_more_info(args) - if quit_eval > 0: - sys.exit() - - return args - - -########################################################################################### -###------------------------------- Script Usage Message --------------------------------### -########################################################################################### - -def usage_msg(): - return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 2b_remove_Bact.py --input_file'\ - ' ../Op_me_Xxma/Op_me_Xxma_NorRNAseqs.fasta'+color.END) - - -########################################################################################## -###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------### -########################################################################################## - -def return_more_info(args): - - valid_arg = 0 - - author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\ - ' maurerax@gmail.com\n\n'+color.END) - - if args.author == True: - print (author) - valid_arg += 1 - - print(args.input_file) - - if args.input_file != None: - if os.path.isfile(args.input_file) != False: - if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])): - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - elif args.input_file.endswith('NorRNAseqs.fasta') != True: - print (color.BOLD+'\n\nInvalid Fasta File! Only Fasta Files that were processed'\ - ' with '+color.GREEN+'2a_remove_rRNA.py '+color.END+color.BOLD+'are valid\n\n'\ - 'However, to bypass that issue, Fasta Files MUST end with '+color.CYAN+\ - '"NorRNAseqs.fas"\n\n'+color.END) - valid_arg += 1 - else: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - - if os.path.isdir(args.databases + '/db_BvsE') != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\ - +color.ORANGE+'db_BvsE Folder!\n\n'+color.END+color.BOLD+'Ensure that this folder '\ - 'can be found in the main '+color.ORANGE+'Databases Folder'+color.END+color.BOLD\ - +'\n\nThen try once again.') - valid_arg += 1 - elif os.path.isfile(args.databases + '/db_BvsE/eukout.dmnd') != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\ - 'Diamond formatted '+color.ORANGE+'Eukaryotic Protein database!\n\n'+color.END+color.BOLD+\ - 'Ensure that it can be found in the '+color.ORANGE+'db_BvsE folder'+color.END+\ - color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\ - color.END+color.BOLD+'\n\nThen try once again.'+color.END) - elif os.path.isfile(args.databases + '/db_BvsE/micout.dmnd') != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\ - 'Diamond formatted '+color.ORANGE+'Bacterial/Archaeal Protein database!\n\n'+color.END+color.BOLD+\ - 'Ensure that it can be found in the '+color.ORANGE+'db_BvsE folder'+color.END+\ - color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\ - color.END+color.BOLD+'\n\nThen try once again.'+color.END) - - valid_arg += 1 - - return valid_arg - - -########################################################################################### -###--------------------------- Does the Inital Folder Prep -----------------------------### -########################################################################################### - -def prep_folders(args): - - BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/' - - if os.path.isdir(BvE_folder) != True: - os.system('mkdir '+BvE_folder) - - -########################################################################################### -###---------------- Runs Diamond on Bact and Euk small RefSeq Databases ----------------### -########################################################################################### - -def ublast_BvE(args, diamond_path): - - BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/' - mic_output = args.input_file.split('/')[-1]+'micresults.' - euk_output = args.input_file.split('/')[-1]+'eukresults.' - - print(color.BOLD+'\n\n"BLAST"-ing against PROK database using DIAMOND: ' + color.DARKCYAN + 'micout.dmnd' + color.END + '\n\n') - - Prok_diamond_cmd = diamond_path + ' blastx -q ' + args.input_file + ' --max-target-seqs 1 -d ' + args.databases + '/db_BvsE/micout.dmnd --evalue 1e-5 --threads 60 --outfmt 6 -o ' + BvE_folder + 'allmicresults.tsv' - - os.system(Prok_diamond_cmd) - - print(color.BOLD+'\n\n"BLAST"-ing against EUK database using DIAMOND: ' + color.DARKCYAN + 'eukout.dmnd' + color.END + '\n\n') - - Euk_diamond_cmd = diamond_path + ' blastx -q ' + args.input_file + ' --max-target-seqs 1 -d ' + args.databases + '/db_BvsE/eukout.dmnd --evalue 1e-5 --threads 60 --outfmt 6 -o ' + BvE_folder + 'alleukresults.tsv' - - os.system(Euk_diamond_cmd) - - - -########################################################################################### -###---------------- Compares Bacterial and Euk Hits for Classification -----------------### -########################################################################################### - -def compare_hits(args): - - BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/' - - EukDict = {} - ProkDict = {} - CompDict = {} - - inFasta = [seq_rec for seq_rec in SeqIO.parse(args.input_file,'fasta')] - - for seq_rec in inFasta: - EukDict[seq_rec.description] = '' - ProkDict[seq_rec.description] = '' - CompDict[seq_rec.description] = [] - - inEukHits = [i for i in open(BvE_folder + 'alleukresults.tsv').readlines()] - inEukHits.sort(key=lambda x: (float(x.split('\t')[-2]), -int(x.split('\t')[3]))) - - inProkHits = [i for i in open(BvE_folder + 'allmicresults.tsv').readlines()] - inProkHits.sort(key=lambda x: (float(x.split('\t')[-2]), -int(x.split('\t')[3]))) - - for i in inEukHits: - if EukDict[i.split('\t')[0]] == '': - EukDict[i.split('\t')[0]] = float(i.split('\t')[-2]) - - for i in inProkHits: - if ProkDict[i.split('\t')[0]] == '': - ProkDict[i.split('\t')[0]] = float(i.split('\t')[-2]) - - for k in CompDict.keys(): - if EukDict[k] != '': - CompDict[k].append(EukDict[k]) - else: - CompDict[k].append('no hit') - if ProkDict[k] != '': - CompDict[k].append(ProkDict[k]) - else: - CompDict[k].append('no hit') - - for k, v in CompDict.items(): - - ### Contigs lacking STRONG Eukaryotic OR Prokaryotic Hits - if v[0] == 'no hit' and v[1] == 'no hit': - CompDict[k].append('UNDETERMINED') - - ### Contigs lacking STRONG Eukaryotic with a Prokaryotic Hit - elif v[0] != 'no hit' and v[1] == 'no hit': - CompDict[k].append('EUKARYOTIC') - - ### Contigs with a Eukaryotic but without a Prokaryotic Hit - elif v[0] == 'no hit' and v[1] != 'no hit': - CompDict[k].append('PROKARYOTIC') - - ### Uses Basic math to determine if contigs with are MORE Eukaryotic than Prokaryotic - else: - try: - prok_euk_ratio = float(v[1])/float(v[0]) - euk_prok_ratio = float(v[0])/float(v[1]) - - if prok_euk_ratio >= 100: - CompDict[k].append('EUKARYOTIC') - - elif euk_prok_ratio >= 1000: - CompDict[k].append('PROKARYOTIC') - - else: - CompDict[k].append('UNDETERMINED') - - except: - CompDict[k].append('divide by zero') - - with open(BvE_folder + 'comparisons.txt','w+') as w: - for k, v in CompDict.items(): - w.write(k+':'+':'.join([str(i) for i in v])+'\n') - - BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/' - BvE_output_base = BvE_folder+args.input_file.split('/')[-1].split('.fas')[0] - -### Gathers the sequences and categorizes them - Euk_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'EUKARYOTIC'), key=lambda x: -int(len(x.seq))) - Prok_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'PROKARYOTIC'), key=lambda x: -int(len(x.seq))) - Und_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'UNDETERMINED'), key=lambda x: -int(len(x.seq))) - Zero_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'divide by zero'), key=lambda x: -int(len(x.seq))) - - -### Writes out all of the categorized sequences - with open(args.input_file.split('NorRNA')[0] + 'WTA_EPU.fasta', 'w') as epu: - with open(BvE_output_base+'.Not_Bact.fasta','w+') as nb: - for euk_seq in Euk_Fasta: - nb.write('>' + euk_seq.description + '\n' + str(euk_seq.seq) + '\n') - epu.write('>' + euk_seq.description + '_E' + '\n' + str(euk_seq.seq) + '\n') - - - with open(BvE_output_base+'.Bact_Hit.fasta','w+') as pr: - for prok_seq in Prok_Fasta: - pr.write('>' + prok_seq.description + '\n' + str(prok_seq.seq) + '\n') - epu.write('>' + prok_seq.description + '_P' + '\n' + str(prok_seq.seq) + '\n') - - with open(BvE_output_base+'.Undetermined.fasta','w+') as und: - for und_seq in Und_Fasta: - und.write('>' + und_seq.description + '\n' + str(und_seq.seq) + '\n') - epu.write('>' + und_seq.description + '_U' + '\n' + str(und_seq.seq) + '\n') - - if len(Zero_Fasta) != 0: - with open(BvE_output_base+'.DivideByZero.fasta','w+') as w: - for zero_seq in Zero_Fasta: - w.write('>' + zero_seq.description + '\n' + str(zero_seq.seq) + '\n') - epu.write('>' + zero_seq.description + '_U' + '\n' + str(zero_seq.seq) + '\n') - else: - pass - - return str(len(Euk_Fasta)), str(len(Prok_Fasta)), str(len(Und_Fasta)) - - -########################################################################################### -###----------------------- Updates Log of Prok vs Euk Comparisons ----------------------### -########################################################################################### - -def update_log(args, Euk_Contigs, Prok_Contigs, Und_Contigs): - - if os.path.isdir('../PostAssembly_Logs/') != True: - os.system('mkdir ../PostAssembly_Logs/') - else: - pass - - print (color.BOLD +'\n\nThere are '+color.RED+Prok_Contigs+' Strongly Prokaryotic contigs'+color.END\ - +color.BOLD+',\n'+color.ORANGE+Euk_Contigs+' Strongly Eukaryotic contigs'+color.END\ - +color.BOLD+',\nand '+color.PURPLE+Und_Contigs+' Undetermined Contigs\n'+color.END\ - +color.BOLD+'in '+args.input_file.split('/')[-1]+color.END) - - for Logname in os.listdir(os.curdir+'./PostAssembly_Logs/'): - if Logname.startswith(args.input_file.split('/')[-1].split('_No')[0]) and Logname.endswith('Log.txt'): # ACL - ??? - with open('../PostAssembly_Logs/'+Logname,'a') as Logfilename: - Logfilename.write('Prokaryotic Contigs\t'+Prok_Contigs+'\tn/a\tn/a\n') - Logfilename.write('Eukaryotic Contigs\t'+Euk_Contigs+'\tn/a\tn/a\n') - Logfilename.write('Undetermined Contigs\t'+Und_Contigs+'\tn/a\tn/a\n') - - -########################################################################################### -###-------------------------------- Next Script Message --------------------------------### -########################################################################################### - -def next_script(args): - - print (color.BOLD+'\nLook for '+color.DARKCYAN+args.input_file.split('/')[-1]\ - .split('NorRNA')[0]+'WTA_EPU.fasta'+color.END+color.BOLD+' in the '\ - +args.input_file.split('/')[1]+' Folder\n\n' + color.END) - print (color.BOLD + 'Next Script is: ' + color.GREEN + '3_CountOGsDiamond.py\n\n'+ color.END) - - -########################################################################################## -###--------------------- Cleans up the Folder and Moves Final Files -------------------### -########################################################################################## - -def clean_up(args): - - home_folder = '/'.join(args.input_file.split('/')[:-1]) - - os.system('cp '+home_folder+'/*WTA_EPU.fasta '+home_folder+'/BvE/') - os.system('mv '+home_folder+'/*NorRNA*fasta '+home_folder+'/rRNA_Removal/') - - -########################################################################################## -###--------------- Checks Command Line Arguments and Calls on Functions ---------------### -########################################################################################## - -def main(): - - usearch_path = check_diamond_path() - - args = check_args() - - prep_folders(args) - - ublast_BvE(args, usearch_path) - - Euk_Contigs, Prok_Contigs, Und_Contigs = compare_hits(args) - - #update_log(args, Euk_Contigs, Prok_Contigs, Und_Contigs) - - clean_up(args) - - next_script(args) - -main() diff --git a/PTL1/Transcriptomes/Scripts/3_CountOGsDiamond.py b/PTL1/Transcriptomes/Scripts/3_CountOGsDiamond.py deleted file mode 100644 index ceac829..0000000 --- a/PTL1/Transcriptomes/Scripts/3_CountOGsDiamond.py +++ /dev/null @@ -1,354 +0,0 @@ -#!/usr/bin/env python3.5 - -##__Updated__: 16_10_2017 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 3_CountOGsDiamond.py --help - - -########################################################################################## -## This script is intended to classify the STRONGLY Eukaryotic and UNDETERMINED/UNKNOWN ## -## contigs into different OGs (e.g. orthologous gene-families) ## -## ## -## For more info about the OGs, check out: OrthoMCL.org ## -## ## -## Prior to running this script, ensure the following: ## -## ## -## 1. You have assembled your transcriptome and COPIED the 'assembly' file ## -## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ## -## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ## -## 3. Removed SSU/LSU sequences from your Fasta File ## -## ## -## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ## -## ## -## Next Script(s) to Run: ## -## 4_StopFrequency.py ## -## ## -########################################################################################## - -import argparse, os, sys -from argparse import RawTextHelpFormatter,SUPPRESS -from distutils import spawn -from Bio import SeqIO - - -#------------------------------ Colors For Print Statements ------------------------------# -class color: - PURPLE = '\033[95m' - CYAN = '\033[96m' - DARKCYAN = '\033[36m' - ORANGE = '\033[38;5;214m' - BLUE = '\033[94m' - GREEN = '\033[92m' - YELLOW = '\033[93m' - RED = '\033[91m' - BOLD = '\033[1m' - UNDERLINE = '\033[4m' - END = '\033[0m' - -#------------------------------- Main Functions of Script --------------------------------# - -########################################################################################### -###---------------------------- UPDATE DIAMOND PATH BELOW! -----------------------------### -########################################################################################### - ## IF Diamond is IN YOUR PATH then no updating is needed... - -def check_diamond_path(): - - diamond_path = '' - - if diamond_path == '': - diamond_path = spawn.find_executable("diamond") - #diamond_path = '/path/to/diamond' - else: - pass - - if diamond_path == None: - print (color.BOLD + '\n\nPlease open this script and check that you have included'\ - +' the PATH to the'+color.BLUE+' "usearch" '+color.END+color.BOLD+'executable.\n\n'+color.END) - print (color.BOLD+color.BLUE+'LOOK FOR:\n\n'+color.RED\ - +'#------------------------------ UPDATE USEARCH PATH BELOW! -------------------------------#'\ - +color.BLUE+'\n\nThis is somewhere around lines 50 - 80...\n\n'+color.END) - - sys.exit() - else: - pass - - return diamond_path - - -########################################################################################### -###--------------------- Parses and Checks Command-Line Arguments ----------------------### -########################################################################################### - -def check_args(): - - parser = argparse.ArgumentParser(description= - color.BOLD + '\n\nThis script will categorize Contigs into'+color.ORANGE+' "Homologous" '\ - +color.END+color.BOLD+'Gene Families (OGs)\nbased on '+color.RED+'OrthoMCL'+color.END\ - +color.BOLD+"'s Gene Family Grouping\n\n\nNotes on this script and "+color.GREEN+\ - 'OrthoMCL Families'+color.END+color.BOLD+' can be found\nat the bottom of '+color.GREEN\ - +'THIS script (3_CountOGsDiamond.py)\n'+color.END+usage_msg(), usage=SUPPRESS, - formatter_class=RawTextHelpFormatter) - - required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END) - - required_arg_group.add_argument('--input_file','-in', action='store', - help=color.BOLD+color.GREEN+'Fasta file of Nucleotide sequences enriched \nwith'\ - ' Eukaryotic protein coding transcripts'+color.END) - required_arg_group.add_argument('--databases','-d', action='store', - help=color.BOLD+color.GREEN+"Path to databases"+color.END) - - optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END) - optional_arg_group.add_argument('--threads','-t', default='2', - help=color.BOLD+color.GREEN+' Number of threads to use for BLAST\n (default = 2)\n'+color.END) - optional_arg_group.add_argument('--evalue','-e', default=1e-5, type = float, - help=color.BOLD+color.GREEN+' Maximum e-value for OG assignment\n (default = 1e-5)\n'+color.END) - optional_arg_group.add_argument('-author', action='store_true', - help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END) - - if len(sys.argv[1:]) == 0: - print (parser.description) - print ('\n') - sys.exit() - - args = parser.parse_args() - - quit_eval = return_more_info(args) - if quit_eval > 0: - sys.exit() - - return args - - -########################################################################################### -###------------------------------- Script Usage Message --------------------------------### -########################################################################################### - -def usage_msg(): - return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 3_CountOGsDiamond.py'\ - ' --input_file ../Op_me_Xxma/Op_me_Xxma_WTA_NBU.fasta'+color.END) - - -########################################################################################## -###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------### -########################################################################################## - -def return_more_info(args): - - valid_arg = 0 - - author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\ - ' maurerax@gmail.com\n\n'+color.END) - - if args.author == True: - print (author) - valid_arg += 1 - - if args.input_file != None: - if os.path.isfile(args.input_file) != False: - if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])): - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - elif args.input_file.endswith('WTA_EPU.fasta') != True: - print (color.BOLD+'\n\nInvalid Fasta File! Only Fasta Files that were processed'\ - ' with '+color.GREEN+'2b_remove_Bact.py '+color.END+color.BOLD+'are valid\n\n'\ - 'However, to bypass that issue, Fasta Files MUST end with '+color.CYAN+\ - '"WTA_NBU.fasta"\n\n'+color.END) - valid_arg += 1 - else: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - - if os.path.isdir(args.databases + '/db_OG') != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\ - +color.ORANGE+'db_OG Folder!\n\n'+color.END+color.BOLD+'Ensure that this folder '\ - 'can be found in the main '+color.ORANGE+'Databases Folder'+color.END+color.BOLD\ - +'\n\nThen try once again\n\n.'+color.END) - valid_arg += 1 - - elif os.path.isfile(args.databases + '/db_OG/OGSout.dmnd') != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\ - 'Diamond formatted '+color.ORANGE+'Gene Family database!\n\n'+color.END+color.BOLD+\ - 'Ensure that it can be found in the '+color.ORANGE+'db_OG folder'+color.END+\ - color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\ - color.END+color.BOLD+'\n\nThen try once again.