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Delete PTL1/Transcriptomes/Scripts/2b_remove_Bact.py
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#!/usr/bin/env python3.5
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##__Updated__: 18_08_2017
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##__Author__: Xyrus Maurer-Alcala; maurerax@gmail.com
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##__Usage__: python 2b_remove_Bact.py --help
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##########################################################################################
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## This script is intended to identify and isolate SSU/LSU sequences ##
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## Prior to running this script, ensure the following: ##
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## ##
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## 1. You have assembled your transcriptome and COPIED the 'assembly' file ##
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## (contigs.fasta, or scaffolds.fasta) to the PostAssembly Folder ##
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## 2. Removed small sequences (usually sequences < 300bp) with ContigFilterPlusStats.py ##
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## 3. Have the Databases set up correctly (e.g. with BLAST or Diamond) and in their ##
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## respective folders! See the manual if you need help ##
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## 4. Run removeSSU.py on your Fasta file ##
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## ##
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## COMMAND Example Below ##
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## ##
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## E-mail Xyrus (author) for help if needed: maurerax@gmail.com ##
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## ##
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## Next Script(s) to Run: ##
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## 3_CountOGsDiamond.py ##
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## ##
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##########################################################################################
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import argparse, os, sys
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from argparse import RawTextHelpFormatter,SUPPRESS
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from distutils import spawn
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from Bio import SeqIO
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#------------------------------ Colors For Print Statements ------------------------------#
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class color:
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PURPLE = '\033[95m'
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CYAN = '\033[96m'
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DARKCYAN = '\033[36m'
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ORANGE = '\033[38;5;214m'
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BLUE = '\033[94m'
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GREEN = '\033[92m'
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YELLOW = '\033[93m'
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RED = '\033[91m'
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BOLD = '\033[1m'
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UNDERLINE = '\033[4m'
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END = '\033[0m'
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#------------------------------- Main Functions of Script --------------------------------#
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###########################################################################################
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###---------------------------- UPDATE DIAMOND PATH BELOW! -----------------------------###
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###########################################################################################
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## IF Diamond is IN YOUR PATH then no updating is needed...
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def check_diamond_path():
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diamond_path = ''
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if diamond_path == '':
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diamond_path = spawn.find_executable("diamond")
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#diamond_path = '/path/to/diamond'
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else:
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pass
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if diamond_path == None:
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print (color.BOLD + '\n\nPlease open this script and check that you have included'\
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+' the PATH to the'+color.BLUE+' "Diamond" '+color.END+color.BOLD+'executable.\n\n'+color.END)
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print (color.BOLD+color.BLUE+'LOOK FOR:\n\n'+color.RED\
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+'#------------------------------ UPDATE DIAMOND PATH BELOW! -------------------------------#'\
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+color.BLUE+'\n\nThis is somewhere around lines 50 - 80...\n\n'+color.END)
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sys.exit()
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else:
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pass
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return diamond_path
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###########################################################################################
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###--------------------- Parses and Checks Command-Line Arguments ----------------------###
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###########################################################################################
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def check_args():
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parser = argparse.ArgumentParser(description=
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color.BOLD + '\nThis script will categorize Contigs as'+color.ORANGE+' STRONGLY '+color.END\
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+color.BOLD+color.RED+'Eukaryotic \nOR Prokaryotic'+color.END+color.BOLD+' using a set of Proteins'\
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' from diverse\n'+color.ORANGE+'Eukaryotes, Bacteria and Archaea'+color.END\
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+color.BOLD+'.'+color.END+usage_msg(), usage=SUPPRESS,formatter_class=RawTextHelpFormatter)
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required_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Required Options'+color.END)
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required_arg_group.add_argument('--input_file','-in', action='store',
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help=color.BOLD+color.GREEN+'Fasta file of Nucleotide sequences (with rRNAs removed)'+color.END)
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required_arg_group.add_argument('--databases','-d', action='store',
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help=color.BOLD+color.GREEN+"Path to databases"+color.END)
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optional_arg_group = parser.add_argument_group(color.ORANGE+color.BOLD+'Options'+color.END)
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optional_arg_group.add_argument('-author', action='store_true',