\n\n'+color.END) - valid_arg += 1 - - return valid_arg - - -########################################################################################### -###--------------------------- Does the Inital Folder Prep -----------------------------### -########################################################################################### - -def prep_folders(args): - - OG_folder = '/'.join(args.input_file.split('/')[:-1]) + '/DiamondOG/' - - if os.path.isdir(OG_folder) != True: - os.system('mkdir '+OG_folder) - - -########################################################################################### -###--------------------- Runs Diamond on Split OrthoMCL Databases ----------------------### -########################################################################################### - -def OG_diamond(args, diamond_path): - - print (color.BOLD+'\nStarting to "BLAST" against OG databases'+color.END) - - OG_folder = '/'.join(args.input_file.split('/')[:-1]) + '/DiamondOG/' - - print (color.BOLD + '\n\n"BLAST"-ing against OG database using DIAMOND: ' + color.DARKCYAN + 'OGSout.dmnd' + color.END + '\n\n') - - OG_diamond_cmd = diamond_path + ' blastx -q ' + args.input_file + ' -d ' + args.databases + '/db_OG/OGSout.dmnd --evalue ' + str(args.evalue) + ' --threads 60 --subject-cover 0.35 --outfmt 6 -o ' + OG_folder + 'allOGresults.tsv' - - os.system(OG_diamond_cmd) - - -########################################################################################### -###--------------- Keeps the Single BEST Hit (HSP-score) Per Transcript ----------------### -########################################################################################### - -def keep_best(args): - - print (color.BOLD+color.PURPLE+'\n\nProcessing OG-database results to keep only the BEST match for each transcript\n\n'+color.END) - - OG_folder = '/'.join(args.input_file.split('/')[:-1]) + '/DiamondOG/' - - inTSV = [i for i in open(OG_folder + 'allOGresults.tsv').readlines()] - - inTSV.sort(key = lambda x: -float(x.split('\t')[-1])) - - keep = [] - for i in inTSV: - if any(i.split('\t')[0] in j for j in keep) != True: - keep.append(i) - - updated_lines = list(set([line.split('\t')[0]+'_'+'_'.join(line.split('\t')[1].split('_')[-2:])+'\t'+'\t'.join(line.split('\t')[1:]) for line in keep])) - - with open(args.input_file.replace('.fasta','.Renamed_allOGCleanresults.tsv'), 'w+') as w: - for i in updated_lines: - w.write(i) - - -########################################################################################### -###-------- Copies and Updates Names of Transcripts With OG Hits to New Fasta ----------### -########################################################################################### - -def update_fasta(args): - - print (color.BOLD+color.PURPLE+'Updating Fasta File Sequence Names with their BEST OG hits\n\n'+color.END) - - Renamed_TSV = args.input_file.replace('.fasta','.Renamed_allOGCleanresults.tsv') - - keep = [i for i in open(Renamed_TSV).readlines() if i != '\n'] - - keep_dict = { line.split('\t')[0].split('_OG5')[0] : line.split('\t')[0].split('_OG5')[0] + '_OG5_' + line.split('\t')[1].split('_')[-1] for line in keep if 'OG5' in line.split('\t')[1] } - - inFasta = [i for i in SeqIO.parse(args.input_file,'fasta')] - - updated_seq_name = ['>'+keep_dict[i.description]+'\n'+str(i.seq)+'\n' for i in inFasta if i.description in keep_dict.keys()] - - seqs_without_OG = ['>'+i.description+'\n'+str(i.seq)+'\n' for i in inFasta if i.description not in keep_dict.keys()] - - with open(args.input_file.replace('.fasta','.Renamed.fasta'),'w+') as w: - for i in updated_seq_name: - w.write(i) - - with open(args.input_file.replace('.fasta','.LackOG.fasta'),'w+') as x: - for i in seqs_without_OG: - x.write(i) - - -########################################################################################### -###-------------------- Updates Log With OG Assignment Information ---------------------### -########################################################################################### - -def update_log(args): - - if os.path.isdir('../PostAssembly_Logs/') != True: - os.system('mkdir ../PostAssembly_Logs/') - else: - pass - - home_folder = '/'.join(args.input_file.split('/')[:-1]) + '/' - - Renamed_TSV = home_folder+args.input_file.split('/')[-1].replace('.fasta','.Renamed_allOGCleanresults.tsv') - - keep = [line for line in open(Renamed_TSV).readlines()] - all_ogs = [line.split('\t')[1].split('_')[-1] for line in keep if 'OG5' in line.split('\t')[1]] - - total_with_ogs = str(len(all_ogs)) - unique_ogs = str(len(set(all_ogs))) - - print (color.BOLD +'There are '+color.BLUE +total_with_ogs+' Contigs'+color.END\ - +color.BOLD+' that hit '+color.DARKCYAN+unique_ogs+' Unique OGs\n'+color.END) - - - for Logname in os.listdir(os.curdir+'./PostAssembly_Logs/'): - if Logname.startswith(args.input_file.split('/')[2].split('_WTA')[0]) and Logname.endswith('Log.txt'): - with open('../PostAssembly_Logs/'+Logname,'a') as LogFile: - LogFile.write('Contigs With OG\t'+total_with_ogs+'\tn/a\tn/a\n') - LogFile.write('Unique OGs\t'+unique_ogs+'\tn/a\tn/a\n') - - -########################################################################################## -###--------------------- Cleans up the Folder and Moves Final Files -------------------### -########################################################################################## - -def clean_up(args): - - OG_folder = '/'.join(args.input_file.split('/')[:-1]) + '/DiamondOG/' - - os.system('rm ' + args.input_file) - - os.system('cp ' + args.input_file.replace('.fasta','.Renamed.fasta') + ' ' + OG_folder) - - os.system('cp ' + args.input_file.replace('.fasta','.Renamed_allOGCleanresults.tsv') + ' ' + OG_folder) - - -########################################################################################### -###-------------------------------- Next Script Message --------------------------------### -########################################################################################### - -def next_script(args): - - home_folder = '../'+args.input_file.split('/')[1]+'/' - - print (color.BOLD+'\nLook for '+color.DARKCYAN+args.input_file.split('/')[-1]\ - .replace('.fasta','WTA_EPU.fasta')+color.END+color.BOLD+' in the '+home_folder\ - +' Folder\n\n' + color.END) - - print (color.BOLD+'Next Script is: '+color.GREEN+'4_InFrameStopFreq.py\n\n'+ color.END) - - -########################################################################################## -###--------------- Checks Command Line Arguments and Calls on Functions ---------------### -########################################################################################## - -def main(): - - usearch_path = check_diamond_path() - - args = check_args() - - prep_folders(args) - - OG_diamond(args, usearch_path) - - keep_best(args) - - update_fasta(args) - - #update_log(args) - - clean_up(args) - - next_script(args) - -main() diff --git a/PTL1/Transcriptomes/Scripts/4_InFrameStopFreq.py b/PTL1/Transcriptomes/Scripts/4_InFrameStopFreq.py deleted file mode 100644 index e5def97..0000000 --- a/PTL1/Transcriptomes/Scripts/4_InFrameStopFreq.py +++ /dev/null @@ -1,790 +0,0 @@ -#!/usr/bin/env python - -##__Updated__: 18_08_2017 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 4_InFrameStopFreq.py --help - - -########################################################################################## -## This script is intended to aid in identifying the genetic code of the data given ## -## ## -## Prior to running this script, ensure the following: ## -## ## -## 1. You have assembled your transcriptome and COPIED the 'assembly' file ## -## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ## -## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ## -## 3. Removed SSU/LSU sequences from your Fasta File ## -## 4. Classified your sequences as Strongly Prokaryotic/Eukaryotic or Undetermined ## -## 5. Classified the Non-Strongly Prokaryotic sequences into OGs ## -## ## -## COMMAND Example Below ## -## Extra Notes at Bottom of Script ## -## ## -## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ## -## ## -## Next Script(s) to Run: ## -## 5_GCodeTranslate.py ## -## ## -########################################################################################## - - -import argparse, os, sys -from argparse import RawTextHelpFormatter,SUPPRESS -from distutils import spawn - -from Bio import SeqIO -from Bio.Seq import Seq -from Bio.Data.CodonTable import CodonTable - - -#-------------------------- Set-up Codon Tables (Genetic Codes) --------------------------# - -tag_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Q', - 'TGT': 'C', 'TGC': 'C', 'TGA': 'Q', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['TAG']) - -c_uncinata_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', 'TAG': 'Q', - 'TGT': 'C', 'TGC': 'C', 'TGA': 'Q', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['TAA']) - -#------------------------------ Colors For Print Statements ------------------------------# -class color: - PURPLE = '\033[95m' - CYAN = '\033[96m' - DARKCYAN = '\033[36m' - ORANGE = '\033[38;5;214m' - BLUE = '\033[94m' - GREEN = '\033[92m' - YELLOW = '\033[93m' - RED = '\033[91m' - BOLD = '\033[1m' - UNDERLINE = '\033[4m' - END = '\033[0m' - -#------------------------------- Main Functions of Script --------------------------------# - -########################################################################################### -###---------------------------- UPDATE DIAMOND PATH BELOW! -----------------------------### -########################################################################################### - ## IF Diamond is IN YOUR PATH then no updating is needed... - -def check_diamond_path(): - - diamond_path = '' - - if diamond_path == '': - diamond_path = spawn.find_executable("diamond") - #diamond_path = '/path/to/diamond' - else: - pass - - if diamond_path == None: - print (color.BOLD + '\n\nPlease open this script and check that you have included'\ - +' the PATH to the'+color.BLUE+' "diamond" '+color.END+color.BOLD+'executable.\n\n'+color.END) - print (color.BOLD+color.BLUE+'LOOK FOR:\n\n'+color.RED\ - +'#------------------------------ UPDATE DIAMOND PATH BELOW! -------------------------------#'\ - +color.BLUE+'\n\nThis is somewhere around lines 50 - 80...\n\n'+color.END) - - sys.exit() - else: - pass - - return diamond_path - - -########################################################################################### -###--------------------- Parses and Checks Command-Line Arguments ----------------------### -########################################################################################### - -def check_args(): - - parser = argparse.ArgumentParser(description= - color.BOLD+'\n\nThis script is intended to '+color.RED+'AID You '+color.END+color.BOLD\ - +'in determining the '+color.RED+'\nLikely Genetic Code'+color.END+color.BOLD+' of a'\ - ' given Fasta File of transcripts\n\nInterpretation of the output (StopFreq.tsv) is difficult \nand so '+color.ORANGE\ - +'TWO EXAMPLES'+color.END+color.BOLD+' can be found in the '+color.CYAN+'NOTES Section'\ - +color.END+color.BOLD+' of\nTHIS Script '+color.GREEN+'(4_InFrameStopFreq.py)\n'+color.END\ - +usage_msg(), usage=SUPPRESS,formatter_class=RawTextHelpFormatter) - - required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END) - - required_arg_group.add_argument('--input_file','-in', action='store', required=True, - help=color.BOLD+color.GREEN+'Fasta file of Nucleotide sequences enriched \nwith'\ - ' Eukaryotic protein coding transcripts'+color.END) - required_arg_group.add_argument('--databases','-d', action='store', - help=color.BOLD+color.GREEN+"Path to databases"+color.END) - - optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END) - optional_arg_group.add_argument('-author', action='store_true', - help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END) - - if len(sys.argv[1:]) == 0: - print (parser.description) - print ('\n') - sys.exit() - - args = parser.parse_args() - - quit_eval = return_more_info(args) - if quit_eval > 0: - sys.exit() - - return args - - -########################################################################################### -###------------------------------- Script Usage Message --------------------------------### -########################################################################################### - -def usage_msg(): - return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 4_InFrameStopFreq.py'\ - ' --input_file ../Op_me_Xxma/Op_me_Xxma_WTA_EPU.Renamed.fasta'+color.END) - - -########################################################################################## -###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------### -########################################################################################## - -def return_more_info(args): - - valid_arg = 0 - - author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\ - ' maurerax@gmail.com\n\n'+color.END) - - if args.author == True: - print (author) - valid_arg += 1 - - if args.input_file != None: - if os.path.isfile(args.input_file) != False: - if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])): - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - elif args.input_file.endswith('WTA_EPU.Renamed.fasta') != True: - print (color.BOLD+'\n\nInvalid Fasta File! Only Fasta Files that were processed'\ - ' with '+color.GREEN+'3_CountOGsUsearcy.py '+color.END+color.BOLD+'are valid\n\n'\ - 'However, to bypass that issue, Fasta Files MUST end with '+color.CYAN+\ - '"WTA_NBU.Renamed.fasta"\n\n'+color.END) - valid_arg += 1 - else: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - - if os.path.isdir(args.databases + '/db_StopFreq') != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\ - +color.ORANGE+'db_StopFreq Folder!\n\n'+color.END+color.BOLD+'Ensure that this folder '\ - 'can be found in the main '+color.ORANGE+'Databases Folder'+color.END+color.BOLD\ - +'\n\nThen try once again\n\n.'+color.END) - valid_arg += 1 - - elif os.path.isfile(args.databases + '/db_StopFreq/RepEukProts.dmnd') != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\ - 'Diamond formatted '+color.ORANGE+'Representative Eukaryotic Protein Database!\n\n'+color.END+color.BOLD+\ - 'Ensure that it can be found in the '+color.ORANGE+'db_StopFreq folder'+color.END+\ - color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\ - color.END+color.BOLD+'\n\nThen try once again.\n\n'+color.END) - valid_arg += 1 - - return valid_arg - - -########################################################################################### -###--------------------------- Does the Inital Folder Prep -----------------------------### -########################################################################################### - -def prep_folders(args): - - Stop_folder = '../'+args.input_file.split('/')[1]+'/StopCodonFreq/' - - if os.path.isdir(Stop_folder) != True: - os.system('mkdir '+Stop_folder) - - if os.path.isdir(Stop_folder+'StopCodonFastas') != True: - os.system('mkdir '+Stop_folder+'StopCodonFastas') - - if os.path.isdir(Stop_folder+'SpreadSheets') != True: - os.system('mkdir '+Stop_folder+'SpreadSheets') - - return Stop_folder+'StopCodonFastas/' - - -########################################################################################### -###--------------------- Translates Sequences with Each Stop Codon ---------------------### -########################################################################################### - -def prep_translations(args): - print (color.BOLD+'\nIdentifying ORFs in the Fasta file based on the output of 3_CountOGsDiamond.py\n'+color.END) - - intsv = [i for i in open(args.input_file.replace('.fasta','_allOGCleanresults.tsv')).readlines() if i != '\n'] - - inFasta = [i for i in SeqIO.parse(args.input_file,'fasta')] - - prot_dict = {} - - for i in intsv: -# print i - prot_dict.setdefault(i.split('\t')[0],[]) - if int(i.split('\t')[6]) < int(i.split('\t')[7]): - prot_dict[i.split('\t')[0]].append('F') - if (int(i.split('\t')[6])) < 5: - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[6])-1) - else: - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[6])-1) - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[7])+3) - if int(i.split('\t')[7]) < int(i.split('\t')[6]): - prot_dict[i.split('\t')[0]].append('RC') - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[6])) - if (int(i.split('\t')[7])-4) < 5: - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[7])) - else: - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[7])-4) - - - #------------- Prep translation with 'TAA' as the only Stop -------------# - - print (color.BOLD+'\n\nTranslating DNA using'+color.RED+' TAA'+color.END\ - +color.BOLD+' as the sole STOP codon\n'+color.END) - - for key, value in prot_dict.items(): - for seq_rec in inFasta: - if key in seq_rec.description: - stop_pos = 0 - if prot_dict[key][0] == 'F': - temp = seq_rec.seq[prot_dict[key][1]:] - temp_prot = str(temp.translate(table=c_uncinata_table)) - if '*' in temp_prot: - stop_pos = (temp_prot.index('*')+1)*3 - prot_dict[key].append(temp[:stop_pos]) - else: - prot_dict[key].append(seq_rec.seq[prot_dict[key][1]:prot_dict[key][2]]) - if prot_dict[key][0] == 'RC': - temp = seq_rec.seq[:prot_dict[key][1]].reverse_complement() - temp_prot = str(temp.translate(table=c_uncinata_table)) - if '*' in temp_prot: - stop_pos = (temp_prot.index('*')+1)*3 - prot_dict[key].append(temp[:stop_pos]) - else: - prot_dict[key].append(seq_rec.seq[prot_dict[key][2]:prot_dict[key][1]].reverse_complement()) - - - #------------- Prep translation with 'TGA' as the only Stop -------------# - print (color.BOLD+'\n\nTranslating DNA using'+color.RED+' TGA'+color.END\ - +color.BOLD+' as the sole STOP codon\n'+color.END) - - for key, value in prot_dict.items(): - for seq_rec in inFasta: - if key in seq_rec.description: - stop_pos = 0 - if prot_dict[key][0] == 'F': - temp = seq_rec.seq[prot_dict[key][1]:] - temp_prot = str(temp.translate(table=6)) - if '*' in temp_prot: - stop_pos = (temp_prot.index('*')+1)*3 - prot_dict[key].append(temp[:stop_pos]) - else: - prot_dict[key].append(seq_rec.seq[prot_dict[key][1]:prot_dict[key][2]]) - if prot_dict[key][0] == 'RC': - temp = seq_rec.seq[:prot_dict[key][1]].reverse_complement() - temp_prot = str(temp.translate(table=6)) - if '*' in temp_prot: - stop_pos = (temp_prot.index('*')+1)*3 - prot_dict[key].append(temp[:stop_pos]) - else: - prot_dict[key].append(seq_rec.seq[prot_dict[key][2]:prot_dict[key][1]].reverse_complement()) - - - #------------- Prep translation with 'TAG' as the only Stop -------------# - print (color.BOLD+'\n\nTranslating DNA using'+color.RED+' TAG'+color.END\ - +color.BOLD+' as the sole STOP codon\n'+color.END) - - - for key, value in prot_dict.items(): - for seq_rec in inFasta: - if key in seq_rec.description: - stop_pos = 0 - if prot_dict[key][0] == 'F': - temp = seq_rec.seq[prot_dict[key][1]:] - temp_prot = str(temp.translate(table=tag_table)) - if '*' in temp_prot: - stop_pos = (temp_prot.index('*')+1)*3 - prot_dict[key].append(temp[:stop_pos]) - else: - prot_dict[key].append(seq_rec.seq[prot_dict[key][1]:prot_dict[key][2]]) - if prot_dict[key][0] == 'RC': - temp = seq_rec.seq[:prot_dict[key][1]].reverse_complement() - temp_prot = str(temp.translate(table=tag_table)) - if '*' in temp_prot: - stop_pos = (temp_prot.index('*')+1)*3 - prot_dict[key].append(temp[:stop_pos]) - else: - prot_dict[key].append(seq_rec.seq[prot_dict[key][2]:prot_dict[key][1]].reverse_complement()) - - #------------ Parsing through data to maintain OG assignments ------------# - inOGs = intsv - inOGs = [i.split('\t')[0]+';'+i.split('\t')[1][-10:] for i in inOGs] - inOGs2 = [] - for i in inOGs: - if 'no_group' not in i.split(';')[1]: - inOGs2.append(i) - else: - inOGs2.append(i.split(';')[0]+';no_group') - inOGs2 = list(set(inOGs2)) - - #---------------- Write file with 'TAA' is the only Stop ----------------# - - with open(args.input_file.split('.fas')[0]+'_taa_ORF.fasta','w+') as w: - print (color.BOLD+'\n\nWriting FASTA files with ORF and Protein sequences with'+color.RED\ - +' TAA '+color.END+color.BOLD+'as only STOP codon\n'+color.END) - - for key, value in prot_dict.items(): - for j in inOGs2: - if key == j.split(';')[0]: - if len(prot_dict[key]) < 4: - pass - else: - w.write('>'+key+'_'+j.split(';')[1]+'\n'+str(value[-3]).upper()+'\n') - - with open(args.input_file.split('.fas')[0]+'_taa_ORF.aa.fasta','w+') as w: - for key, value in prot_dict.items(): - for j in inOGs2: - if key == j.split(';')[0]: - if len(prot_dict[key]) < 4: - pass - else: - w.write('>'+key+'_'+j.split(';')[1]+'\n'+str(Seq(str(value[-3])).translate(table=c_uncinata_table)).upper()+'\n') - - #---------------- Write file with 'TGA' is the only Stop ----------------# - - with open(args.input_file.split('.fas')[0]+'_tga_ORF.fasta','w+') as w: - print (color.BOLD+'\n\nWriting FASTA files with ORF and Protein sequences with'+color.RED\ - +' TGA '+color.END+color.BOLD+'as only STOP codon\n'+color.END) - - for key, value in prot_dict.items(): - for j in inOGs2: - if key == j.split(';')[0]: - if len(prot_dict[key]) < 4: - pass - else: - w.write('>'+key+'_'+j.split(';')[1]+'\n'+str(value[-2]).upper()+'\n') - - with open(args.input_file.split('.fas')[0]+'_tga_ORF.aa.fasta','w+') as w: - for key, value in prot_dict.items(): - for j in inOGs2: - if key == j.split(';')[0]: - if len(prot_dict[key]) < 4: - pass - else: - w.write('>'+key+'_'+j.split(';')[1]+'\n'+str(Seq(str(value[-2])).translate(table=6)).upper()+'\n') - - #---------------- Write file with 'TAG' is the only Stop ----------------# - - with open(args.input_file.split('.fas')[0]+'_tag_ORF.fasta','w+') as w: - print (color.BOLD+'\n\nWriting FASTA files with ORF and Protein sequences with'+color.RED\ - +' TAG '+color.END+color.BOLD+'as only STOP codon\n'+color.END) - - for key, value in prot_dict.items(): - for j in inOGs2: - if key == j.split(';')[0]: - if len(prot_dict[key]) < 4: - pass - else: - w.write('>'+key+'_'+j.split(';')[1]+'\n'+str(value[-1]).upper()+'\n') - - with open(args.input_file.split('.fas')[0]+'_tag_ORF.aa.fasta','w+') as w: - for key, value in prot_dict.items(): - for j in inOGs2: - if key == j.split(';')[0]: - if len(prot_dict[key]) < 4: - pass - else: - w.write('>'+key+'_'+j.split(';')[1]+'\n'+str(Seq(str(value[-1])).translate(table=tag_table)).upper()+'\n') - - -########################################################################################### -###---------- Diamonds the Translations Against a SMALL Euk Protein Database ----------### -########################################################################################### - -def diamond_ProtDB(args, diamond_path): - os.system(diamond_path + ' blastp -q ' + args.input_file.split('.fas')[0] + '_tag_ORF.aa.fasta -d ' + args.databases + '/db_StopFreq/RepEukProts.dmnd --evalue 1e-5 --max-target-seqs 1 --threads 60 --outfmt 6 -o ' + args.input_file.split('.fas')[0] + '_tag_ORF.RepEukProts.tsv') - - os.system(diamond_path + ' blastp -q ' + args.input_file.split('.fas')[0] + '_tga_ORF.aa.fasta -d ' + args.databases + '/db_StopFreq/RepEukProts.dmnd --evalue 1e-5 --max-target-seqs 1 --threads 60 --outfmt 6 -o ' + args.input_file.split('.fas')[0] + '_tga_ORF.RepEukProts.tsv') - - os.system(diamond_path + ' blastp -q ' + args.input_file.split('.fas')[0] + '_taa_ORF.aa.fasta -d ' + args.databases + '/db_StopFreq/RepEukProts.dmnd --evalue 1e-5 --max-target-seqs 1 --threads 60 --outfmt 6 -o ' + args.input_file.split('.fas')[0] + '_taa_ORF.RepEukProts.tsv') - - -########################################################################################### -###-------------------- Manages the search for In-Frame Stop Codons --------------------### -########################################################################################### - - -def hunt_for_stops(args): - - #------------------------ Open Fasta Files ------------------------# - try: - TAGinFasta = [i for i in SeqIO.parse(args.input_file.split('.fas')[0]+'_tag_ORF.fasta','fasta') if str(i.seq).endswith('TAG')] - print (color.BOLD+'\n\nGathering Sequence information from FASTA and TSV files\n'+color.END) - - except: - print (color.BOLD+color.RED+'\n\nMissing Necessary Inputs: Open Script for Usage'\ - ' Information\n\n'+color.END) - sys.exit() - - TGAinFasta = [i for i in SeqIO.parse(args.input_file.split('.fas')[0]+'_tga_ORF.fasta','fasta') if str(i.seq).endswith('TGA')] - - TAAinFasta = [i for i in SeqIO.parse(args.input_file.split('.fas')[0]+'_taa_ORF.fasta','fasta') if str(i.seq).endswith('TAA')] - - ## This section originally ONLY considered sequences WITH OG assignments: - ## TAAinFasta = [i for i in TAAinFasta if 'no_group' not in i.description and str(i.seq).endswith('TAA')] - ## This has been taken out for now - - #----------------------- Open BLAST Reports -----------------------# - - TAGinTSV = [i for i in open(args.input_file.split('.fas')[0]+'_tag_ORF.RepEukProts.tsv').read().split('\n') if i != ''] - - TGAinTSV = [i for i in open(args.input_file.split('.fas')[0]+'_tga_ORF.RepEukProts.tsv').read().split('\n') if i != ''] - - TAAinTSV = [i for i in open(args.input_file.split('.fas')[0]+'_taa_ORF.RepEukProts.tsv').read().split('\n') if i != ''] - -## This section originally ONLY considered sequences WITH OG assignments: - ## TAAinTSV = i for i in TAAinTSV if i != ''and 'no_group' not in i.split('\t')[0]] - ## This has been taken out for now - - - #------------ Set-up Genetic Code Specific Dictionaries ------------# - - tag_dict = {} - for i in TAGinTSV: - tag_dict.setdefault(i.split('\t')[0].replace('_TAG',''),[]).append(int(i.split('\t')[-6])) - tag_dict.setdefault(i.split('\t')[0].replace('_TAG',''),[]).append(int(i.split('\t')[-5])) - - tga_dict = {} - for i in TGAinTSV: - tga_dict.setdefault(i.split('\t')[0].replace('_Ciliate',''),[]).append(int(i.split('\t')[-6])) - tga_dict.setdefault(i.split('\t')[0].replace('_Ciliate',''),[]).append(int(i.split('\t')[-5])) - - taa_dict = {} - for i in TAAinTSV: - taa_dict.setdefault(i.split('\t')[0].replace('_Chilo',''),[]).append(int(i.split('\t')[-6])) - taa_dict.setdefault(i.split('\t')[0].replace('_Chilo',''),[]).append(int(i.split('\t')[-5])) - - #-------------- Preparing In-Frame Stop Codon Counts --------------# - -# All the data when TGA is the sole stop codon - tga_codons = 0 - tga_data_tag = 0 - tga_data_tga = 0 - tga_data_taa = 0 - tga_seq_count = 0 - -# All the data when TAG is the sole stop codon - tag_codons = 0 - tag_data_tag = 0 - tag_data_tga = 0 - tag_data_taa = 0 - tag_seq_count = 0 - -# All the data when TAA is the sole stop codon - taa_codons = 0 - taa_data_tag = 0 - taa_data_tga = 0 - taa_data_taa = 0 - taa_seq_count = 0 - -# All the data for each stop codon combined - tga_inframe = 0 - tag_inframe = 0 - taa_inframe = 0 - total_codons = 0 - total_seq_counts = len(open(args.input_file).read().split('>'))-1 - - - #-------- Gathering In-frame Stop Codon Density Information --------# - -### Collect in-frame stop information for "TAA" and "TAG" when TGA is the ONLY stop - print (color.BOLD+'\nCollecting in-frame stop codon information when'+color.RED\ - +' TGA'+color.END+color.BOLD+' is the only STOP\n'+color.END) - - for i in TGAinFasta: - try: - if tga_dict[i.description][0] == 1: - for n in range((tga_dict[i.description][0]-1),((tga_dict[i.description][1])*3)-3,3): - if str(i.seq).upper()[n:n+3] == 'TAG': - tga_data_tag += 1 - tag_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TAA': - tga_data_taa += 1 - taa_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TGA': - tga_data_tga += 1 - tga_inframe += 1 - tga_codons += 1 - total_codons += 1 - tga_seq_count += 1 - - else: - for n in range(((tga_dict[i.description][0]-1)*3),((tga_dict[i.description][1])*3)-3,3): - if str(i.seq).upper()[n:n+3] == 'TAG': - tga_data_tag += 1 - tag_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TAA': - tga_data_taa += 1 - taa_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TGA': - tga_data_tga += 1 - tga_inframe += 1 - tga_codons += 1 - total_codons += 1 - tga_seq_count += 1 - except: - pass - -### Collect in-frame stop information for "TAA" and "TGA" when TAG is the ONLY stop - print (color.BOLD+'\nCollecting in-frame stop codon information when'+color.RED\ - +' TAG'+color.END+color.BOLD+' is the only STOP\n'+color.END) - - for i in TAGinFasta: - try: - if tag_dict[i.description][0] == 1: - for n in range((tag_dict[i.description][0]-1),((tag_dict[i.description][1])*3)-3,3): - if str(i.seq).upper()[n:n+3] == 'TAG': - tag_data_tag += 1 - tag_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TAA': - tag_data_taa += 1 - taa_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TGA': - tag_data_tga += 1 - tga_inframe += 1 - tag_codons += 1 - total_codons += 1 - tag_seq_count += 1 - - else: - for n in range(((tag_dict[i.description][0]-1)*3),(tag_dict[i.description][1]*3)-3,3): - if str(i.seq).upper()[n:n+3] == 'TAG': - tag_data_tag += 1 - tag_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TAA': - tag_data_taa += 1 - taa_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TGA': - tag_data_tga += 1 - tga_inframe += 1 - tag_codons += 1 - total_codons += 1 - tag_seq_count += 1 - except: - pass - - -### Collect in-frame stop information for "TGA" and "TAG" when TAA is the ONLY stop - print (color.BOLD+'\nCollecting in-frame stop codon information when'+color.RED\ - +' TAA'+color.END+color.BOLD+' is the only STOP\n'+color.END) - - for i in TAAinFasta: - try: - if taa_dict[i.description][0] == 1: - for n in range((taa_dict[i.description][0]-1),((taa_dict[i.description][1])*3)-3,3): - if str(i.seq).upper()[n:n+3] == 'TAG': - taa_data_tag += 1 - tag_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TAA': - taa_data_taa += 1 - taa_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TGA': - taa_data_tga += 1 - tga_inframe += 1 - taa_codons += 1 - total_codons += 1 - taa_seq_count += 1 - - else: - for n in range(((taa_dict[i.description][0]-1)*3),(taa_dict[i.description][1]*3)-3,3): - if str(i.seq).upper()[n:n+3] == 'TAG': - taa_data_tag += 1 - tag_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TAA': - taa_data_taa += 1 - taa_inframe += 1 - if str(i.seq).upper()[n:n+3].upper() == 'TGA': - taa_data_tga += 1 - tga_inframe += 1 - tag_codons += 1 - total_codons += 1 - taa_seq_count += 1 - except: - pass - - #-------------- Writing Data Out and Print Statement --------------# - - with open(args.input_file.split('.fas')[0]+'_StopCodonStats.tsv','w+') as w: - w.write('Stop Codon\tNumber of Seqs Analyzed\tIn-frame TAG\tIn-frame TGA\tIn-frame TAA\tTotal Codons\tIn-frame TAG density\tIn-frame TGA density\tIn-frame TAA density\n') - if tga_codons != 0: - w.write('TGA\t'+str(tga_seq_count)+'\t'+str(tga_data_tag)+'\t'+str(tga_data_tga)+'\t'+str(tga_data_taa)+'\t'+str(tga_codons)\ - +'\t'+"%.2f" % ((float(tga_data_tag)*1000)/float(tga_codons))+'\t'+"%.2f" % ((float(tga_data_tga)*1000)/float(tga_codons))+'\t'\ - +"%.2f" % ((float(tga_data_taa)*1000)/float(tga_codons))+'\n') - else: - w.write('TGA\t0\t0\t0\t0\t0\t0\t0\t0\n') - - if tag_codons != 0: - w.write('TAG\t'+str(tag_seq_count)+'\t'+str(tag_data_tag)+'\t'+str(tag_data_tga)+'\t'+str(tag_data_taa)+'\t'+str(tag_codons)\ - +'\t'+"%.2f" % ((float(tag_data_tag)*1000)/float(tag_codons))+'\t'+"%.2f" % ((float(tag_data_tga)*1000)/float(tag_codons))+'\t'\ - +"%.2f" % ((float(tag_data_taa)*1000)/float(tag_codons))+'\n') - else: - w.write('TAG\t0\t0\t0\t0\t0\t0\t0\t0\n') - if taa_codons != 0: - w.write('TAA\t'+str(taa_seq_count)+'\t'+str(taa_data_tag)+'\t'+str(taa_data_tga)+'\t'+str(taa_data_taa)+'\t'+str(taa_codons)\ - +'\t'+"%.2f" % ((float(taa_data_tag)*1000)/float(taa_codons))+'\t'+"%.2f" % ((float(taa_data_tga)*1000)/float(taa_codons))+'\t'\ - +"%.2f" % ((float(taa_data_taa)*1000)/float(taa_codons))+'\n') - else: - w.write('TAA\t0\t0\t0\t0\t0\t0\t0\t0\n') - - w.write('\n \n') - w.write('Summary\t'+str(tga_seq_count+tag_seq_count+taa_seq_count)+'\t'+str(tag_inframe)+'\t'+str(tga_inframe)+'\t'+str(taa_inframe)\ - +'\t'+str(total_codons)+'\t'+"%.2f" % ((float(tag_inframe)*1000)/float(total_codons))+'\t'+"%.2f" % ((float(tga_inframe)*1000)/float(total_codons))\ - +'\t'+"%.2f" % ((float(taa_inframe)*1000)/float(total_codons))+'\n') - w.write('\nTotal Seqs in Fasta\t'+str(total_seq_counts)) - -# print color.BOLD + color.BLUE + '\nSummary\t'+str(tag_inframe)+'\t'+str(tga_inframe)+'\t'+str(taa_inframe)+'\t'+str(total_codons)+'\t'+"%.2f" % ((float(tag_inframe)*1000)/float(total_codons))+'\t'\ -# +"%.2f" % ((float(tga_inframe)*1000)/float(total_codons))+'\t'+"%.2f" % ((float(taa_inframe)*1000)/float(total_codons))+'\n\n'\ -# + str(tag_seq_count) + '\t' + str(tga_seq_count) + '\t' + str(taa_seq_count) + color.END - - -########################################################################################## -###--------------------- Cleans up the Folder and Moves Final Files -------------------### -########################################################################################## - -def clean_up(args): - if os.path.isdir('/'.join(args.input_file.split('/')[:-1]) + '/StopCodonFreq') != True: - os.system('mkdir ' + '/'.join(args.input_file.split('/')[:-1]) + '/StopCodonFreq/') - else: - pass - - os.system('mkdir ' + '/'.join(args.input_file.split('/')[:-1]) + '/StopCodonFreq/StopCodonFastas/') - os.system('mkdir ' + '/'.join(args.input_file.split('/')[:-1]) + '/StopCodonFreq/SpreadSheets/') - os.system('mv ' + args.input_file.split('.fas')[0]+'_t*_ORF.*fasta ' + '/'.join(args.input_file.split('/')[:-1]) + '/StopCodonFreq/StopCodonFastas/') - os.system('mv ' + args.input_file.split('.fas')[0]+'_t*Prots.tsv ' + '/'.join(args.input_file.split('/')[:-1]) + '/StopCodonFreq/SpreadSheets/') - - -########################################################################################### -###-------------------------------- Next Script Message --------------------------------### -########################################################################################### - -def next_script(args): - - home_folder = '/'.join(args.input_file.split('/')[:-1]) - - print (color.BOLD+'\nLook for '+color.DARKCYAN+args.input_file.split('/')[-1]\ - .replace('.fasta','_StopCodonStats.tsv')+color.END+color.BOLD+' in the '+home_folder\ - +' Folder\n\n' + color.END) - - print (color.BOLD+'Next Script is: '+color.GREEN+'5_GCodeTranslate.py\n\n'+ color.END) - - -########################################################################################## -###--------------- Checks Command Line Arguments and Calls on Functions ---------------### -########################################################################################## - -def main(): - - diamond_path = check_diamond_path() - - args = check_args() - - prep_translations(args) - - diamond_ProtDB(args, diamond_path) - - hunt_for_stops(args) - - clean_up(args) - - next_script(args) - -main() - - -#----------------------------------------- NOTES -----------------------------------------# -# -# This script is designed to HELP you make an informed decision about the genetic code being -# used by your particular organism. Be aware that it will be limited by the quality of the -# data given to it! -# -# You will need: -# -# Diamond, BioPython, AND the output from '3_CountOGSDiamond.py' -# -# If you are not using the Author's database, update your database name(s) in lines: 345-360 -# -# katzlab$ python StopFrequency.py YourFastaFile.fasta -# -# -#------------------------------- Interpretation of Results -------------------------------# -# -# FORMATTED BELOW WITH TEXTWRANGLER... -# -# Example output using CILIATE (TGA) genetic Code (NOTE THE In-Frame Densities): -# -# Stop Codon Number_of_Seqs_Analyzed In-frame TAG In-frame TGA In-frame TAA Total Codons In-frame TAG density In-frame TGA density In-frame TAA density -# TGA 341 14 0 22 113156 1.2 0 0.92 -# TAG 424 0 0 34 140085 0 0 0.78 -# TAA 205 14 0 0 16714 0.84 0 0 -# Summary 970 28 0 56 269955 2.04 0 1.7 -# -# VALUES in summary line (OR SUM of Density) that are > 1.5 likely indicate that the STOP -# codon has been reassigned... in the case above, TAG and TAA look like they have been -# reassigned. -# -# -# Example output using UNIVERSAL genetic Code (NOTE THE In-Frame Densities): -# -# Stop Codon Number_of_Seqs_Analyzed In-frame TAG In-frame TGA In-frame TAA Total Codons In-frame TAG density In-frame TGA density In-frame TAA density -# TGA 341 1 0 2 113156 0.2 0 0.05 -# TAG 424 0 2 4 140085 0 0 0.08 -# TAA 205 1 0 0 16714 0.04 0 0 -# Summary 970 2 2 6 269955 0.15 0 0.06 -# -# VALUES in summary line (OR SUM of Density) that are > 0.5 likely indicate that the STOP -# codon still acts as STOP... in the case above, TAG, TGA and TAA look like they still behave -# as a stop codon. -# -# THIS IS A ROUGH GUIDE FOR INTERPRETING THE RESULTS!!!! BE VERY VERY WARY! NUMBER OF TOTAL -# SEQUENCES AND TOTAL CODONS OBSERVED ARE IMPORTANT (TOO FEW AND ANY INTERPRETATION IS DEVOID -# OF ANY MEANING). diff --git a/PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py b/PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py deleted file mode 100644 index 4ea3c08..0000000 --- a/PTL1/Transcriptomes/Scripts/5_GCodeTranslate.py +++ /dev/null @@ -1,770 +0,0 @@ -#!/usr/bin/env python3.5 - -##__Updated__: 20_09_2017 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 5_GCodeTranslate.py --help - - -########################################################################################## -## This script is intended to aid in identifying the genetic code of the data given ## -## ## -## Prior to running this script, ensure the following: ## -## ## -## 1. You have assembled your transcriptome and COPIED the 'assembly' file ## -## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ## -## 2. Removed small sequences (usually sequences < 300bp) with 1_ContigFiltStats.py ## -## 3. Removed SSU/LSU sequences from your Fasta File ## -## 4. Classified your sequences as Strongly Prokaryotic/Eukaryotic or Undetermined ## -## 5. Classified the Non-Strongly Prokaryotic sequences into OGs ## -## 6. You either know (or have inferred) the genetic code of the organism ## -## ## -## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ## -## ## -## Next Script(s) to Run: ## -## 6_FilterPatials.py (in FinalizeTranscripts Folder) ## -## ## -########################################################################################## - -import argparse, os, re, sys -from argparse import RawTextHelpFormatter,SUPPRESS - -from Bio import SeqIO -from Bio.Seq import Seq -from Bio.Data.CodonTable import CodonTable - - -#-------------------------- Set-up Codon Tables (Genetic Codes) --------------------------# - -blepharisma_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', - 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['TAA','TAG']) - -condylostoma_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Q', 'TAG': 'Q', - 'TGT': 'C', 'TGC': 'C', 'TGA': 'W', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['']) - -c_uncinata_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', 'TAG': 'Q', - 'TGT': 'C', 'TGC': 'C', 'TGA': 'Q', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['TAA']) - -euplotes_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', - 'TGT': 'C', 'TGC': 'C', 'TGA': 'C', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['TAA','TAG']) - -myrionecta_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Y', 'TAG': 'Y', - 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['TGA']) - -no_stop_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'X', 'TAG': 'X', - 'TGT': 'C', 'TGC': 'C', 'TGA': 'X', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['']) - -peritrich_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'E', 'TAG': 'E', - 'TGT': 'C', 'TGC': 'C', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['TGA']) - -tag_table = CodonTable(forward_table={ - 'TTT': 'F', 'TTC': 'F', 'TTA': 'L', 'TTG': 'L', - 'TCT': 'S', 'TCC': 'S', 'TCA': 'S', 'TCG': 'S', - 'TAT': 'Y', 'TAC': 'Y', 'TAA': 'Q', - 'TGT': 'C', 'TGC': 'C', 'TGA': 'Q', 'TGG': 'W', - 'CTT': 'L', 'CTC': 'L', 'CTA': 'L', 'CTG': 'L', - 'CCT': 'P', 'CCC': 'P', 'CCA': 'P', 'CCG': 'P', - 'CAT': 'H', 'CAC': 'H', 'CAA': 'Q', 'CAG': 'Q', - 'CGT': 'R', 'CGC': 'R', 'CGA': 'R', 'CGG': 'R', - 'ATT': 'I', 'ATC': 'I', 'ATA': 'I', 'ATG': 'M', - 'ACT': 'T', 'ACC': 'T', 'ACA': 'T', 'ACG': 'T', - 'AAT': 'N', 'AAC': 'N', 'AAA': 'K', 'AAG': 'K', - 'AGT': 'S', 'AGC': 'S', 'AGA': 'R', 'AGG': 'R', - 'GTT': 'V', 'GTC': 'V', 'GTA': 'V', 'GTG': 'V', - 'GCT': 'A', 'GCC': 'A', 'GCA': 'A', 'GCG': 'A', - 'GAT': 'D', 'GAC': 'D', 'GAA': 'E', 'GAG': 'E', - 'GGT': 'G', 'GGC': 'G', 'GGA': 'G', 'GGG': 'G'}, - start_codons = [ 'ATG'], - stop_codons = ['TAG']) - - -#------------------------------ Colors For Print Statements ------------------------------# -class color: - PURPLE = '\033[95m' - CYAN = '\033[96m' - DARKCYAN = '\033[36m' - ORANGE = '\033[38;5;214m' - PURPLE = '\033[94m' - GREEN = '\033[92m' - YELLOW = '\033[93m' - RED = '\033[91m' - BOLD = '\033[1m' - UNDERLINE = '\033[4m' - END = '\033[0m' - - -#------------------------------- Main Functions of Script --------------------------------# - -########################################################################################### -###------------------------- Checks the Command Line Arguments -------------------------### -########################################################################################### - -def check_args(): - - parser = argparse.ArgumentParser(description= - color.BOLD + '\n\nThis script will '+color.RED+'Translate '+color.END+color.BOLD+'a '\ - 'given Fasta file of CDS\nsequences using a given'+color.PURPLE+' Genetic Code.'