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help=color.BOLD+color.GREEN+' Print author contact information\n'+color.END)
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if len(sys.argv[1:]) == 0:
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print (parser.description)
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print ('\n')
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sys.exit()
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args = parser.parse_args()
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quit_eval = return_more_info(args)
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if quit_eval > 0:
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sys.exit()
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return args
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###########################################################################################
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###------------------------------- Script Usage Message --------------------------------###
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###########################################################################################
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def usage_msg():
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return (color.BOLD+color.RED+'\n\nExample usage:'+color.CYAN+' python 2b_remove_Bact.py --input_file'\
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' ../Op_me_Xxma/Op_me_Xxma_NorRNAseqs.fasta'+color.END)
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##########################################################################################
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###-------- Storage for LARGE (Annoying) Print Statements for Flagged Options ---------###
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##########################################################################################
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def return_more_info(args):
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valid_arg = 0
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author = (color.BOLD+color.ORANGE+'\n\n\tQuestions/Comments? Email Xyrus (author) at'\
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' maurerax@gmail.com\n\n'+color.END)
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if args.author == True:
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print (author)
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valid_arg += 1
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print(args.input_file)
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if args.input_file != None:
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if os.path.isfile(args.input_file) != False:
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if args.input_file.split('/')[-1] not in os.listdir('/'.join(args.input_file.split('/')[:-1])):
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\
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'('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
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' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
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valid_arg += 1
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elif args.input_file.endswith('NorRNAseqs.fasta') != True:
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print (color.BOLD+'\n\nInvalid Fasta File! Only Fasta Files that were processed'\
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' with '+color.GREEN+'2a_remove_rRNA.py '+color.END+color.BOLD+'are valid\n\n'\
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'However, to bypass that issue, Fasta Files MUST end with '+color.CYAN+\
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'"NorRNAseqs.fas"\n\n'+color.END)
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valid_arg += 1
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else:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' The provided Fasta file '\
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'('+color.DARKCYAN+args.input_file.split('/')[-1]+color.END+color.BOLD+')\ndoes not'\
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' exist or is incorrectly formatted.\n\nDouble-check then try again!\n\n'+color.END)
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valid_arg += 1
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if os.path.isdir(args.databases + '/db_BvsE') != True:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
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+color.ORANGE+'db_BvsE Folder!\n\n'+color.END+color.BOLD+'Ensure that this folder '\
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'can be found in the main '+color.ORANGE+'Databases Folder'+color.END+color.BOLD\
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+'\n\nThen try once again.')
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valid_arg += 1
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elif os.path.isfile(args.databases + '/db_BvsE/eukout.dmnd') != True:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
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'Diamond formatted '+color.ORANGE+'Eukaryotic Protein database!\n\n'+color.END+color.BOLD+\
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'Ensure that it can be found in the '+color.ORANGE+'db_BvsE folder'+color.END+\
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color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\
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color.END+color.BOLD+'\n\nThen try once again.'+color.END)
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elif os.path.isfile(args.databases + '/db_BvsE/micout.dmnd') != True:
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print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
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'Diamond formatted '+color.ORANGE+'Bacterial/Archaeal Protein database!\n\n'+color.END+color.BOLD+\
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'Ensure that it can be found in the '+color.ORANGE+'db_BvsE folder'+color.END+\
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color.BOLD+',\nwhich can be found in the main '+color.ORANGE+'Databases Folder'+\
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color.END+color.BOLD+'\n\nThen try once again.'+color.END)
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valid_arg += 1
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return valid_arg
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###########################################################################################
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###--------------------------- Does the Inital Folder Prep -----------------------------###
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###########################################################################################
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def prep_folders(args):
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BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/'
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if os.path.isdir(BvE_folder) != True:
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os.system('mkdir '+BvE_folder)
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###########################################################################################
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###---------------- Runs Diamond on Bact and Euk small RefSeq Databases ----------------###
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###########################################################################################
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def ublast_BvE(args, diamond_path):
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BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/'
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mic_output = args.input_file.split('/')[-1]+'micresults.'