+color.END+\ - color.BOLD+usage_msg(), usage=SUPPRESS, formatter_class=RawTextHelpFormatter) - - - required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END) - - required_arg_group.add_argument('--input_file','-in', action='store', - help=color.BOLD+color.GREEN+' Fasta file with CDSs\n'+color.END) - - optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END) - - optional_arg_group.add_argument('--genetic_code','-g', action='store', default='universal', - help=color.BOLD+color.GREEN+' Genetic code to use for translation\n (default = '\ - '"universal")\n'+color.END) - - optional_arg_group.add_argument('--no_RP','-no_RP', action='store_true', - help=color.BOLD+color.GREEN+' Allows files to "skip" the removal\n of Partial Transcripts\n'\ - +color.END) - - optional_arg_group.add_argument('--list_codes','-codes', action='store_true', - help=color.BOLD+color.GREEN+' Lists supported genetic codes\n'+color.END) - - optional_arg_group.add_argument('-author', action='store_true', - help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END) - - - if len(sys.argv[1:]) == 0: - print (parser.description) - print ('\n') - sys.exit() - - args = parser.parse_args() - - quit_eval = return_more_info(args) - if quit_eval > 0: - sys.exit() - - ### Adding in names to 'arg' class for more easy use throughout the script - args.ntd_out = args.input_file.split('.fas')[0]+'_'+args.genetic_code.title()+'_NTD.ORF.fasta' - args.aa_out = args.input_file.split('.fas')[0]+'_'+args.genetic_code.title()+'_AA.ORF.fasta' - args.tsv_out = args.input_file.split('.fas')[0]+'_'+args.genetic_code.title()+'_allOGCleanresults.tsv' - - args.home_folder = '/'.join(args.input_file.split('/')[:-1]) - args.Diamond_Folder = args.home_folder+'/DiamondOG' - args.StopFreq = args.home_folder+'/StopCodonFreq' - args.all_output_folder = '/'.join(args.input_file.split('/')[:-2]) + '/' - - args.tsv_file = args.input_file.split('.fas')[0]+ '_allOGCleanresults.tsv' - - - - - - - return args - - -########################################################################################### -###------------------------------- Script Usage Message --------------------------------### -########################################################################################### - -def usage_msg(): - return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 5g_GCodeTranslate.py'\ - ' --input_file ../Stentor_coeruleus.WGS.CDS.Prep/Stentor_coeruleus.WGS.CDS.Renamed.fasta'\ - ' --genetic_code Universal'+color.END) - - -########################################################################################## -###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------### -########################################################################################## - -def return_more_info(args): - - valid_arg = 0 - - supported_gcodes_names = ['bleph','blepharisma','chilo','chilodonella','condy',\ - 'condylostoma','none','eup','euplotes','peritrich','vorticella','ciliate','universal',\ - 'taa','tag','tga','mesodinium'] - - supported_gcodes_list = ['Blepharisma\t(TGA = W)','Chilodonella\t(TAG/TGA = Q)','Ciliate\t\t(TAR = Q)',\ - 'Condylostoma\t(TAR = Q, TGA = W)','Euplotes\t(TGA = C)','Peritrich\t(TAR = E)','None\t\t(TGA/TAG/TAA = X)',\ - 'Universal\t(TGA/TAG/TAA = STOP)','TAA\t\t(TAG/TGA = Q)', 'TAG\t\t(TRA = Q)', 'TGA\t\t(TAR = Q)'] - - author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\ - ' maurerax@gmail.com\n\n'+color.END) - - - if args.genetic_code != None and args.genetic_code.lower() not in supported_gcodes_names: - print (color.BOLD+color.RED+'\nProvided genetic code is currently unsupported.\n\n'\ - 'If you have a new genetic code, please contact the author (with some evidence).\n\n'\ - 'Otherwise, use one of the currently supported genetic codes.\n'+color.END) - print (color.BOLD+color.ORANGE+'\n'.join(supported_gcodes_list)+'\n\n'+color.END) - print (author) - valid_arg += 1 - else: - if args.list_codes == True: - print (color.BOLD+color.RED+'\nThese are the currently supported genetic codes.\n'+color.END) - print (color.BOLD+color.ORANGE+'\n'.join(supported_gcodes_list)+'\n\n'+color.END) - valid_arg += 1 - - if args.author == True: - print (author) - valid_arg += 1 - - if args.input_file != None: - if os.path.isfile(args.input_file) != False: - if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])): - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - elif args.input_file.endswith('WTA_EPU.Renamed.fasta') != True: - print (color.BOLD+'\n\nInvalid Fasta File! Only Fasta Files that were processed'\ - ' with '+color.GREEN+'3_CountOGsDiamond.py '+color.END+color.BOLD+'are valid\n\n'\ - 'However, to bypass that issue, Fasta Files MUST end with '+color.CYAN+\ - '"WTA_EPU.Renamed.fasta"\n\n'+color.END) - valid_arg += 1 - else: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\ - '('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_arg += 1 - - return valid_arg - - -########################################################################################### -###--------------------------- Does the Inital Folder Prep -----------------------------### -########################################################################################### - -def prep_folders(args): - - OG_folder = '/'.join(args.input_file.split('/')[:-1]) + '/DiamondOG/' - - if os.path.isdir(OG_folder) != True: - os.system('mkdir '+OG_folder) - - if os.path.isdir(args.all_output_folder + 'TranslatedTranscriptomes') != True: - os.system('mkdir ' + args.all_output_folder + 'TranslatedTranscriptomes') - - - -########################################################################################## -###---------------- Scans 5-Prime End of Transcript for In-Frame "ATG" ----------------### -########################################################################################## - -def check_new_start_new(some_seq, low_lim, upper_lim, old_start, codon_table): - - ## Looks for in-frame STOP codons in the UTR of the transcript - prime5 = str(Seq(some_seq[low_lim:upper_lim]).translate(table=codon_table)).replace('*','x') - in_frame_stops = [stops.start() for stops in re.finditer('x',prime5)] - - ## Looks for in-frame START codons in the UTR of the transcript - in_frame_starts = [starts.start() for starts in re.finditer('M',prime5)] - - ## Checks that there are NO in-frame STOP codons between the possible "new" START codon - ## and the aligned portion of the transcript -- THIS is double checked! - if len(in_frame_starts) != 0: - if len(in_frame_stops) != 0: - if in_frame_stops[-1] < in_frame_starts[-1]: - new_start = low_lim+in_frame_starts[-1]*3 - else: - new_start = old_start - else: - new_start = low_lim+in_frame_starts[-1]*3 - else: - new_start = old_start - - ## Skips the double-checking if there are no GOOD potential START codons - if new_start == old_start: - updated_start = old_start - - else: - ## Double checks that there are NO IN-FRAME stop codons between the NEW-SUGGESTED Start - ## position and the OLD-SUPPORTED stop position! - between_new_old_start = str(Seq(some_seq[new_start:old_start]).translate(table=1)).replace('*','x') - in_frame_stops_check = [stops.start() for stops in re.finditer('x',between_new_old_start)] - in_frame_starts_check = [starts.start() for starts in re.finditer('M',between_new_old_start)] - if len(in_frame_starts_check) != 0: - if len(in_frame_stops_check) != 0: - if in_frame_stops_check[-1] < in_frame_starts_check[-1]: - updated_start = new_start+in_frame_starts_check[-1]*3 - else: - updated_start = old_start - else: - updated_start = new_start - else: - updated_start = new_start - - return updated_start - - -########################################################################################## -###--------------- Extracts the ORF from the Fasta File and SpreadSheet ---------------### -########################################################################################## - -def extract_ORF(prot_dict, codon_table, args): - - print (color.BOLD+'\n\nExtracting '+color.PURPLE+'ORFs'+color.END+color.BOLD+' from'\ - ' the transcriptomic data-set\n\n'+color.END) - - for k, v in prot_dict.items(): - - ## Attempting to find the most-likely START (ATG) position in the transcript (tricky) - ## Skips this if the initial Methionine (ATG) is likely present - ## (e.g. the alignment position of the protein = '1') - prot_start = int(v[3].split('..')[0]) - old_start = v[1] - if prot_start != 1: - min_dist, max_dist = round_down_three(prot_start) - min_start = old_start-min_dist - max_start = old_start-max_dist - if min_start < 0: - min_start = old_start - if max_start < 0: - max_start = min_start%3 -# print k+'\tOld_start\t'+str(old_start)+'\tMin_Dist/Start\t'+str(min_dist)+'/'+str(min_start)+'\tMax_Dist/Start\t'+str(max_dist)+'/'+str(max_start)+'\n' - updated_start = check_new_start_new(v[-1], max_start, min_start, old_start, codon_table) - else: - updated_start = old_start - temp = prot_dict[k][-1][updated_start:] - - ## Uses the given genetic code to identify the stop position of the ORF - temp_prot = str(Seq(temp).translate(table=codon_table)) - if '*' in temp_prot: - stop_pos = (temp_prot.index('*')+1)*3 - prot_dict[k].append(temp[:stop_pos]) - else: - stop_pos = prot_dict[k][2] - prot_dict[k][1] - prot_dict[k].append(temp[:stop_pos]) - - ## Awkward_list is populated with unexpectedly SHORT ORFs! - ## Reasons for being short include: - # An error Xyrus introduced - # Not as great genetic code decision (in-frame stop) - # Crummy sequence/assembly quality (false in-frame stop codons) - - awkward_list = [] - look_good = [] - - for k, v in prot_dict.items(): - expected_min = len(v[-2][v[1]:v[2]])-1 - if len(v[-1]) < expected_min: - awkward_list.append(k) - else: - look_good.append(k) - - if len(awkward_list) != 0: - with open('UnexpexctedShortStuffBlameXyrus.txt','w+') as x: - for entry in awkward_list: - x.write(entry+'\n') - else: - pass - - print (color.BOLD+'\n\nTranslating '+color.PURPLE+'ORFs'+color.END+color.BOLD+' from'\ - ' using the '+color.DARKCYAN+args.genetic_code.title()+' genetic code'+color.END) - - for k, v in prot_dict.items(): - prot_dict[k].append(str(Seq(v[-1]).translate(table=codon_table)).rstrip('*')) - - return prot_dict - -########################################################################################## -###------------ Grabs the Coding Coordinates from the OG-BLAST SpreadSheet ------------### -########################################################################################## - -def prep_translations(args): - - print (color.BOLD+'\n\nGrabbing useful info from the '+color.ORANGE+args.input_file\ - .split('/')[-1]+color.END+color.BOLD+' Fasta File\nand from the '+color.ORANGE+args.tsv_file\ - .split('/')[-1]+color.END+color.BOLD+' OG-Assignment Spreadsheet'+color.END) - - inTSV = ['\t'.join(i.rstrip('\n').split('\t')[:-1]) for i in open(args.tsv_file).readlines() if i != '\n'] - inFasta = [i for i in SeqIO.parse(args.input_file,'fasta')] - - # ORF identification step here, uses the 'allOGCleanresults.tsv file to identify the ORF - prot_dict = {} - - # Special scenario! Only for when the genetic code is not particularly useful ... - if args.genetic_code.lower() == 'none' or args.genetic_code.lower() == 'condylostoma' or args.genetic_code.lower() == 'condy': - for i in inTSV: - prot_dict.setdefault(i.split('\t')[0],[]) - if int(i.split('\t')[6]) < int(i.split('\t')[7]): - ## Saves the Transcript Orientation (Coding vs. Template Strand) - prot_dict[i.split('\t')[0]].append('F') - ## Collects initial Start and Stop positions from the BLAST alignment - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[6])-1) - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[7])+3) - ## Implied Amino Acid alignment positions (e.g. does the alignment start at the 1st Methionine?) - prot_dict[i.split('\t')[0]].append('..'.join(i.split('\t')[-4:-2])) - - if int(i.split('\t')[7]) < int(i.split('\t')[6]): - ## Saves the Transcript Orientation (Coding vs. Template Strand) - prot_dict[i.split('\t')[0]].append('RC') - ## Collects initial Start and Stop positions from the BLAST alignment - prot_dict[i.split('\t')[0]].append(int(i.split('_Len')[1].split('_')[0])-int(i.split('\t')[6])) - prot_dict[i.split('\t')[0]].append(int(i.split('_Len')[1].split('_')[0])-int(i.split('\t')[7])+1) - ## Implied Amino Acid alignment positions (e.g. does the alignment start at the 1st Methionine?) - prot_dict[i.split('\t')[0]].append('..'.join(i.split('\t')[-4:-2])) - - ## Makes sure that the dictionary has the transcript in the correct orientation - for i in inFasta: - if i.description in prot_dict.keys(): - if 'RC' == prot_dict[i.description][0]: - prot_dict[i.description].append(str(i.seq.reverse_complement())) - else: - prot_dict[i.description].append(str(i.seq)) - - else: - for i in inTSV: - prot_dict.setdefault(i.split('\t')[0],[]) - if int(i.split('\t')[6]) < int(i.split('\t')[7]): - ## Saves the Transcript Orientation (Coding vs. Template Strand) - prot_dict[i.split('\t')[0]].append('F') - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[6])-1) - prot_dict[i.split('\t')[0]].append(int(i.split('\t')[7])+3) - ## Implied Amino Acid alignment positions (e.g. does the alignment start at the 1st Methionine?) - prot_dict[i.split('\t')[0]].append('..'.join(i.split('\t')[-4:-2])) - if int(i.split('\t')[7]) < int(i.split('\t')[6]): - ## Saves the Transcript Orientation (Coding vs. Template Strand) - prot_dict[i.split('\t')[0]].append('RC') - ## Collects initial Start and Stop positions from the BLAST alignment (but in the "correct" orientation) - prot_dict[i.split('\t')[0]].append(int(i.split('_Len')[1].split('_')[0])-int(i.split('\t')[6])) - prot_dict[i.split('\t')[0]].append(int(i.split('_Len')[1].split('_')[0])-int(i.split('\t')[7])+1) - ## Implied Amino Acid alignment positions (e.g. does the alignment start at the 1st Methionine?) - prot_dict[i.split('\t')[0]].append('..'.join(i.split('\t')[-4:-2])) - - ## Makes sure that the dictionary has the transcript in the correct orientation - for i in inFasta: - if i.description in prot_dict.keys(): - if 'RC' == prot_dict[i.description][0]: - prot_dict[i.description].append(str(i.seq.reverse_complement())) - else: - prot_dict[i.description].append(str(i.seq)) - - return prot_dict - - -########################################################################################## -###------------------------ Rounds Down Values to Nearest "3" -------------------------### -########################################################################################## - -def round_down_three(num): - min_val = int(num*3*.5)-int(num*3*.5)%3 - max_val = int(num*6)-int(num*6)%3 - return min_val, max_val - - -########################################################################################## -###--------------------- Makes Translation Steps (Later) Easier -----------------------### -########################################################################################## - -def standardize_gcode(given_code): - if given_code == 'ciliate' or given_code == 'tga': - codon_table = 6 - elif given_code == 'chilodonella' or given_code == 'chilo' or given_code == 'taa': - codon_table = c_uncinata_table - elif given_code == 'blepharisma' or given_code == 'bleph': - codon_table = blepharisma_table - elif given_code == 'euplotes' or given_code == 'eup': - codon_table = euplotes_table - elif given_code == 'myrionecta' or given_code == 'mesodinium': - codon_table = myrionecta_table - elif given_code == 'peritrich' or given_code == 'vorticella': - codon_table = peritrich_table - elif given_code == 'none': - codon_table = no_stop_table - elif given_code == 'condylostoma' or given_code == 'condy': - codon_table = condylostoma_table - elif given_code == 'tag': - codon_table = tag_table - elif given_code == 'universal': - codon_table = 1 - else: - print (color.BOLD+color.RED+'\n\nNo valid genetic code provided!\n\n'+color.END+\ - color.BOLD+'Using the "Universal" genetic code (by default)\n\nPlease check that the'\ - ' code you wish to use is supported:'+color.CYAN+'\n\npython 5_GCodeTranslate.py'\ - ' -list_codes\n\n'+color.END) - codon_table = 1 - - return codon_table - - -########################################################################################### -###------------------ Updates Spreadsheet with Updated Contig Names --------------------### -########################################################################################### - -def update_spreadsheet(args, updated_spreadsheet_dict): - if os.path.isdir(args.home_folder + '/DiamondOG/') != True: - os.system(args.home_folder + '/DiamondOG/') - else: - pass - - inTSV = [line.rstrip('\n') for line in open(args.tsv_file).readlines() if line != '\n' and line.split('\t')[0] in updated_spreadsheet_dict.keys()] - - updatedTSV = [updated_spreadsheet_dict[line.split('\t')[0]]+'\t'+'\t'.join(line.split('\t')[1:]) for line in inTSV] - - with open(args.tsv_out,'w+') as w: - w.write('\n'.join(updatedTSV)) - - -########################################################################################### -###-------------------- Updates Log With OG Assignment Information ---------------------### -########################################################################################### - -def update_log(filename, codon_table): - - if os.path.isdir('../PostAssembly_Logs/') != True: - os.system('mkdir ../PostAssembly_Logs/') - else: - pass - - ntd_ORF = [i for i in SeqIO.parse(filename.split('.fas')[0]+'_'+gcode.title()+'_ORF.fasta','fasta')] - aa_ORF = [i for i in SeqIO.parse(filename.split('.fas')[0]+'_'+gcode.title()+'_ORF.aa.fasta','fasta')] - - min_ntd_ORF = str(min([len(i.seq) for i in ntd_ORF])) - max_ntd_ORF = str(max([len(i.seq) for i in ntd_ORF])) - avg_ntd_ORF = '%.2f' % (sum([len(i.seq) for i in ntd_ORF])/float(len(ntd_ORF))) - - min_aa_ORF = str(min([len(i.seq) for i in aa_ORF])) - max_aa_ORF = str(max([len(i.seq) for i in aa_ORF])) - avg_aa_ORF = '%.2f' % (sum([len(i.seq) for i in aa_ORF])/float(len(aa_ORF))) - - for Logname in os.listdir(os.curdir+'./PostAssembly_Logs/'): - if Logname.startswith(filename.split('/')[2].split('_WTA')[0]) and Logname.endswith('Log.txt'): - with open('../PostAssembly_Logs/'+Logname,'a') as LogFile: - LogFile.write('Nucleotide ORFs\t'+str(len(ntd_ORF))+'\tn/a\tn/a\n') - LogFile.write('Nucleotide ORF Lengths\t'+avg_ntd_ORF+'\t'+min_ntd_ORF+'\t'+max_ntd_ORF+'\n') - LogFile.write('Protein ORFs\t'+str(len(aa_ORF))+'\tn/a\tn/a\n') - LogFile.write('Protein ORF Lengths\t'+avg_aa_ORF+'\t'+min_aa_ORF+'\t'+max_aa_ORF+'\n') - - -########################################################################################## -###----------------------- Write File with Provided Genetic Code ----------------------### -########################################################################################## - -def write_data_out(prot_dict, codon_table, args): - - update_spreadsheet_dict = {} - - #The code below only works if rnaspades was used; constrained by addition of script 6b - for k, v in prot_dict.items(): - #if 'Cov' in k: - new_name = k.split('_Len')[0]+'_Len'+str(len(v[-2]))+'_'+'_'.join(k.split('_')[-3:]) - #update_spreadsheet_dict[k] = new_name - update_spreadsheet_dict[k] = k - #else: - #new_name = k.split('_Len')[0]+'_Len'+str(len(v[-2]))+'_'+'_'.join(k.split('_')[-2:]) - #update_spreadsheet_dict[k] = new_name - #update_spreadsheet_dict[k] = k - - with open(args.ntd_out,'w+') as w: - print (color.BOLD+'\n\nWriting FASTA file with '+color.PURPLE+'ORF'+color.END+color.BOLD\ - +' sequences using the '+color.DARKCYAN+args.genetic_code.title()+' genetic code'+color.END) - - for k, v in prot_dict.items(): - w.write('>'+update_spreadsheet_dict[k]+'\n'+str(v[-2])+'\n') - - with open(args.aa_out, 'w+') as w: - print (color.BOLD+'\n\nWriting FASTA file with '+color.PURPLE+'Translated ORF'+color.END+color.BOLD\ - +' sequences using the '+color.DARKCYAN+args.genetic_code.title()+' genetic code'+color.END) - - for k, v in prot_dict.items(): - w.write('>'+update_spreadsheet_dict[k]+'\n'+str(v[-1])+'\n') - - return update_spreadsheet_dict - - -########################################################################################## -###--------------------- Cleans up the Folder and Moves Final Files -------------------### -########################################################################################## - -def clean_up(args): - - if args.input_file.split('.fas')[0].split('/')[-1] + '_StopCodonStats.tsv' in os.listdir(args.home_folder): - os.system('mv ' + args.input_file.split('.fas')[0] + '_StopCodonStats.tsv ' + args.StopFreq) - - os.system('mv '+args.tsv_file+' '+args.Diamond_Folder) - os.system('mv '+args.input_file+' '+args.Diamond_Folder) - - if args.no_RP == True: - if os.path.isdir(args.all_output_folder + 'ToRename/') != True: - os.system('mkdir ' + args.all_output_folder + 'ToRename/') - - os.system('cp ' + args.ntd_out + ' ' + args.all_output_folder + 'ToRename/') - os.system('cp ' + args.aa_out + ' ' + args.all_output_folder + 'ToRename/') - os.system('cp ' + args.tsv_out + ' ' + args.all_output_folder + 'ToRename/') - - else: - os.system('cp ' + args.tsv_out + ' ' + args.all_output_folder) - os.system('cp ' + args.ntd_out + ' ' + args.all_output_folder) - os.system('cp ' + args.aa_out + ' ' + args.all_output_folder) - - os.system('mv ' + args.home_folder + ' ' + args.all_output_folder + 'TranslatedTranscriptomes') - - -########################################################################################### -###-------------------------------- Next Script Message --------------------------------### -########################################################################################### - -def next_script(args): - - print (color.BOLD+'\n\nLook for '+color.DARKCYAN+args.ntd_out.split('/')[-1]+color.END+\ - color.BOLD+',\n'+color.DARKCYAN+args.aa_out.split('/')[-1]+color.END+color.BOLD+', and\n'\ - +color.DARKCYAN+args.tsv_out.split('/')[-1]+color.END+color.BOLD+',\nwhich are in the '+\ - color.ORANGE+args.home_folder.split('/')[-1]+' Folder'+color.END) - - if args.no_RP == True: - print(color.BOLD+'\n\nNext Script is: '+color.GREEN+'7_FinalRename.py'+color.END+color.BOLD+\ - ' in the '+color.PURPLE+'RemovePartials Folder'+color.END+color.BOLD+'\nwith a copy of'\ - ' the outputs of this script!'+color.END) - print(color.BOLD+'\n\nRemember that you have chosen '+color.RED+'NOT '+color.END+color.BOLD+\ - 'to remove partials\nand are skipping to the renaming step!\n\n'+color.END) - - else: - print(color.BOLD+'\n\nNext Script is: '+color.GREEN+'6_FilterPartials.py'+color.END+color.BOLD+\ - ' in the '+color.PURPLE+'FinalizeTranscripts Folder'+color.END+color.BOLD+'\nwith a copy of'\ - ' the outputs of this script!\n\n'+color.END) - - -########################################################################################## -###--------------- Checks Command Line Arguments and Calls on Functions ---------------### -########################################################################################## - -def main(): - - args = check_args() - - prep_folders(args) - - codon_table = standardize_gcode(args.genetic_code.lower()) - - prot_dict_Prepped = prep_translations(args) - - prot_dict_Final = extract_ORF(prot_dict_Prepped, codon_table, args) - - new_spreadsheet_names = write_data_out(prot_dict_Final, codon_table, args) - - update_spreadsheet(args, new_spreadsheet_names) - -# update_log(fasta_file, gcode) - - clean_up(args) - - next_script(args) - -main() \ No newline at end of file diff --git a/PTL1/Transcriptomes/Scripts/6_FilterPartials.py b/PTL1/Transcriptomes/Scripts/6_FilterPartials.py deleted file mode 100644 index 73be7f4..0000000 --- a/PTL1/Transcriptomes/Scripts/6_FilterPartials.py +++ /dev/null @@ -1,607 +0,0 @@ -#!/usr/bin/env python3.5 - -##__Updated__: 2020-11-29 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com; xyrus.maurer-alcala@izb.unibe.ch -##__Usage__: python 6_FilterPartials.py --help - - -################################################################################################## -## This script is intended to remove incomplete transcripts that have a more complete mate ## -## ## -## Prior to running this script, ensure the following: ## -## ## -## 1. You have assembled your transcriptome and COPIED the 'assembly' file ## -## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ## -## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ## -## 3. Removed SSU/LSU sequences from your Fasta File ## -## 4. Classified your sequences as Strongly Prokaryotic/Eukaryotic or Undetermined ## -## 5. Classified the Non-Strongly Prokaryotic sequences into OGs ## -## 6. You either know (or have inferred) the genetic code of the organism ## -## 7. You have translated the sequences and checked for the data in the RemovePartials folder ## -## ## -## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ## -## ## -## Next Script(s) to Run: ## -## 7_FinalRename.py ## -## ## -################################################################################################## - -from Bio import SeqIO -from Bio.Seq import Seq - -from distutils import spawn -import argparse, os, sys, time -from argparse import RawTextHelpFormatter,SUPPRESS - - - -#------------------------------ Colors For Print Statements ------------------------------# -class color: - PURPLE = '\033[95m' - CYAN = '\033[96m' - DARKCYAN = '\033[36m' - ORANGE = '\033[38;5;214m' - BLUE = '\033[94m' - GREEN = '\033[92m' - YELLOW = '\033[93m' - RED = '\033[91m' - BOLD = '\033[1m' - UNDERLINE = '\033[4m' - END = '\033[0m' - - -#------------------------------- Main Functions of Script --------------------------------# - -########################################################################################### -###---------------------------- UPDATE DIAMOND PATH BELOW! -----------------------------### -########################################################################################### - ## IF Diamond is IN YOUR PATH then no updating is needed... - -def check_diamond_path(): - - diamond_path = '' - - if diamond_path == '': - diamond_path = spawn.find_executable("diamond") - #diamond_path = '/path/to/diamond' - else: - pass - - if diamond_path == None: - print (color.BOLD + '\n\nPlease open this script and check that you have included'\ - +' the PATH to the'+color.BLUE+' "diamond" '+color.END+color.BOLD+'executable.\n\n'+color.END) - print (color.BOLD+color.BLUE+'LOOK FOR:\n\n'+color.RED\ - +'#------------------------------ UPDATE DIAMOND PATH BELOW! -------------------------------#'\ - +color.BLUE+'\n\nThis is somewhere around lines 50 - 80...\n\n'+color.END) - - sys.exit() - else: - pass - - return diamond_path - -########################################################################################### -###--------------------- Parses and Checks Command-Line Arguments ----------------------### -########################################################################################### - -def check_args(): - - parser = argparse.ArgumentParser(description= - color.BOLD + '\n\nThis script is intended to '+color.RED+'Identify and Collapse '+color.END\ - +color.BOLD+'partial '+color.PURPLE+'ORFS\n'+color.END+color.BOLD+'present within a '\ - +color.RED+'Given'+color.END+color.BOLD+' transcriptome (or replicate) transcriptome(s)'\ - +usage_msg(), usage=SUPPRESS, formatter_class=RawTextHelpFormatter) - - required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END) - - required_arg_group.add_argument('--file_prefix','-fp', action='store', - help=color.BOLD+color.GREEN+' File prefix that is unique (or common)\n to the files '\ - 'to be processed\n'+color.END) - - optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END) - - optional_arg_group.add_argument('--identity','-id', type=float, action='store', default=0.98, - help=color.BOLD+color.GREEN+' Identity threshold for identifying \n "partials" to larger'\ - ' contigs\n (default = 0.98)\n'+color.END) - optional_arg_group.add_argument('-author', action='store_true', - help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END) - - if len(sys.argv[1:]) == 0: - print (parser.description) - print ('\n') - sys.exit() - - args = parser.parse_args() - - args.id_print = str(int(float(args.identity)*100)) - - args.all_output_folder = '/'.join(args.file_prefix.split('/')[:-1]) + '/' - args.file_prefix = args.file_prefix.split('/')[-1] - - args.file_listNTD = [args.all_output_folder + i for i in os.listdir(args.all_output_folder) if args.file_prefix in i and i.endswith('NTD.ORF.fasta')] - - args.file_listAA = [args.all_output_folder + i for i in os.listdir(args.all_output_folder) if args.file_prefix in i and i.endswith('AA.ORF.fasta')] - - args.file_listTSV = [args.all_output_folder + i for i in os.listdir(args.all_output_folder) if args.file_prefix in i and i.endswith('results.tsv')] - - quit_eval = return_more_info(args) - if quit_eval > 0: - print ('\n') - sys.exit() - - return args - - -########################################################################################### -###------------------------------- Script Usage Message --------------------------------### -########################################################################################### - -def usage_msg(): - return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 6_RemovePartials.py'\ - ' --file_prefix Op_me_Xxma'+color.END) - - -########################################################################################## -###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------### -########################################################################################## - -def return_more_info(args): - - valid_arg = 0 - - author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\ - ' maurerax@gmail.com\n\n'+color.END) - - if args.author == True: - print (author) - valid_arg += 1 - - if args.file_listNTD == []: - print (color.BOLD+'\n\nNo '+color.ORANGE+'Nucleotide Fasta Files'+color.END+color.BOLD+\ - ' found!\n\nCheck that your'+color.GREEN+' File Prefix'+color.END+color.BOLD+\ - 'is present in\nthe files of interest') - valid_arg += 1 - - if args.file_listAA == []: - print (color.BOLD+'\n\nNo '+color.ORANGE+'Protein Fasta Files'+color.END+color.BOLD+\ - ' found!\n\nCheck that your'+color.GREEN+' File Prefix'+color.END+color.BOLD+\ - 'is present in\nthe files of interest') - valid_arg += 1 - - if args.file_listTSV == []: - print (color.BOLD+'\n\nNo '+color.ORANGE+'OG-Assignment Spreadsheets'+color.END+color.BOLD+\ - ' found!\n\nCheck that your'+color.GREEN+' File Prefix'+color.END+color.BOLD+\ - 'is present in\nthe files of interest') - valid_arg += 1 - - if len(args.file_listNTD) == len(args.file_listAA) == len(args.file_listTSV): - pass - else: - print (color.BOLD+color.RED+'\n\nError:'+color.END+color.BOLD+' Unequal numbers of'\ - ' input files found.\n\nDouble-check that there are:'+color.CYAN+'SINGLE'+color.END\ - +color.BOLD+' Nucleotide and Protein fasta files and OG-assignment Spreadsheet for'\ - ' each transcriptome\n\nThen try once again.'+color.END) - valid_arg += 1 - - return valid_arg - - -########################################################################################## -###------------------------- Creates Folders For Storing Data -------------------------### -########################################################################################## - -def prep_folders(args): - - if os.path.isdir(args.all_output_folder + 'ToRename') != True: - os.system('mkdir ' + args.all_output_folder + 'ToRename') - - if os.path.isdir(args.all_output_folder + args.file_prefix) != True: - os.system('mkdir ' + args.all_output_folder + args.file_prefix) - - if os.path.isdir(args.all_output_folder + args.file_prefix + '/Original') != True: - os.system('mkdir ' + args.all_output_folder + args.file_prefix + '/Original') - os.system('mkdir ' + args.all_output_folder + args.file_prefix + '/Original/SpreadSheets') - os.system('mkdir ' + args.all_output_folder + args.file_prefix + '/Original/Concatenated/') - os.system('mkdir ' + args.all_output_folder + args.file_prefix + '/Original/Concatenated/SpreadSheets') - - if os.path.isdir(args.all_output_folder + args.file_prefix + '/Processed') != True: - os.system('mkdir ' + args.all_output_folder + args.file_prefix + '/Processed') - os.system('mkdir ' + args.all_output_folder + args.file_prefix + '/Processed/SpreadSheets') - - -########################################################################################## -###-------------------- Merges Fasta Files When Replicates Present --------------------### -########################################################################################## - -def merge_fasta_replicates(args, type): - - cat_folder = args.all_output_folder + args.file_prefix + '/Original/Concatenated/' - - count = 0 - fasta_to_merge = [] - - if type == 'NTD': - fasta_list = args.file_listNTD - else: - fasta_list = args.file_listAA - - for file in fasta_list: - fasta_to_merge += ['>'+str(count)+'_'+i for i in open(file).read().split('>') if i != ''] - count += 1 - - with open(cat_folder+args.file_prefix+'.'+type+'.Concatenated.fasta','w+') as w: - w.write(''.join(fasta_to_merge)) - - time.sleep(.75) - - -########################################################################################## -###--------------------- Merges TSV Files When Replicates Present ---------------------### -########################################################################################## - -def merge_tsv_replicates(args): - - cat_folder = args.all_output_folder + args.file_prefix + '/Original/Concatenated/SpreadSheets/' - - count = 0 - tsv_to_merge = [] - - for file in args.file_listTSV: - tsv_to_merge += [str(count)+'_'+i for i in open(file).read().split('\n') if i != ''] - count += 1 - - with open(cat_folder+args.file_prefix+'_Concatenated.allOGCleanresults.tsv','w+') as w: - w.write('\n'.join(tsv_to_merge)) - - time.sleep(.75) - - -########################################################################################## -###------------------ Calls on the other Merge Functions by Data Type -----------------### -########################################################################################## - -def merge_relevant_data(args): - - print (color.BOLD+'\n\nMerging Transcriptome data together.'+color.END) - - merge_fasta_replicates(args, 'NTD') - merge_fasta_replicates(args, 'AA') - merge_tsv_replicates(args) - - -########################################################################################## -###------------------- Uses Diamond to perform Self-vs-Self "BLAST" -------------------### -########################################################################################## - -def self_blast(args, diamond_path): - - cat_folder = args.all_output_folder + args.file_prefix + '/Original/Concatenated/' - - diamond_makedb = diamond_path + ' makedb --in ' + cat_folder + args.file_prefix + '.AA.Concatenated.fasta -d ' + cat_folder + args.file_prefix + '.AA.Concatenated' - - diamond_self = diamond_path + ' blastp -q ' + cat_folder + args.file_prefix + '.AA.Concatenated.fasta -d ' + cat_folder + args.file_prefix + '.AA.Concatenated --strand plus --no-self-hits --id '+str(args.identity)+\ - ' --query-cover 0.7 --evalue 1e-15 --threads 60 --outfmt 6 -o ' + cat_folder + 'SpreadSheets/' + args.file_prefix + '.Concatenated.Self.'+str(args.id_print)+'ID.tsv' - - print (color.BOLD+'\n\nBinning ALL '+color.ORANGE+'Nucleotide ORFs'+color.END+color.BOLD\ - +' for '+color.GREEN+args.file_prefix+color.END+color.BOLD+' at '+args.id_print\ - +'% identity.\n\n'+color.END) - - os.system(diamond_makedb) - os.system(diamond_self) - - return cat_folder+'SpreadSheets/'+args.file_prefix+'.Concatenated.Self.'+str(args.id_print)+'ID.tsv' - - -########################################################################################## -###------------------- Uses USearch to perform Self-vs-Self "BLAST" -------------------### -########################################################################################## - -def check_Self_vs_Self(tsv_file): - - evaluation = '' - - tsv_in = [i for i in open(tsv_file).read().split('\n') if i != ''] - - if len(tsv_in) == 0: - evaluation = 'empty' - with open(tsv_file,'w+') as w: - w.write('No Self-vs-Self hits were found') - else: - evaluation = 'continue' - - return evaluation - - - -########################################################################################## -###-------------------- Removes Nearly Identical ORFs from Data Set -------------------### -########################################################################################## - -def filter_NTD_data(args): - - cat_folder = args.all_output_folder + args.file_prefix + '/Original/Concatenated/' - proc_folder = args.all_output_folder + args.file_prefix + '/Processed/' - - ########################################## - ## Set-up Useful Lists and Dictionaries ## - ########################################## - - nuc_Above98_hit = {} - seqs_to_toss = [] - prepped_NTD = [] - prepped_AA = [] - - nuc_tsv_100 = 0 - - replicates = '' - - if len(args.file_listNTD) > 1: - replicates = 'yes' - else: - replicates = 'nope' - - ### Update values and names if you have used an alternative Database of Proteins! - ### Last updated on Nov 29, 2020 - OGLenDB = {'OG5_150345': 641, 'OG5_143398': 227, 'OG5_150228': 828, 'OG5_134588': 197, 'OG5_153040': 615, 'OG5_153047': 430, 'OG5_153046': 241, 'OG5_153045': 394, 'OG5_134580': 420, 'OG5_134582': 414, 'OG5_134584': 794, 'OG5_150344': 279, 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'OG5_128434': 346, 'OG5_128435': 549, 'OG5_128436': 1096, 'OG5_128437': 581, 'OG5_129749': 470, 'OG5_129748': 202, 'OG5_150368': 1442, 'OG5_129218': 656, 'OG5_129741': 195, 'OG5_129740': 336, 'OG5_129743': 859, 'OG5_129742': 188, 'OG5_129213': 284, 'OG5_129744': 315, 'OG5_129211': 566, 'OG5_129210': 791, 'OG5_169785': 533, 'OG5_150756': 667, 'OG5_150757': 269, 'OG5_150752': 884, 'OG5_150753': 3285, 'OG5_126951': 220, 'OG5_126950': 387, 'OG5_126953': 256, 'OG5_126952': 479, 'OG5_126955': 419, 'OG5_126954': 449, 'OG5_126957': 212, 'OG5_126956': 200, 'OG5_126959': 455, 'OG5_131622': 139, 'OG5_131621': 263, 'OG5_131620': 983, 'OG5_131626': 280, 'OG5_131624': 298, 'OG5_130461': 273, 'OG5_128292': 598, 'OG5_147262': 406, 'OG5_169804': 355, 'OG5_141536': 252, 'OG5_129745': 792, 'OG5_138708': 433, 'OG5_138706': 1083, 'OG5_135963': 558, 'OG5_138703': 456, 'OG5_135965': 605, 'OG5_135967': 701, 'OG5_128980': 690, 'OG5_155635': 108, 'OG5_128981': 342, 'OG5_147266': 272, 'OG5_128982': 291, 'OG5_128983': 673, 'OG5_146764': 135, 'OG5_128984': 300, 'OG5_146761': 225, 'OG5_128985': 439, 'OG5_128986': 460, 'OG5_128987': 309, 'OG5_135486': 1025, 'OG5_178580': 313, 'OG5_147269': 100, 'OG5_158973': 382, 'OG5_164910': 128, 'OG5_134517': 1166, 'OG5_153386': 237, 'OG5_128988': 510, 'OG5_129746': 409, 'OG5_153439': 243, 'OG5_155864': 440, 'OG5_141710': 146, 'OG5_137708': 480, 'OG5_137709': 412, 'OG5_141712': 428, 'OG5_141713': 121, 'OG5_154720': 489, 'OG5_148411': 843, 'OG5_156580': 484, 'OG5_156582': 276, 'OG5_176474': 629, 'OG5_146358': 960, 'OG5_156587': 937, 'OG5_156586': 532, 'OG5_156589': 313, 'OG5_146357': 299, 'OG5_146351': 691, 'OG5_134617': 898, 'OG5_161984': 919, 'OG5_128920': 769, 'OG5_130282': 577, 'OG5_130283': 322, 'OG5_130280': 851, 'OG5_130281': 316, 'OG5_130286': 1243, 'OG5_130287': 409, 'OG5_130284': 994, 'OG5_130285': 383, 'OG5_137834': 351, 'OG5_130288': 415, 'OG5_130289': 422, 'OG5_137832': 267, 'OG5_136613': 810, 'OG5_136610': 561, 'OG5_129622': 322, 'OG5_137651': 340, 'OG5_136619': 563, 'OG5_133069': 518, 'OG5_142696': 258, 'OG5_133061': 470, 'OG5_133060': 330, 'OG5_133067': 546, 'OG5_133066': 414, 'OG5_133065': 206, 'OG5_133064': 456, 'OG5_129623': 538, 'OG5_137652': 367, 'OG5_155580': 95, 'OG5_132937': 899, 'OG5_135480': 142, 'OG5_145957': 586, 'OG5_145955': 345, 'OG5_130908': 1242, 'OG5_146970': 491, 'OG5_146973': 997, 'OG5_146975': 406, 'OG5_146974': 260, 'OG5_146977': 302, 'OG5_140279': 193, 'OG5_145128': 253, 'OG5_162681': 451, 'OG5_126799': 946, 'OG5_126798': 554, 'OG5_126797': 283, 'OG5_126796': 592, 'OG5_126795': 620, 'OG5_126794': 147, 'OG5_126793': 348, 'OG5_126792': 190, 'OG5_126791': 1909, 'OG5_126790': 483, 'OG5_137994': 819, 'OG5_147005': 291, 'OG5_141894': 716, 'OG5_155059': 300, 'OG5_129903': 174, 'OG5_161490': 607, 'OG5_163187': 263, 'OG5_161496': 589, 'OG5_129905': 486, 'OG5_129904': 677, 'OG5_162600': 194, 'OG5_132628': 1472, 'OG5_132627': 449, 'OG5_132622': 385, 'OG5_132999': 1028, 'OG5_132621': 645, 'OG5_132878': 562, 'OG5_149938': 209, 'OG5_145048': 139, 'OG5_129624': 246, 'OG5_127795': 150, 'OG5_133938': 1211, 'OG5_152704': 276, 'OG5_142695': 247, 'OG5_133930': 728, 'OG5_133933': 423, 'OG5_133934': 632, 'OG5_133937': 317, 'OG5_143355': 427, 'OG5_153811': 516, 'OG5_142697': 433, 'OG5_129625': 686, 'OG5_156440': 404, 'OG5_132931': 488, 'OG5_142692': 1136, 'OG5_133335': 547, 'OG5_156443': 318, 'OG5_143655': 678, 'OG5_179960': 603, 'OG5_131012': 972, 'OG5_134361': 683, 'OG5_146519': 375, 'OG5_146518': 622, 'OG5_181722': 189, 'OG5_134360': 339, 'OG5_158986': 655, 'OG5_146511': 577, 'OG5_141230': 358, 'OG5_146516': 293, 'OG5_141235': 307, 'OG5_141725': 68, 'OG5_141724': 1020, 'OG5_141727': 1212, 'OG5_141726': 323, 'OG5_141721': 138, 'OG5_141720': 576, 'OG5_141723': 575, 'OG5_131013': 183, 'OG5_141729': 3688, 'OG5_151342': 178, 'OG5_151343': 402, 'OG5_130919': 727, 'OG5_130912': 540, 'OG5_130913': 403, 'OG5_130910': 1121, 'OG5_151349': 288, 'OG5_130916': 242, 'OG5_130917': 138, 'OG5_130915': 151, 'OG5_129914': 252, 'OG5_164765': 235, 'OG5_129916': 1690, 'OG5_129917': 706, 'OG5_129910': 489, 'OG5_129911': 665, 'OG5_129913': 408, 'OG5_135397': 130, 'OG5_135396': 282, 'OG5_135395': 478, 'OG5_135394': 429, 'OG5_135393': 310, 'OG5_129919': 305, 'OG5_135391': 215, 'OG5_133574': 393, 'OG5_165494': 186, 'OG5_153277': 244, 'OG5_134376': 213, 'OG5_134377': 857, 'OG5_134375': 574, 'OG5_134379': 279, 'OG5_135187': 154, 'OG5_128355': 407, 'OG5_128354': 457, 'OG5_128357': 496, 'OG5_128356': 429, 'OG5_128351': 401, 'OG5_128353': 297, 'OG5_139394': 403, 'OG5_139428': 384, 'OG5_160472': 281, 'OG5_160473': 195, 'OG5_128359': 894, 'OG5_128358': 456, 'OG5_160476': 285, 'OG5_130707': 368, 'OG5_137078': 295, 'OG5_130705': 660, 'OG5_130872': 296, 'OG5_130875': 840, 'OG5_130702': 297, 'OG5_130701': 413, 'OG5_130700': 983, 'OG5_130879': 168, 'OG5_130878': 216, 'OG5_163262': 543, 'OG5_163264': 245, 'OG5_163265': 185, 'OG5_130709': 190, 'OG5_130708': 352, 'OG5_135570': 500, 'OG5_135576': 456, 'OG5_135574': 976, 'OG5_135579': 530, 'OG5_129195': 683, 'OG5_137079': 352, 'OG5_131476': 470, 'OG5_132954': 304, 'OG5_131474': 1584, 'OG5_131475': 373, 'OG5_134112': 207, 'OG5_131473': 697, 'OG5_131470': 1025, 'OG5_132955': 317, 'OG5_146426': 507, 'OG5_127262': 137, 'OG5_131478': 2041, 'OG5_131479': 171, 'OG5_127967': 759, 'OG5_127966': 733, 'OG5_160515': 683, 'OG5_127964': 233, 'OG5_127963': 290, 'OG5_127962': 994, 'OG5_127961': 570, 'OG5_127960': 846, 'OG5_132950': 643, 'OG5_129196': 362, 'OG5_139648': 896, 'OG5_127969': 688, 'OG5_127968': 95, 'OG5_137545': 156, 'OG5_160464': 217, 'OG5_132953': 1112, 'OG5_126822': 616, 'OG5_126976': 522, 'OG5_170160': 307, 'OG5_129197': 313, 'OG5_175054': 454, 'OG5_144852': 363, 'OG5_144853': 328, 'OG5_144854': 244, 'OG5_144855': 545, 'OG5_144857': 1478, 'OG5_144859': 304, 'OG5_175404': 300, 'OG5_172007': 632, 'OG5_129008': 249, 'OG5_129009': 366, 'OG5_179243': 119, 'OG5_152583': 235, 'OG5_152582': 167, 'OG5_129002': 426, 'OG5_129003': 369, 'OG5_129000': 307, 'OG5_129001': 287, 'OG5_129007': 618, 'OG5_129004': 310, 'OG5_129005': 371, 'OG5_155247': 590, 'OG5_137012': 300, 'OG5_145725': 687, 'OG5_145727': 189, 'OG5_145726': 487, 'OG5_145729': 315, 'OG5_145728': 166, 'OG5_130843': 441, 'OG5_129191': 705, 'OG5_150560': 871, 'OG5_152613': 113, 'OG5_132289': 380, 'OG5_141396': 380, 'OG5_130563': 977, 'OG5_130177': 638, 'OG5_163273': 274, 'OG5_152632': 328, 'OG5_141392': 313, 'OG5_138112': 391, 'OG5_138113': 299, 'OG5_177212': 413, 'OG5_141393': 220, 'OG5_138116': 613, 'OG5_137138': 536, 'OG5_138115': 280, 'OG5_161644': 155, 'OG5_130562': 1546, 'OG5_147326': 304, 'OG5_161641': 94, 'OG5_136849': 580, 'OG5_136846': 280, 'OG5_136844': 358, 'OG5_163995': 293, 'OG5_136842': 373, 'OG5_136840': 503, 'OG5_136436': 642, 'OG5_128419': 224, 'OG5_171260': 1234, 'OG5_135503': 393, 'OG5_131890': 353, 'OG5_131891': 436, 'OG5_131892': 389, 'OG5_131894': 487, 'OG5_131895': 232, 'OG5_131896': 658, 'OG5_131897': 378, 'OG5_131898': 309, 'OG5_131899': 528, 'OG5_137372': 285, 'OG5_132554': 1864, 'OG5_177637': 407, 'OG5_156249': 417, 'OG5_134750': 947, 'OG5_132556': 356, 'OG5_138551': 128, 'OG5_134105': 655, 'OG5_134107': 657, 'OG5_138569': 298, 'OG5_136262': 713, 'OG5_136260': 758, 'OG5_136261': 344, 'OG5_136267': 486, 'OG5_136264': 424, 'OG5_136265': 272, 'OG5_134752': 1173, 'OG5_146540': 376, 'OG5_178741': 284, 'OG5_153867': 471, 'OG5_158620': 253, 'OG5_160547': 227, 'OG5_147088': 98, 'OG5_141643': 592, 'OG5_134210': 453, 'OG5_139226': 395, 'OG5_127369': 497, 'OG5_127368': 198, 'OG5_127365': 112, 'OG5_127364': 1216, 'OG5_127367': 320, 'OG5_127366': 173, 'OG5_127361': 190, 'OG5_127360': 1103, 'OG5_127363': 277, 'OG5_127362': 436, 'OG5_163728': 541, 'OG5_175845': 577, 'OG5_147083': 462, 'OG5_163725': 160, 'OG5_163721': 490, 'OG5_156636': 305, 'OG5_156635': 463, 'OG5_147081': 2587, 'OG5_133337': 536, 'OG5_147086': 291, 'OG5_133236': 748, 'OG5_133725': 493, 'OG5_133234': 304, 'OG5_133232': 601, 'OG5_133230': 243, 'OG5_133231': 281, 'OG5_133728': 597, 'OG5_133238': 423, 'OG5_133239': 649, 'OG5_127181': 349, 'OG5_127180': 403, 'OG5_127183': 1000, 'OG5_127182': 529, 'OG5_127187': 267, 'OG5_127186': 581, 'OG5_145289': 450, 'OG5_127188': 576, 'OG5_137408': 266, 'OG5_149527': 359, 'OG5_160288': 447, 'OG5_163095': 260, 'OG5_135769': 248, 'OG5_135766': 435, 'OG5_135765': 272, 'OG5_135762': 1087, 'OG5_135763': 131, 'OG5_135760': 353, 'OG5_128737': 358, 'OG5_150363': 109, 'OG5_150362': 348, 'OG5_126588': 633, 'OG5_126589': 1246, 'OG5_150367': 476, 'OG5_149728': 175, 'OG5_150365': 334, 'OG5_150364': 262, 'OG5_126582': 482, 'OG5_126583': 311, 'OG5_150369': 328, 'OG5_149726': 538, 'OG5_126587': 183, 'OG5_149723': 469, 'OG5_149890': 552, 'OG5_141530': 439, 'OG5_128989': 460, 'OG5_141532': 380, 'OG5_184704': 296, 'OG5_128638': 708, 'OG5_128639': 398, 'OG5_128636': 272, 'OG5_128637': 1402, 'OG5_128634': 315, 'OG5_128635': 276, 'OG5_128632': 351, 'OG5_128633': 561, 'OG5_128630': 184, 'OG5_128631': 486, 'OG5_142840': 528, 'OG5_142842': 647, 'OG5_136083': 193, 'OG5_129589': 332, 'OG5_129588': 422, 'OG5_129587': 1028, 'OG5_129586': 290, 'OG5_129585': 359, 'OG5_129584': 277, 'OG5_129582': 923, 'OG5_129580': 292, 'OG5_140623': 314, 'OG5_149862': 633, 'OG5_140620': 321, 'OG5_140626': 583, 'OG5_145022': 184, 'OG5_155859': 375, 'OG5_155854': 524, 'OG5_145020': 317, 'OG5_158571': 355, 'OG5_128180': 421, 'OG5_128181': 970, 'OG5_128182': 635, 'OG5_128183': 217, 'OG5_128184': 379, 'OG5_128185': 372, 'OG5_128186': 151, 'OG5_128187': 488, 'OG5_128188': 315, 'OG5_145026': 486, 'OG5_134557': 475, 'OG5_145027': 117, 'OG5_129763': 484, 'OG5_129762': 352, 'OG5_129761': 331, 'OG5_129760': 653, 'OG5_129767': 117, 'OG5_129766': 218, 'OG5_129765': 310, 'OG5_129764': 274, 'OG5_135182': 534, 'OG5_135183': 486, 'OG5_129769': 1621, 'OG5_129768': 779, 'OG5_135186': 338, 'OG5_149860': 182, 'OG5_155407': 384, 'OG5_135185': 375, 'OG5_126979': 495, 'OG5_126978': 241, 'OG5_128656': 574, 'OG5_126973': 681, 'OG5_126972': 584, 'OG5_126971': 224, 'OG5_126970': 198, 'OG5_126977': 534, 'OG5_145028': 545, 'OG5_126975': 655, 'OG5_126974': 436, 'OG5_141398': 557, 'OG5_131648': 394, 'OG5_131645': 466, 'OG5_131644': 631, 'OG5_131647': 441, 'OG5_131646': 702, 'OG5_131641': 216, 'OG5_131640': 80, 'OG5_131643': 346, 'OG5_131642': 567, 'OG5_139091': 261, 'OG5_128657': 495, 'OG5_169909': 222, 'OG5_134555': 474, 'OG5_135982': 308, 'OG5_149620': 266, 'OG5_135980': 519, 'OG5_177023': 288, 'OG5_135984': 690, 'OG5_138270': 288, 'OG5_135989': 653, 'OG5_128650': 542, 'OG5_153263': 823, 'OG5_146704': 211, 'OG5_150260': 569, 'OG5_149867': 684, 'OG5_159313': 297, 'OG5_146709': 126, 'OG5_134553': 587, 'OG5_149629': 485} - - print (color.BOLD+'\n\nRemoving Partial '+color.PURPLE+'ORFs'+color.END+color.BOLD+\ - ' with >'+args.id_print+'% Nucleotide Identity over >70% of\ntheir length when '\ - 'compared to more complete '+color.PURPLE+'ORFs '+color.END+color.BOLD+'from: '\ - +color.CYAN+args.file_prefix+'\n\n'+color.END) - - ##################################################################### - ## Self-v-self BLAST Output Parsing - first checks for Seq-length! ## - ##################################################################### - - nuc_tsv_raw = [i.rstrip('\n') for i in open(cat_folder+'SpreadSheets/'+args.file_prefix\ - +'.Concatenated.Self.'+str(args.id_print)+'ID.tsv').readlines() if i != '\n'] -# +'.Concatenated.Self.'+str(args.identity)+'ID.tsv').readlines() if i != '\n'] - - for line in nuc_tsv_raw: - if line.split('OG5_')[-1].split('\t')[0] in OGLenDB.keys(): - ### Checks that the NTD is not 150% the Protein length (so 4.5x due to CODONS!) - if int(line.split('Len')[-1].split('_')[0]) > 4.5*OGLenDB['OG5_'+line.split('OG5_')[-1].split('\t')[0]]: - seqs_to_toss.append(line.split('\t')[1]) - too_long += 1 - - nuc_tsv = [line for line in nuc_tsv_raw if line.split('\t')[1] not in seqs_to_toss] - - if 'Cov' in nuc_tsv[0].split('\t')[0].split('_')[-3]: - nuc_tsv.sort(key=lambda x: (-int(x.split('\t')[1].split('Len')[-1].split('_')[0]),-int(x.split('\t')[1].split('Cov')[-1].split('_')[0]))) - else: - nuc_tsv.sort(key=lambda x: -int(x.split('\t')[1].split('Len')[-1].split('_')[0])) - - - for line in nuc_tsv: - if line.split('\t')[1] not in seqs_to_toss: - nuc_Above98_hit.setdefault(line.split('\t')[1],[]).append(line.split('\t')[0]) - seqs_to_toss.append(line.split('\t')[0]) - if line.split('\t')[2] == '100.0': - nuc_tsv_100 += 1 - - seqs_to_toss = list(set(seqs_to_toss)) - inFasta_NTD_rawLen = [i for i in SeqIO.parse(cat_folder+args.file_prefix+'.NTD.Concatenated.fasta', 'fasta') if i.description] - inFasta_NTD = [i for i in inFasta_NTD_rawLen if i.description not in seqs_to_toss] - inFasta_AA = [i for i in SeqIO.parse(cat_folder+args.file_prefix+'.AA.Concatenated.fasta','fasta') if i.description not in seqs_to_toss] - - if replicates != '': - for i in inFasta_NTD: - if i.description not in nuc_Above98_hit.keys(): - prepped_NTD.append('>'+'_'.join(i.description.split('_')[1:])+'_Trans1\n'+str(i.seq)) - else: - Rep_Num = str(len(set([i.description.split('_')[0]]+[j.split('_')[0] for j in nuc_Above98_hit[i.description]]))) - prepped_NTD.append('>'+'_'.join(i.description.split('_')[1:])+'_Trans'+Rep_Num+'\n'+str(i.seq)) - for i in inFasta_AA: - if i.description not in nuc_Above98_hit.keys(): - prepped_AA.append('>'+'_'.join(i.description.split('_')[1:])+'_Trans1\n'+str(i.seq).replace('*','X')) - else: - Rep_Num = str(len(set([i.description.split('_')[0]]+[j.split('_')[0] for j in nuc_Above98_hit[i.description]]))) - prepped_AA.append('>'+'_'.join(i.description.split('_')[1:])+'_Trans'+Rep_Num+'\n'+str(i.seq).replace('*','X')) - else: - for i in inFasta_NTD: - if i.description not in nuc_Above98_hit.keys(): - prepped_NTD.append('>'+i.description+'\n'+str(i.seq)) - else: - prepped_NTD.append('>'+i.description+'\n'+str(i.seq)) - for i in inFasta_AA: - if i.description not in nuc_Above98_hit.keys(): - prepped_AA.append('>'+i.description+'\n'+str(i.seq).replace('*','X')) - else: - prepped_AA.append('>'+i.description+'\n'+str(i.seq).replace('*','X')) - - with open(args.all_output_folder + args.file_prefix + '/'+args.file_prefix+'_SeqPairsAbove98.txt','w+') as w: - for k, v in nuc_Above98_hit.items(): - w.write(k+'\t'+'\t'.join(v)+'\n') - - ################################################################################### - ## Check for abnormally short sequences for the taxon for every Gene Family (OG) ## - ################################################################################### - - print (color.BOLD+'Removing Abnormally Short (70% length) OR Long (200% length)'\ - +color.PURPLE+' ORFs'+color.END+color.BOLD+'\ncompared to typical '+color.ORANGE+'Gene '\ - 'Family '+color.END+color.BOLD+'member length for: '+color.CYAN+args.file_prefix+'\n\n'+color.END) - - self_OGLenDB={} ## - seqs_to_toss = [] ## - too_long = too_short = 0 ## - - for i in prepped_NTD: - self_OGLenDB.setdefault(i.split('\n')[0].split('OG5_')[-1].split('_')[0],[]).append(len(i.split('\n')[-1])) - - good_NTD_names = [i.split('\n')[0] for i in prepped_NTD if (0.7*sum(self_OGLenDB[i.split('\n')[0].split('OG5_')[-1].split('_')[0]])/float(len(self_OGLenDB[i.split('\n')[0].split('OG5_')[-1].split('_')[0]]))) <= len(i.split('\n')[-1]) <= (2*sum(self_OGLenDB[i.split('\n')[0].split('OG5_')[-1].split('_')[0]])/float(len(self_OGLenDB[i.split('\n')[0].split('OG5_')[-1].split('_')[0]])))] - good_NTD_seqs = [i for i in prepped_NTD if i.split('\n')[0] in good_NTD_names] - good_AA_seqs = [i for i in prepped_AA if i.split('\n')[0] in good_NTD_names] - - too_short = len(prepped_NTD) - len(good_NTD_names) - - #################################################################### - ## Finalized Outputs are Summarized and Written Out to New Fastas ## - #################################################################### - - print (color.BOLD+'There were '+color.CYAN+str(len(inFasta_NTD_rawLen))+color.END+color.BOLD\ - +color.PURPLE+' ORFs '+color.END+color.BOLD+'originally, with '+color.ORANGE+\ - str(nuc_tsv_100)+color.END+color.BOLD+' Partial '+color.PURPLE+'ORFs'+color.END+\ - color.BOLD+' that\nwere '+color.RED+'100% Identical'+color.END+color.BOLD+' to larger'\ - +color.PURPLE+' ORFs.\n\n'+color.END) - - print(color.BOLD+'Of the '+color.CYAN+str(len(inFasta_NTD_rawLen))+color.END+color.BOLD\ - +' original'+color.PURPLE+' ORFs'+color.END+color.BOLD+', '+color.ORANGE+str(len(set(seqs_to_toss)))+\ - color.END+color.BOLD+' are '+color.PURPLE+'Partial ORFs '+color.END+color.BOLD+'(e.g. '+\ - color.RED+'> '+args.id_print+'%'+color.END+color.BOLD+'\nNUCLEOTIDE identity) to larger'\ - +color.PURPLE+' ORFs'+color.END+color.BOLD+' with '+color.ORANGE+str(too_short+too_long)\ - +color.END+color.BOLD+' additional'+color.PURPLE+' ORFs\n'+color.END+color.BOLD+'that were either '+\ - color.RED+'TOO LONG or SHORT.\n\n'+color.END) - - print (color.BOLD+'Overall, there are '+color.GREEN+str(len(good_NTD_seqs))+' Unique ORFs'\ - +color.END+color.BOLD+' for '+color.CYAN+args.file_prefix+'\n'+color.END) - - with open(proc_folder+args.file_prefix+'_Filtered.Final.NTD.ORF.fasta','w+') as w: - for i in good_NTD_seqs: - w.write(i+'\n') - with open(proc_folder+args.file_prefix+'_Filtered.Final.AA.ORF.fasta','w+') as x: - for i in good_AA_seqs: - x.write(i+'\n') - - return good_NTD_names - - -########################################################################################## -###------------------- Updates SpreadSheet with Update Sequence Names -----------------### -########################################################################################## - -def update_tsv(args, NTD_list_names): - - cat_folder = args.all_output_folder + args.file_prefix + '/Original/Concatenated/SpreadSheets/' - proc_folder = args.all_output_folder + args.file_prefix + '/Processed/' - - inTSV = {'_'.join(i.split('\t')[0].split('_')[1:]):'\t'.join(i.split('\t')[1:]) for i in open(cat_folder+\ - args.file_prefix+'_Concatenated.allOGCleanresults.tsv').readlines() if i != '\n'} - - Updated_inTSV = [i.strip('>')+'\t'+inTSV[i.split('_Trans')[0].strip('>')] for i in NTD_list_names] - - with open(proc_folder+'/SpreadSheets/'+args.file_prefix+'_Filtered.Final.allOGCleanresults.tsv','w+') as w: - for line in Updated_inTSV: - w.write(line+'\n') - - -def no_partials_present(args): - - print (color.BOLD+color.RED+'\n\nWarning:'+color.END+color.BOLD+' No partial sequences'\ - ' were found with > '+str(args.id_print)+'% nucleotide identity.\n\nThe data will still be '\ - 'checked for ORFs that are unexpectedly '+color.ORANGE+'Short'+color.END+color.BOLD+' or'\ - +color.ORANGE+' Long.\n\n'+color.END) - - cat_folder = args.all_output_folder + args.file_prefix + '/Original/Concatenated/' - proc_folder = args.all_output_folder + args.file_prefix + '/Processed/' - - NTD_file = cat_folder+args.file_prefix+'.NTD.Concatenated.fasta' - AA_file = cat_folder+args.file_prefix+'.AA.Concatenated.fasta' - TSV_file = cat_folder+'/SpreadSheets/'+args.file_prefix+'_Concatenated.allOGCleanresults.tsv' - - ### Update values and names if you have used an alternative Database of Proteins! - ### Last updated on Nov 29, 2020 - OGLenDB = {'OG5_150345': 641, 'OG5_143398': 227, 'OG5_150228': 828, 'OG5_134588': 197, 'OG5_153040': 615, 'OG5_153047': 430, 'OG5_153046': 241, 'OG5_153045': 394, 'OG5_134580': 420, 'OG5_134582': 414, 'OG5_134584': 794, 'OG5_150344': 279, 'OG5_168666': 362, 'OG5_143132': 370, 'OG5_150229': 557, 'OG5_130112': 910, 'OG5_130113': 572, 'OG5_130110': 754, 'OG5_130116': 601, 'OG5_130117': 563, 'OG5_130114': 2107, 'OG5_130115': 616, 'OG5_137728': 671, 'OG5_130118': 568, 'OG5_130119': 430, 'OG5_169392': 445, 'OG5_136451': 238, 'OG5_136982': 361, 'OG5_136453': 354, 'OG5_136452': 558, 'OG5_136455': 374, 'OG5_136986': 746, 'OG5_142597': 400, 'OG5_136984': 716, 'OG5_136988': 187, 'OG5_139243': 978, 'OG5_141897': 269, 'OG5_146376': 2370, 'OG5_134631': 194, 'OG5_134630': 186, 'OG5_134637': 331, 'OG5_134636': 615, 'OG5_134635': 349, 'OG5_134634': 291, 'OG5_155711': 841, 'OG5_134639': 1049, 'OG5_159186': 493, 'OG5_139602': 1164, 'OG5_159187': 296, 'OG5_153510': 230, 'OG5_142406': 414, 'OG5_148208': 623, 'OG5_137585': 686, 'OG5_137586': 1016, 'OG5_137855': 362, 'OG5_137580': 673, 'OG5_159182': 492, 'OG5_137582': 255, 'OG5_137583': 655, 'OG5_141458': 1086, 'OG5_137858': 185, 'OG5_137859': 1373, 'OG5_136674': 804, 'OG5_144663': 670, 'OG5_169714': 659, 'OG5_136672': 226, 'OG5_136679': 285, 'OG5_133008': 315, 'OG5_144629': 239, 'OG5_144628': 1211, 'OG5_133005': 547, 'OG5_133004': 280, 'OG5_133006': 653, 'OG5_133001': 461, 'OG5_144622': 419, 'OG5_133003': 1044, 'OG5_129447': 225, 'OG5_153048': 841, 'OG5_142276': 130, 'OG5_142275': 158, 'OG5_142903': 699, 'OG5_145106': 1030, 'OG5_131653': 391, 'OG5_145976': 431, 'OG5_129448': 399, 'OG5_128658': 838, 'OG5_146952': 702, 'OG5_146951': 711, 'OG5_141634': 264, 'OG5_126771': 1175, 'OG5_126770': 780, 'OG5_126773': 340, 'OG5_126772': 600, 'OG5_126775': 423, 'OG5_126774': 1080, 'OG5_126777': 305, 'OG5_126776': 411, 'OG5_126779': 971, 'OG5_126778': 284, 'OG5_171684': 114, 'OG5_147026': 359, 'OG5_147027': 467, 'OG5_155565': 469, 'OG5_132286': 286, 'OG5_147023': 222, 'OG5_147029': 871, 'OG5_136189': 247, 'OG5_127119': 1807, 'OG5_136183': 666, 'OG5_136182': 825, 'OG5_136181': 264, 'OG5_136180': 1763, 'OG5_136187': 407, 'OG5_136186': 331, 'OG5_172133': 906, 'OG5_155117': 722, 'OG5_155113': 881, 'OG5_160211': 453, 'OG5_144666': 742, 'OG5_132600': 124, 'OG5_132353': 419, 'OG5_132350': 367, 'OG5_132351': 364, 'OG5_132356': 642, 'OG5_132357': 469, 'OG5_132354': 262, 'OG5_132607': 534, 'OG5_132609': 202, 'OG5_132358': 619, 'OG5_127117': 1081, 'OG5_182858': 103, 'OG5_144665': 304, 'OG5_137725': 314, 'OG5_133913': 568, 'OG5_133917': 801, 'OG5_133915': 273, 'OG5_144664': 775, 'OG5_169823': 388, 'OG5_171419': 113, 'OG5_164059': 496, 'OG5_164056': 328, 'OG5_170942': 89, 'OG5_156795': 403, 'OG5_158960': 324, 'OG5_158963': 243, 'OG5_158962': 88, 'OG5_141259': 500, 'OG5_141709': 1082, 'OG5_141708': 245, 'OG5_141255': 125, 'OG5_146574': 263, 'OG5_141705': 215, 'OG5_141703': 341, 'OG5_141250': 622, 'OG5_141253': 339, 'OG5_158450': 395, 'OG5_127648': 246, 'OG5_127649': 399, 'OG5_129840': 159, 'OG5_136025': 475, 'OG5_127642': 200, 'OG5_127643': 907, 'OG5_127640': 800, 'OG5_127641': 126, 'OG5_127646': 867, 'OG5_127647': 254, 'OG5_127644': 527, 'OG5_127645': 317, 'OG5_130938': 213, 'OG5_130939': 916, 'OG5_129978': 639, 'OG5_129979': 373, 'OG5_129976': 554, 'OG5_129977': 466, 'OG5_129974': 117, 'OG5_129975': 339, 'OG5_129972': 155, 'OG5_129973': 155, 'OG5_129970': 247, 'OG5_129971': 565, 'OG5_135371': 191, 'OG5_159307': 558, 'OG5_135373': 251, 'OG5_135372': 151, 'OG5_135375': 458, 'OG5_135374': 222, 'OG5_135376': 660, 'OG5_135379': 473, 'OG5_135378': 228, 'OG5_130330': 180, 'OG5_139208': 280, 'OG5_134354': 353, 'OG5_134355': 211, 'OG5_139408': 490, 'OG5_134350': 802, 'OG5_128379': 897, 'OG5_128378': 1497, 'OG5_128377': 118, 'OG5_137456': 224, 'OG5_128375': 527, 'OG5_128374': 399, 'OG5_128373': 703, 'OG5_128372': 178, 'OG5_128371': 116, 'OG5_128370': 372, 'OG5_160493': 576, 'OG5_130859': 409, 'OG5_160497': 316, 'OG5_139204': 363, 'OG5_130853': 127, 'OG5_130852': 875, 'OG5_130851': 429, 'OG5_130850': 799, 'OG5_130857': 506, 'OG5_130856': 444, 'OG5_130855': 183, 'OG5_130854': 487, 'OG5_146377': 932, 'OG5_128828': 300, 'OG5_139201': 474, 'OG5_145371': 854, 'OG5_145377': 141, 'OG5_146374': 589, 'OG5_135511': 682, 'OG5_135510': 431, 'OG5_135513': 711, 'OG5_135512': 684, 'OG5_144362': 410, 'OG5_144361': 412, 'OG5_144364': 256, 'OG5_146372': 579, 'OG5_129666': 585, 'OG5_176372': 208, 'OG5_139669': 96, 'OG5_129667': 118, 'OG5_130005': 466, 'OG5_139664': 480, 'OG5_139663': 393, 'OG5_139539': 365, 'OG5_147623': 231, 'OG5_129398': 1423, 'OG5_129399': 337, 'OG5_130589': 1129, 'OG5_130588': 168, 'OG5_129392': 1365, 'OG5_129393': 1939, 'OG5_130587': 515, 'OG5_130586': 420, 'OG5_130581': 1440, 'OG5_129397': 379, 'OG5_129394': 1223, 'OG5_129395': 221, 'OG5_129192': 924, 'OG5_178923': 253, 'OG5_150094': 300, 'OG5_150096': 398, 'OG5_150091': 331, 'OG5_150090': 786, 'OG5_149285': 484, 'OG5_150098': 432, 'OG5_154938': 441, 'OG5_134268': 660, 'OG5_140919': 297, 'OG5_154937': 245, 'OG5_139536': 399, 'OG5_182054': 211, 'OG5_129028': 253, 'OG5_129029': 315, 'OG5_129024': 1349, 'OG5_129025': 189, 'OG5_129026': 103, 'OG5_129027': 547, 'OG5_129020': 362, 'OG5_129021': 436, 'OG5_129022': 227, 'OG5_129023': 488, 'OG5_133753': 585, 'OG5_150549': 1216, 'OG5_131459': 1016, 'OG5_131328': 470, 'OG5_131329': 572, 'OG5_131450': 519, 'OG5_131320': 305, 'OG5_131321': 599, 'OG5_131326': 344, 'OG5_131327': 1225, 'OG5_131324': 568, 'OG5_131325': 793, 'OG5_130329': 324, 'OG5_130328': 452, 'OG5_137118': 773, 'OG5_137117': 459, 'OG5_137440': 517, 'OG5_130323': 119, 'OG5_130322': 602, 'OG5_137113': 521, 'OG5_130324': 557, 'OG5_130327': 802, 'OG5_130326': 1181, 'OG5_138138': 982, 'OG5_127797': 453, 'OG5_138137': 636, 'OG5_138133': 500, 'OG5_136860': 632, 'OG5_136865': 171, 'OG5_136866': 222, 'OG5_136867': 893, 'OG5_136868': 377, 'OG5_136869': 625, 'OG5_175544': 1142, 'OG5_137587': 755, 'OG5_142336': 497, 'OG5_146590': 1539, 'OG5_171107': 168, 'OG5_146595': 465, 'OG5_136217': 113, 'OG5_156261': 578, 'OG5_171108': 146, 'OG5_163918': 204, 'OG5_136248': 563, 'OG5_143026': 629, 'OG5_136244': 230, 'OG5_136245': 231, 'OG5_136247': 201, 'OG5_136240': 73, 'OG5_136241': 269, 'OG5_153680': 87, 'OG5_139986': 493, 'OG5_139987': 465, 'OG5_139985': 470, 'OG5_139980': 1297, 'OG5_160930': 1020, 'OG5_139988': 329, 'OG5_139989': 821, 'OG5_127347': 389, 'OG5_127346': 765, 'OG5_127345': 134, 'OG5_127344': 766, 'OG5_127343': 525, 'OG5_127342': 498, 'OG5_127341': 434, 'OG5_127340': 1938, 'OG5_127439': 643, 'OG5_127438': 434, 'OG5_127349': 574, 'OG5_127348': 389, 'OG5_175825': 74, 'OG5_156659': 387, 'OG5_156658': 302, 'OG5_156654': 235, 'OG5_156948': 440, 'OG5_156656': 225, 'OG5_159170': 123, 'OG5_133219': 279, 'OG5_149919': 265, 'OG5_133748': 426, 'OG5_133749': 356, 'OG5_133211': 199, 'OG5_133212': 561, 'OG5_133213': 390, 'OG5_133214': 327, 'OG5_149917': 293, 'OG5_149914': 308, 'OG5_133217': 549, 'OG5_144487': 487, 'OG5_144486': 159, 'OG5_142480': 831, 'OG5_142483': 161, 'OG5_142482': 110, 'OG5_142485': 180, 'OG5_142486': 198, 'OG5_135740': 528, 'OG5_135741': 80, 'OG5_135742': 238, 'OG5_135743': 311, 'OG5_135744': 311, 'OG5_135745': 240, 'OG5_135746': 237, 'OG5_144626': 289, 'OG5_135749': 436, 'OG5_140399': 674, 'OG5_144480': 416, 'OG5_149707': 338, 'OG5_144550': 670, 'OG5_144553': 772, 'OG5_144552': 608, 'OG5_144555': 300, 'OG5_150300': 230, 'OG5_144557': 483, 'OG5_149876': 249, 'OG5_144559': 239, 'OG5_144623': 254, 'OG5_150309': 305, 'OG5_128610': 366, 'OG5_128611': 185, 'OG5_128612': 510, 'OG5_128613': 919, 'OG5_128614': 796, 'OG5_128615': 1064, 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'OG5_158620': 253, 'OG5_160547': 227, 'OG5_147088': 98, 'OG5_141643': 592, 'OG5_134210': 453, 'OG5_139226': 395, 'OG5_127369': 497, 'OG5_127368': 198, 'OG5_127365': 112, 'OG5_127364': 1216, 'OG5_127367': 320, 'OG5_127366': 173, 'OG5_127361': 190, 'OG5_127360': 1103, 'OG5_127363': 277, 'OG5_127362': 436, 'OG5_163728': 541, 'OG5_175845': 577, 'OG5_147083': 462, 'OG5_163725': 160, 'OG5_163721': 490, 'OG5_156636': 305, 'OG5_156635': 463, 'OG5_147081': 2587, 'OG5_133337': 536, 'OG5_147086': 291, 'OG5_133236': 748, 'OG5_133725': 493, 'OG5_133234': 304, 'OG5_133232': 601, 'OG5_133230': 243, 'OG5_133231': 281, 'OG5_133728': 597, 'OG5_133238': 423, 'OG5_133239': 649, 'OG5_127181': 349, 'OG5_127180': 403, 'OG5_127183': 1000, 'OG5_127182': 529, 'OG5_127187': 267, 'OG5_127186': 581, 'OG5_145289': 450, 'OG5_127188': 576, 'OG5_137408': 266, 'OG5_149527': 359, 'OG5_160288': 447, 'OG5_163095': 260, 'OG5_135769': 248, 'OG5_135766': 435, 'OG5_135765': 272, 'OG5_135762': 1087, 'OG5_135763': 131, 'OG5_135760': 353, 'OG5_128737': 358, 'OG5_150363': 109, 'OG5_150362': 348, 'OG5_126588': 633, 'OG5_126589': 1246, 'OG5_150367': 476, 'OG5_149728': 175, 'OG5_150365': 334, 'OG5_150364': 262, 'OG5_126582': 482, 'OG5_126583': 311, 'OG5_150369': 328, 'OG5_149726': 538, 'OG5_126587': 183, 'OG5_149723': 469, 'OG5_149890': 552, 'OG5_141530': 439, 'OG5_128989': 460, 'OG5_141532': 380, 'OG5_184704': 296, 'OG5_128638': 708, 'OG5_128639': 398, 'OG5_128636': 272, 'OG5_128637': 1402, 'OG5_128634': 315, 'OG5_128635': 276, 'OG5_128632': 351, 'OG5_128633': 561, 'OG5_128630': 184, 'OG5_128631': 486, 'OG5_142840': 528, 'OG5_142842': 647, 'OG5_136083': 193, 'OG5_129589': 332, 'OG5_129588': 422, 'OG5_129587': 1028, 'OG5_129586': 290, 'OG5_129585': 359, 'OG5_129584': 277, 'OG5_129582': 923, 'OG5_129580': 292, 'OG5_140623': 314, 'OG5_149862': 633, 'OG5_140620': 321, 'OG5_140626': 583, 'OG5_145022': 184, 'OG5_155859': 375, 'OG5_155854': 524, 'OG5_145020': 317, 'OG5_158571': 355, 'OG5_128180': 421, 'OG5_128181': 970, 'OG5_128182': 635, 'OG5_128183': 217, 'OG5_128184': 379, 'OG5_128185': 372, 'OG5_128186': 151, 'OG5_128187': 488, 'OG5_128188': 315, 'OG5_145026': 486, 'OG5_134557': 475, 'OG5_145027': 117, 'OG5_129763': 484, 'OG5_129762': 352, 'OG5_129761': 331, 'OG5_129760': 653, 'OG5_129767': 117, 'OG5_129766': 218, 'OG5_129765': 310, 'OG5_129764': 274, 'OG5_135182': 534, 'OG5_135183': 486, 'OG5_129769': 1621, 'OG5_129768': 779, 'OG5_135186': 338, 'OG5_149860': 182, 'OG5_155407': 384, 'OG5_135185': 375, 'OG5_126979': 495, 'OG5_126978': 241, 'OG5_128656': 574, 'OG5_126973': 681, 'OG5_126972': 584, 'OG5_126971': 224, 'OG5_126970': 198, 'OG5_126977': 534, 'OG5_145028': 545, 'OG5_126975': 655, 'OG5_126974': 436, 'OG5_141398': 557, 'OG5_131648': 394, 'OG5_131645': 466, 'OG5_131644': 631, 'OG5_131647': 441, 'OG5_131646': 702, 'OG5_131641': 216, 'OG5_131640': 80, 'OG5_131643': 346, 'OG5_131642': 567, 'OG5_139091': 261, 'OG5_128657': 495, 'OG5_169909': 222, 'OG5_134555': 474, 'OG5_135982': 308, 'OG5_149620': 266, 'OG5_135980': 519, 'OG5_177023': 288, 'OG5_135984': 690, 'OG5_138270': 288, 'OG5_135989': 653, 'OG5_128650': 542, 'OG5_153263': 823, 'OG5_146704': 211, 'OG5_150260': 569, 'OG5_149867': 684, 'OG5_159313': 297, 'OG5_146709': 126, 'OG5_134553': 587, 'OG5_149629': 485} - - self_OGLenDB = {} - seqs_to_toss = [] - too_long, too_short = 0, 0 - - ## Small changes in this section for Auden (ought to work now) - ## Lists -> Dictionaries and some data curation steps - - inFasta = {i.description:str(i.seq) for i in SeqIO.parse(NTD_file,'fasta')} - - for k,v in inFasta.items(): - OG5 = 'OG5_'+k.split('_OG5_')[-1].split('_')[0] - if len(v) >= 4.5*OGLenDB[OG5]: - seqs_to_toss.append(k) - too_long+= 1 - - prepped_NTD = [i for i in inFasta if i not in seqs_to_toss] - - print (color.BOLD+'Removing Abnormally Short (70% length) OR Long (200% length)'\ - +color.PURPLE+' ORFs'+color.END+color.BOLD+'\ncompared to typical '+color.ORANGE+'Gene '\ - 'Family '+color.END+color.BOLD+'member length for: '+color.CYAN+args.file_prefix+'\n\n'+color.END) - - ## toss those sequences from the sequence dictonary (less headache) - for crap_seq in seqs_to_toss: - del inFasta[crap_seq] - - for k, v in inFasta.items(): - self_OGLenDB.setdefault(k.split('OG5_')[-1].split('_')[0],[]).append(len(v)) - - self_OGLenDB_Final = {k:sum(v)/len(v) for k, v in self_OGLenDB.items()} - - good_NTD_data = {k:v for k, v in inFasta.items() if 0.7*self_OGLenDB_Final[k.split('OG5_')[-1].split('_')[0]] <= len(v) - <= 2*self_OGLenDB_Final[k.split('OG5_')[-1].split('_')[0]]} - - good_AA_data = {i.description:str(i.seq) for i in SeqIO.parse(AA_file,'fasta') if i.description in good_NTD_data.keys()} - - good_TSV_data = [i for i in open(cat_folder+'/SpreadSheets/'+args.file_prefix+'_Concatenated.allOGCleanresults.tsv')\ - .read().split('\n') if i != '' and i.split('\t')[0] in good_NTD_data.keys()] - - renamed_TSV_data = [i.split('\t')[0]+'_Trans1\t'+'\t'.join(i.split('\t')[1:]) for i in good_TSV_data] - - - with open(proc_folder+args.file_prefix+'_Filtered.Final.NTD.ORF.fasta','w+') as w: - for k,v in good_NTD_data.items(): - w.write('>'+k+'_Trans1\n'+v+'\n') - - with open(proc_folder+args.file_prefix+'_Filtered.Final.AA.ORF.fasta','w+') as x: - for k, v in good_AA_data.items(): - x.write('>'+k+'_Trans1\n'+v+'\n') - - with open(proc_folder+'/SpreadSheets/'+args.file_prefix+'_Filtered.Final.allOGCleanresults.tsv','w+') as y: - y.write('\n'.join(renamed_TSV_data)) - - -########################################################################################## -###--------------------- Cleans up the Folder and Moves Final Files -------------------### -########################################################################################## - -def clean_up(args): - - for i in args.file_listNTD: - os.system('mv ' + i + ' ' + args.all_output_folder + args.file_prefix + '/Original/') - os.system('mv ' + i.replace('NTD.ORF.fasta','AA.ORF.fasta') + ' ' + args.all_output_folder + args.file_prefix + '/Original/') - os.system('mv ' + i.split('named')[0]+'named*allOGCleanresults.tsv ' + args.all_output_folder + args.file_prefix + '/Original/SpreadSheets/') - - -########################################################################################### -###-------------------------------- Next Script Message --------------------------------### -########################################################################################### - -def next_script(): - - print(color.BOLD+'\nNext Script is: '+color.GREEN+'6b_update_cov_post_removepartials.py\n\n'+color.END) - - -########################################################################################## -###------------------- Checks Command Line Arguments and Calls Steps ------------------### -########################################################################################## - -def main(): - - diamond_path = check_diamond_path() - - args = check_args() - - prep_folders(args) - - merge_relevant_data(args) - - self_BLAST_out = self_blast(args, diamond_path) - - evaluation = check_Self_vs_Self(self_BLAST_out) - - if evaluation != 'empty': - NTD_names = filter_NTD_data(args) - update_tsv(args, NTD_names) - else: - no_partials_present(args) - - clean_up(args) - - next_script() - -main() diff --git a/PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py b/PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py deleted file mode 100644 index 828d591..0000000 --- a/PTL1/Transcriptomes/Scripts/6b_update_cov_post_removepartials.py +++ /dev/null @@ -1,81 +0,0 @@ -#!/usr/bin/python -from __future__ import print_function - -__author__ = "Jean-David Grattepanche" -__version__ = "2, August 28, 2017" -__email__ = "jeandavid.grattepanche@gmail.com" - - -import sys -import os -import re -import time -import string -import os.path -from Bio import SeqIO -from sys import argv - - -def Addcoverage(code): - seqfolder = code - all_output_folder = '/'.join(code.split('/')[:-1]) - code = code.split('/')[-1] - - covupd = {} - for seqcoll in open(seqfolder + '/' + code + '_SeqPairsAbove98.txt','r'): - CL = 0 - for transc in seqcoll.split('\t'): - if CL == 0: - reftrans = ('_').join(transc.split('_')[1:]) - coverage = int(transc.split('Cov')[1].split('_')[0]) - Length = int(transc.split('Len')[1].split('_')[0]) - CL += coverage * Length - covupd[reftrans] = CL - - if os.path.isdir(seqfolder + '/Updated_Coverage/') != True: - os.system('mkdir ' + seqfolder + '/Updated_Coverage/') - if os.path.isdir(seqfolder + '/Updated_Coverage/SpreadSheets/') != True: - os.system('mkdir ' + seqfolder + '/Updated_Coverage/SpreadSheets/') - - for spreadsh in os.listdir(seqfolder + '/Processed/SpreadSheets/'): - if spreadsh.endswith('.tsv'): - outtsvtokeep = open(seqfolder + '/Updated_Coverage/SpreadSheets/' + spreadsh.split('Final')[0] + 'UC.Final' + spreadsh.split('Final')[1],'w+') - for row in open(seqfolder + '/Processed/SpreadSheets/'+ spreadsh, 'r'): - if row.split('_Trans')[0] in covupd: - newcov2= covupd[row.split('_Trans')[0]] / int(row.split('_Len')[1].split('_')[0]) - outtsvtokeep.write(row.split('Cov')[0]+'Cov'+str(newcov2)+'_OG5' +row.split('OG5')[1].split('_Trans')[0] +'\t' +('\t').join(row.split('\t')[1:])) - else: - if 'Trans' in row: - outtsvtokeep.write(row.split('_Trans')[0]+ '\t' +('\t').join(row.split('\t')[1:])) - else: - outtsvtokeep.write(row) - outtsvtokeep.close() - - for seqfile in os.listdir(seqfolder + '/Processed'): - if seqfile.endswith('.fasta'): - outseqtokeep = open(seqfolder + '/Updated_Coverage/' + seqfile.split('Final')[0] + 'UC.Final' + seqfile.split('Final')[1],'w+') - for Seq in SeqIO.parse(seqfolder + '/Processed/' + seqfile ,'fasta'): - if Seq.description.split('_Trans')[0] not in covupd: - outseqtokeep.write('>'+Seq.description.split('_Trans')[0]+ '\n'+str(Seq.seq) +'\n') - else: - newcov= covupd[Seq.description.split('_Trans')[0]] / int(Seq.description.split('_Len')[1].split('_')[0]) - outseqtokeep.write('>'+Seq.description.split('Cov')[0]+'Cov'+str(newcov)+'_OG5' +Seq.description.split('OG5')[1].split('_Trans')[0]+ '\n'+str(Seq.seq) +'\n') - outseqtokeep.close() - - if os.path.isdir(all_output_folder + '/ToRename') != True: - os.system('mkdir ' + all_output_folder + '/ToRename') - - os.system('cp ' + seqfolder + '/Updated_Coverage/*fasta ' + all_output_folder + '/ToRename/') - os.system('cp ' + seqfolder + '/Updated_Coverage/SpreadSheets/*tsv ' + all_output_folder + '/ToRename/') - - -def main(): - script, code = argv - Addcoverage(code) -main() - - - - - - diff --git a/PTL1/Transcriptomes/Scripts/7_FinalizeName.py b/PTL1/Transcriptomes/Scripts/7_FinalizeName.py deleted file mode 100644 index 677a836..0000000 --- a/PTL1/Transcriptomes/Scripts/7_FinalizeName.py +++ /dev/null @@ -1,398 +0,0 @@ -#!/usr/bin/env python3.5 - -##__Updated__: 31_08_2017 -##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com -##__Usage__: python 6_FilterPartials.py --help - -################################################################################################## -## This script is intended to rename the outputs of the FilterPartials script ## -## to a given 10-character that is used in the Katz lab Phylogenomic Tree building methods ## -## ## -## Prior to r`ning this script, ensure the following: ## -## ## -## 1. You have assembled your transcriptome and COPIED the 'assembly' file ## -## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ## -## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ## -## 3. Removed SSU/LSU sequences from your Fasta File ## -## 4. Classified your sequences as Strongly Prokaryotic/Eukaryotic or Undetermined ## -## 5. Classified the Non-Strongly Prokaryotic sequences into OGs ## -## 6. You either know (or have inferred) the genetic code of the organism ## -## 7. You have translated the sequences and checked for the data in the RemovePartials folder ## -## 8. Partial sequences have been removed from the transcriptomic data sets ## -## ## -## COMMAND Example Below ## -## Extra Notes at Bottom of Script ## -## ## -## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ## -## ## -## Next Script(s) to Run: ## -## NONE! You're FINISHED! :D ## -## ## -################################################################################################## - -import argparse, os, sys -from argparse import RawTextHelpFormatter,SUPPRESS - -#----------------------- Solely to Make Print Statements Colorful -----------------------# - -class color: - PURPLE = '\033[95m' - CYAN = '\033[96m' - DARKCYAN = '\033[36m' - ORANGE = '\033[38;5;214m' - BLUE = '\033[94m' - GREEN = '\033[92m' - YELLOW = '\033[93m' - RED = '\033[91m' - BOLD = '\033[1m' - UNDERLINE = '\033[4m' - END = '\033[0m' - - -#------------------------------- Main Functions of Script --------------------------------# - -########################################################################################### -###--------------------- Parses and Checks Command-Line Arguments ----------------------### -########################################################################################### - -def check_args(): - - parser = argparse.ArgumentParser(description= - color.BOLD + '\n\nThis script is intended to '+color.RED+'Rename '+color.END\ - +color.BOLD+'the core set of '+color.PURPLE+'ORFS\n'+color.END+color.BOLD+'with a valid '\ - +color.RED+'10-character code'+color.END+color.BOLD+' for use in the KatzLab\nPhylogenomic Pipeline'\ - +usage_msg(), usage=SUPPRESS, formatter_class=RawTextHelpFormatter) - - required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END) - - required_arg_group.add_argument('--input_file','-in', action='store', - help=color.BOLD+color.GREEN+' One of the Fasta files that is to be renamed\n'+color.END) - required_arg_group.add_argument('--name','-n', action='store', - help=color.BOLD+color.GREEN+' A valid 10-Character code for updating the data\n'+color.END) - - - optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END) - - optional_arg_group.add_argument('-author', action='store_true', - help=color.BOLD+color.GREEN+' Prints author contact information\n'+color.END) - - if len(sys.argv[1:]) == 0: - print (parser.description) - print ('\n') - sys.exit() - - args = parser.parse_args() - - quit_eval = return_more_info(args) - if quit_eval > 0: - print ('\n') - sys.exit() - - args.all_output_folder = '/'.join(args.input_file.split('/')[:-2]) - - if '.allOGCleanresults' in args.input_TSV: - args.out_XML = args.name+'_XX_'+args.input_TSV.split('/')[-1].replace('.allOGCleanresults.','.AA.ORF.')\ - .replace('.tsv','.fasta')+'_1e-10keepall_BlastOutall.oneHit' - else: - args.out_XML = args.name+'_XX_'+args.input_TSV.split('/')[-1].replace('_allOGCleanresults.','_AA.ORF.')\ - .replace('.tsv','.fasta')+'_1e-10keepall_BlastOutall.oneHit' - - args.file_prefix = args.input_file.split('/')[-1].split('_Filtered.Final')[0] - if 'fasta' in args.file_prefix: - args.file_prefix = args.name - - args.r2g_aa = args.all_output_folder + '/ReadyToGo/ReadyToGo_AA/' - args.r2g_ntd = args.all_output_folder + '/ReadyToGo/ReadyToGo_NTD/' - args.r2g_tsv = args.all_output_folder + '/ReadyToGo/ReadyToGo_TSV/' - args.r2g_xml = args.all_output_folder + '/ReadyToGo/ReadyToGo_XML/' - - - return args - - -########################################################################################### -###------------------------------- Script Usage Message --------------------------------### -########################################################################################### - -def usage_msg(): - return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 7_FinalizeName.py'\ - ' --input_file ../ToRename/Op_me_Xxma_Filtered.Final.AA.ORF.fasta --name Op_me_Xxma'+color.END) - - -########################################################################################## -###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------### -########################################################################################## - -def return_more_info(args): - - valid_args = 0 - - author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\ - ' maurerax@gmail.com\n\n'+color.END) - - if args.author == True: - print (author) - valid_args += 1 - - if args.input_file.endswith('AA.ORF.fasta'): - args.input_NTD = args.input_file.replace('AA.ORF.fasta','NTD.ORF.fasta') - args.input_AA = args.input_file -# args.input_TSV = ('/').join(args.input_file.split('/')[:-1])+'/SpreadSheets/'+args.input_file.split('/')[-1].replace('AA.ORF.fasta','allOGCleanresults.tsv') - args.input_TSV = args.input_file.replace('AA.ORF.fasta','allOGCleanresults.tsv') - - elif args.input_file.endswith('NTD.ORF.fasta'): - args.input_NTD = args.input_file - args.input_AA = args.input_file.replace('NTD.ORF.fasta','AA.ORF.fasta') -# args.input_TSV = ('/').join(args.input_file.split('/')[:-1])+'/SpreadSheets/'+args.input_file.split('/')[-1].replace('NTD.ORF.fasta','allOGCleanresults.tsv') - args.input_TSV = args.input_file.replace('AA.ORF.fasta','allOGCleanresults.tsv') - print(args.input_TSV) - - if os.path.isfile(args.input_NTD) != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Nucleotide '\ - 'Fasta file ('+color.DARKCYAN+args.input_NTD.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_args += 1 - - if os.path.isfile(args.input_AA) != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Protein '\ - 'Fasta file ('+color.DARKCYAN+args.input_AA.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_args += 1 - - if os.path.isfile(args.input_TSV) != True: - print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided TSV '\ - ' file ('+color.DARKCYAN+args.input_TSV.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\ - ' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END) - valid_args += 1 - - return valid_args - -########################################################################################### -###-------------------- Double Checks Format for 10-Character Code ---------------------### -########################################################################################### - -def check_code(args): - - check_name = args.name.split('_') - - if len(args.name) != 10: - print (color.BOLD+'\n\nNew Species Prefix is not 10 characters long\n\n') - print ('Three examples below:\n'+color.CYAN+'\n\tSr_ci_Cunc\n\n\tOp_me_Hsap\n\n\t'\ - 'Am_ar_Ehis\n\n'+color.END) - sys.exit() - - elif args.name.count('_') != 2: - print (color.BOLD+'\n\nCheck the format of your Species Prefix!\n\n') - print ('Three examples below:\n'+color.CYAN+'\n\tSr_ci_Cunc\n\n\tOp_me_Hsap\n\n\t'\ - 'Am_ar_Ehis\n\n'+color.END) - - sys.exit() - - if len(check_name[0]) == 2 and len(check_name[1]) == 2 and len(check_name[2]) == 4: - print (color.BOLD+"\n\nRenaming "+color.ORANGE+args.input_file.split('/')[-1]\ - .split('_Filtered')[0]+color.END+color.BOLD+"'s files with the following 10-character\n"\ - "code: "+color.CYAN+args.name+color.END+'\n') - else: - print (color.BOLD+'\n\nCheck the format of your Species Prefix!\n\n') - print ('Three examples below:\n'+color.CYAN+'\n\tSr_ci_Cunc\n\n\tOp_me_Hsap\n\n\t'\ - 'Am_ar_Ehis\n\n'+color.END) - sys.exit() - - -########################################################################################## -###------------------------- Creates Folders For Storing Data -------------------------### -########################################################################################## - -def prep_folders(args): - - - if os.path.isdir(args.all_output_folder + '/ReadyToGo/') != True: - os.system('mkdir ' + args.all_output_folder + '/ReadyToGo') - - - if os.path.isdir(args.r2g_ntd) != True: - os.system('mkdir ' + args.r2g_ntd) - if os.path.isdir(args.r2g_aa) != True: - os.system('mkdir ' + args.r2g_aa) - if os.path.isdir(args.r2g_tsv) != True: - os.system('mkdir ' + args.r2g_tsv) - if os.path.isdir(args.r2g_xml) != True: - os.system('mkdir ' + args.r2g_xml) - - if os.path.isdir(args.all_output_folder + '/' + args.file_prefix + '/Renamed') != True: - os.system('mkdir ' + args.all_output_folder + '/' + args.file_prefix + '/Renamed') - -########################################################################################### -###----------- Renames the NTD and AA CDSs with the Given 10-Character Code ------------### -########################################################################################### - -def rename_paralogs(args): - - home_folder = args.all_output_folder + '/' + args.file_prefix + '/Renamed/' - - print (color.BOLD+'\nRenaming Translated (Protein) '+color.PURPLE+'ORFs\n'+color.END) - renamed_Final_Prots = open(args.input_AA).read().replace('>','>'+args.name+'_XX_') - - print (color.BOLD+'\nRenaming Nucleotide '+color.PURPLE+'ORFs\n'+color.END) - renamed_Final_Nucs = open(args.input_NTD).read().replace('>','>'+args.name+'_XX_') - - - print (color.BOLD+'\nUpdating CDS Names in the Spreadsheet'+color.END) - if '\n\n' in open(args.input_TSV).read(): - renamed_Final_tsv = args.name+'_XX_'+open(args.input_TSV).read().rstrip('\n')\ - .replace('\n\n','\n'+args.name+'_XX_') - else: - renamed_Final_tsv = args.name+'_XX_'+open(args.input_TSV).read().rstrip('\n')\ - .replace('\n','\n'+args.name+'_XX_') - - with open(home_folder+args.name+'_XX_'+args.input_AA.split('/')[-1],'w+') as w: - w.write(renamed_Final_Prots) - - with open(home_folder+args.name+'_XX_'+args.input_NTD.split('/')[-1],'w+') as x: - x.write(renamed_Final_Nucs) - - - with open(home_folder+args.name+'_XX_'+args.input_TSV.split('/')[-1],'w+') as y: - y.write(renamed_Final_tsv) - - -########################################################################################### -###--------------------------------- Header/Tail Lines ---------------------------------### -########################################################################################### - -def header_tail(): - header = '\n\n'\ - '\n blastp\n BLASTP 2.2.29+\n'\ - ' 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.\n'\ - ' ../OGBlastDB/renamed_aa_seqs_OrthoMCL-5_12653.fasta\n Query_1\n' - - tail = '\n' - return header, tail - - -########################################################################################### -###------------------------------- TSV to XML Conversion -------------------------------### -########################################################################################### - -def convert_TSV_data(args): - - home_folder = args.all_output_folder + '/' + args.file_prefix + '/Renamed/' - - TSVforConvert = home_folder+args.name+'_XX_'+args.input_TSV.split('/')[-1] - - inTSV = [line.rstrip('\n') for line in open(TSVforConvert).readlines() if line != '\n'] - - iterations = [] - - for n in range(len(inTSV)): - if n == 0: - iterations.append(' '+inTSV[n].split('\t')[0]+'\n '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'\n'\ - ' \n \n BLOSUM62\n 1e-10\n'\ - ' 11\n 1\n F\n'\ - ' \n \n\n\n 1\n Query_1\n'\ - ' '+inTSV[n].split('\t')[0]+'\n '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'\n'\ - '\n\n 1\n Fake_Entry\n '+inTSV[n].split('\t')[1]+'\n Fake_Accession\n'\ - ' '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'\n \n \n 1\n 1234\n'\ - ' '+inTSV[n].split('\t')[-1]+'\n '+inTSV[n].split('\t')[-2]+'\n '+inTSV[n].split('\t')[-4]+'\n'\ - ' '+inTSV[n].split('\t')[-3]+'\n '+inTSV[n].split('\t')[-4]+'\n '+inTSV[n].split('\t')[-3]+'\n'\ - ' 0\n 0\n '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'\n'\ - ' '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'\n 0\n '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'\n'\ - ' \n \n \n \n \n\n'\ - '\n\n \n \n 379660\n 197499634\n'\ - ' 123\n 184705217500\n 0.041\n'\ - ' 0.267\n 0.14\n \n \n\n') - else: - iterations.append('\n '+str(n+1)+'\n Query_'+str(n+1)+'\n'\ - ' '+inTSV[n].split('\t')[0]+'\n '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'\n'\ - '\n\n 1\n Fake_Entry\n '+inTSV[n].split('\t')[1]+'\n Fake_Accession\n'\ - ' '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])+1))+'\n \n \n 1\n 1234\n'\ - ' '+inTSV[n].split('\t')[-1]+'\n '+inTSV[n].split('\t')[-2]+'\n '+inTSV[n].split('\t')[-4]+'\n'\ - ' '+inTSV[n].split('\t')[-3]+'\n '+inTSV[n].split('\t')[-4]+'\n '+inTSV[n].split('\t')[-3]+'\n'\ - ' 0\n 0\n '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'\n'\ - ' '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'\n 0\n '+str(abs(int(inTSV[n].split('\t')[-3])-int(inTSV[n].split('\t')[-4])))+'\n'\ - ' \n \n \n \n \n\n'\ - '\n\n \n \n 379660\n 197499634\n'\ - ' 123\n 184705217500\n 0.041\n'\ - ' 0.267\n 0.14\n \n \n\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() \ No newline at end of file diff --git a/PTL1/Transcriptomes/Scripts/wrapper.py b/PTL1/Transcriptomes/Scripts/wrapper.py deleted file mode 100644 index 4e6dddd..0000000 --- a/PTL1/Transcriptomes/Scripts/wrapper.py +++ /dev/null @@ -1,215 +0,0 @@ -#Dependencies -import os, sys, re -import shutil -import argparse - - -def get_args(): - - parser = argparse.ArgumentParser( - prog = 'PhyloToL v6.0 Part 1 for Transcriptomes', - description = "Updated January 19th, 2023 by Auden Cote-L'Heureux. Link to GitHub: https://github.com/AudenCote/PhyloToL_v6.0" - ) - - parser.add_argument('-s', '--script', default = -1, type = int, choices = { 1, 2, 3, 4, 5, 6, 7 }, help = 'Script to run if you are only running one script') - parser.add_argument('-1', '--first_script', default = -1, type = int, choices = { 1, 2, 3, 4, 5, 6 }, help = 'First script to run') - parser.add_argument('-2', '--last_script', default = -1, type = int, choices = { 2, 3, 4, 5, 6, 7 }, help = 'First script to run') - parser.add_argument('-a', '--assembled_transcripts', type = str, help = 'Path to a folder of assembled transcripts, assembled by rnaSPAdes. Each assembled transcript file name should start with a unique 10 digit code, and end in "_assembledTranscripts.fasta", E.g. Op_me_hsap_assembledTranscripts.fasta') - parser.add_argument('-o', '--output', default = '../', type = str, help = 'An "Output" folder will be created at this directory to contain all output files. By default this folder will be created at the parent directory of the Scripts folder') - parser.add_argument('-x', '--xplate_contam', action = 'store_true', help = 'Run cross-plate contamination removal (includes all files)') - parser.add_argument('-g', '--genetic_code', type = str, help = 'If all of your taxa use the same genetic code, you may enter it here (to be used in script 5). Otherwise, stop at script 4 and fill in "gcode_output.tsv" before running script 5') - parser.add_argument('-l', '--minlen', type = int, default = 200, help = 'Minimum transcript length') - parser.add_argument('-d', '--databases', type = str, default = '../Databases', help = 'Path to databases folder') - - return parser.parse_args() - - -#running the first script on all the bare files -def script_one(args, ten_digit_codes): - for file in os.listdir(args.assembled_transcripts): - if file[10:] == '_assembledTranscripts.fasta' and file[:10] in ten_digit_codes: - os.system('python 1a_ContigFiltStats.py --input_file ' + args.assembled_transcripts + '/' + file + ' --output_file ' + args.output + '/Output/' + file[:10] + ' --minLen ' + str(args.minlen) + ' --spades') #SPADES ARGUMENT?? - - if args.xplate_contam: - os.system('python 1b_XSpeciesContaminationAgnes.py ' + args.output + '/Output/XlaneBleeding ' + str(args.minlen)) - - -def script_two(args): - - for folder in os.listdir(args.output + '/Output/'): - if os.path.isfile(args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta'): - os.system('python 2a_remove_rRNA.py --input_file ' + args.output + '/Output/' + folder + '/SizeFiltered/' + folder + '.' + str(args.minlen) + 'bp.fasta --databases ' + args.databases) - - fasta_withBact = args.output + '/Output/' + folder + '/' + folder + '_NorRNAseqs.fasta' - os.system('python 2b_remove_Bact.py --input_file ' + fasta_withBact + ' --databases ' + args.databases) - -#NEED TO SORT OUT FILE NAMES ETC. BELOW HERE - -#running the third script -def script_three(args): - for folder in os.listdir(args.output + '/Output'): - if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.fasta'): - os.system('python 3_CountOGsDiamond.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.fasta --evalue 1e-15 --databases ' + args.databases) - - -#running the fourth script -def script_four(args): - for folder in os.listdir(args.output + '/Output'): - if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta'): - os.system('python 4_InFrameStopFreq.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --databases ' + args.databases) - - #putting all of the gcode summaries produced by fourth script into a spreadsheet - gcode_info = [] - for folder in os.listdir(args.output + '/Output'): - if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed_StopCodonStats.tsv'): - with open(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed_StopCodonStats.tsv') as f: - for line in f: - line_sep = line.split('\t') - if line_sep[0] == 'Summary': - gcode_info.append([folder, line_sep[6], line_sep[7], line_sep[8][:-1]]) - - with open(args.output + '/Output/gcode_output.tsv', 'w') as g: - g.writelines('10 Digit Code\tIn-frame TAG Density\tIn-frame TGA Density\tIn-frame TAA Density\tGenetic Code\n') - for row in gcode_info: - g.writelines(row[0] + '\t' + row[1] + '\t' + row[2] + '\t' + row[3] + '\n') - -#fifth script - to be run after the spreadsheet of the genetic code types (template with codon counts generated by script 4) is filled out -def script_five(args): - - valid_codes = ['universal', 'blepharisma', 'chilodonella', 'condylostoma', 'euplotes', 'peritrich', 'vorticella', 'mesodinium', 'tag', 'tga', 'taa', 'none'] - - if args.genetic_code != None and args.genetic_code.lower() in valid_codes: - for folder in os.listdir(args.output + '/Output'): - if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta'): - os.system('python 5_GCodeTranslate.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --genetic_code ' + args.genetic_code.lower()) - else: - lines = [line.strip().split('\t') for line in open(args.output + '/Output/gcode_output.tsv', 'r')] - with open(args.output + '/Output/gcode_output.tsv', 'r') as g: - for folder in os.listdir(args.output + '/Output'): - if os.path.isfile(args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta'): - for line in lines: - if line[0] == folder and line[-1].lower() in valid_codes: - os.system('python 5_GCodeTranslate.py --input_file ' + args.output + '/Output/' + folder + '/' + folder + '_WTA_EPU.Renamed.fasta --genetic_code ' + line[-1]) - elif line[-1].lower() not in valid_codes and line[-1] != 'Genetic Code': - print('\n' + line[-1] + ' is not a valid genetic code. Skipping taxon ' + folder + '.\n') - - -def script_six(args): - - prefixes = [] - for file in os.listdir(args.output + '/Output'): - if file[10:] in ('_WTA_EPU.Renamed_Universal_AA.ORF.fasta', '_WTA_EPU.Renamed_Universal_allOGCleanresults.tsv', '_WTA_EPU.Renamed_Universal_NTD.ORF.fasta'): - prefixes.append(file[:10]) - - unique_prefixes = list(dict.fromkeys(prefixes)) - - for prefix in unique_prefixes: - os.system('python 6_FilterPartials.py --file_prefix ' + args.output + '/Output/' + prefix) - - for prefix in unique_prefixes: - os.system('python 6b_update_cov_post_removepartials.py ' + args.output + '/Output/' + prefix) - - -def script_seven(args): - - for file in os.listdir(args.output + '/Output/ToRename'): - if '.AA.ORF.fasta' in file: - os.system('python 7_FinalizeName.py --input_file ' + args.output + '/Output/ToRename/' + file + ' --name ' + file[:10]) - - os.mkdir(args.output + '/Output/Intermediate') - - for file in os.listdir(args.output + '/Output'): - if file != 'ReadyToGo' and file != 'Intermediate': - os.system('mv ' + args.output + '/Output/' + file + ' ' + args.output + '/Output/Intermediate') - - - -if __name__ == "__main__": - - args = get_args() - - if (args.first_script == 1 or args.script == 1) and not os.path.isdir(args.assembled_transcripts): - print('\nERROR: If starting at the first script, a valid path to a folder of assembled transcript files (which must end in .fasta, .fa, or .fna) should be input using the --assembled_transcripts argument') - quit() - - if args.genetic_code == None and args.script == -1: - if args.first_script < 5 and args.last_script >= 5: - print('\nERROR: You cannot run script 5 without giving a genetic code! If all of the taxa in the run use the same genetic code, then use the --genetic_code argument (e.g. -g Universal). Otherwise, stop after script 4, fill out the spreadsheet called "gcode_translate.tsv," and then run scripts 5-7. If this does not make sense, please ask for help.') - quit() - - ten_digit_codes = [] - if args.first_script == 1 or args.script == 1: - for file in os.listdir(args.assembled_transcripts): - if file[10:] == '_assembledTranscripts.fasta': - ten_digit_codes.append(file[:10]) - else: - if not os.path.isdir(args.output + '/Output'): - print('\nERROR: A folder called "Output" is not found at the given output path. Enter the correct path for --output or start from script 1.\n') - quit() - - if(len(ten_digit_codes) > len(list(dict.fromkeys(ten_digit_codes)))): - print('\nERROR: Duplicate 10-digit codes are not allowed.\n') - quit() - - for code in ten_digit_codes: - for c, char in enumerate(code): - if (c != 2 and c != 5 and char not in 'qwertyuiopasdfghjklzxcvbnmQWERTYUIOPASDFGHJKLZXCVBNM1234567890') or ((c == 2 or c == 5) and char != '_'): - print('\nERROR: ' + code + ' is an invalid 10-digit code sample identifier. It must of the format Op_me_hsap (Homo sapiens for example). Please ask for help if this does not make sense.\n') - quit() - - if os.path.isdir(args.output + '/Output') and (args.first_script == 1 or args.script == 1): - print('\nERROR: An "Output" folder already exists at the given path. Please delete or rename this folder and try again.\n') - quit() - elif not os.path.isdir(args.output + '/Output'): - os.mkdir(args.output + '/Output') - - scripts = [0, script_one, script_two, script_three, script_four, script_five, script_six, script_seven] - - if args.script == -1: - if args.first_script < args.last_script: - for i in range(1 + args.last_script - args.first_script): - print('\nRunning script ' + str(i + args.first_script) + '...\n') - if i + args.first_script == 1: - if len(ten_digit_codes) == 0: - print('\nNo properly-named assembled transcripts files found.\n') - quit() - else: - scripts[i + args.first_script](args, ten_digit_codes) - else: - scripts[i + args.first_script](args) - else: - print('\nERROR: Invalid script combination: the first script must be less than the last script. If you want to use only once script, use the --script argument.\n') - quit() - else: - if args.script == 1: - if len(ten_digit_codes) == 0: - print('\nNo properly-named assembled transcripts files found.\n') - quit() - else: - scripts[args.script](args, ten_digit_codes) - else: - scripts[args.script](args) - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/PTL1/Transcriptomes/Scripts/wrapper_submit.sh b/PTL1/Transcriptomes/Scripts/wrapper_submit.sh deleted file mode 100644 index 58874ee..0000000 --- a/PTL1/Transcriptomes/Scripts/wrapper_submit.sh +++ /dev/null @@ -1,23 +0,0 @@ -#!/bin/bash -# -#SBATCH --job-name=PTL1 -#SBATCH --output=PTL1.%j.out # Stdout (%j expands to jobId) -#SBATCH --nodes=1 -#SBATCH --ntasks=1 -#SBATCH --ntasks-per-node=64 ##change to number of srun when running multiple instances -#SBATCH --mem=160G -#SBATCH --mail-type=ALL -#SBATCH --mail-user=pleasedontemailauden@smith.edu - -module purge #Cleans up any loaded modules -module use /gridapps/modules/all #make sure module locations is loaded - -module load slurm -module load Biopython/1.75-foss-2019b-Python-3.7.4 -module load BLAST+ -module load DIAMOND/0.9.30-GCC-8.3.0 - -export PATH=$PATH:/Users/katzlab/scratch/katzlab/grid_phylotol_setup/programs/standard-RAxML-master -export PATH=$PATH:/Users/katzlab/scratch/katzlab/grid_vsearch_setup/vsearch-2.15.1-linux-x86_64/bin - -python wrapper.py --first_script 1 --last_script 7 -a ../TestData --xplate_contam --genetic_code Universal --databases ../Databases --evalue 1e-5 \ No newline at end of file