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euk_output = args.input_file.split('/')[-1]+'eukresults.'
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print(color.BOLD+'\n\n"BLAST"-ing against PROK database using DIAMOND: ' + color.DARKCYAN + 'micout.dmnd' + color.END + '\n\n')
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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'
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os.system(Prok_diamond_cmd)
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print(color.BOLD+'\n\n"BLAST"-ing against EUK database using DIAMOND: ' + color.DARKCYAN + 'eukout.dmnd' + color.END + '\n\n')
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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'
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os.system(Euk_diamond_cmd)
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###########################################################################################
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###---------------- Compares Bacterial and Euk Hits for Classification -----------------###
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###########################################################################################
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def compare_hits(args):
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BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/'
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EukDict = {}
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ProkDict = {}
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CompDict = {}
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inFasta = [seq_rec for seq_rec in SeqIO.parse(args.input_file,'fasta')]
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for seq_rec in inFasta:
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EukDict[seq_rec.description] = ''
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ProkDict[seq_rec.description] = ''
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CompDict[seq_rec.description] = []
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inEukHits = [i for i in open(BvE_folder + 'alleukresults.tsv').readlines()]
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inEukHits.sort(key=lambda x: (float(x.split('\t')[-2]), -int(x.split('\t')[3])))
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inProkHits = [i for i in open(BvE_folder + 'allmicresults.tsv').readlines()]
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inProkHits.sort(key=lambda x: (float(x.split('\t')[-2]), -int(x.split('\t')[3])))
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for i in inEukHits:
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if EukDict[i.split('\t')[0]] == '':
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EukDict[i.split('\t')[0]] = float(i.split('\t')[-2])
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for i in inProkHits:
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if ProkDict[i.split('\t')[0]] == '':
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ProkDict[i.split('\t')[0]] = float(i.split('\t')[-2])
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for k in CompDict.keys():
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if EukDict[k] != '':
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CompDict[k].append(EukDict[k])
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else:
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CompDict[k].append('no hit')
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if ProkDict[k] != '':
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CompDict[k].append(ProkDict[k])
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else:
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CompDict[k].append('no hit')
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for k, v in CompDict.items():
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### Contigs lacking STRONG Eukaryotic OR Prokaryotic Hits
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if v[0] == 'no hit' and v[1] == 'no hit':
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CompDict[k].append('UNDETERMINED')
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### Contigs lacking STRONG Eukaryotic with a Prokaryotic Hit
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elif v[0] != 'no hit' and v[1] == 'no hit':
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CompDict[k].append('EUKARYOTIC')
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### Contigs with a Eukaryotic but without a Prokaryotic Hit
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elif v[0] == 'no hit' and v[1] != 'no hit':
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CompDict[k].append('PROKARYOTIC')
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### Uses Basic math to determine if contigs with are MORE Eukaryotic than Prokaryotic
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else:
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try:
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prok_euk_ratio = float(v[1])/float(v[0])
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euk_prok_ratio = float(v[0])/float(v[1])
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if prok_euk_ratio >= 100:
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CompDict[k].append('EUKARYOTIC')
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elif euk_prok_ratio >= 1000:
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CompDict[k].append('PROKARYOTIC')
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else:
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CompDict[k].append('UNDETERMINED')
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except:
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CompDict[k].append('divide by zero')
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with open(BvE_folder + 'comparisons.txt','w+') as w:
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for k, v in CompDict.items():
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w.write(k+':'+':'.join([str(i) for i in v])+'\n')
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BvE_folder = '/'.join(args.input_file.split('/')[:-1]) + '/BvE/'
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BvE_output_base = BvE_folder+args.input_file.split('/')[-1].split('.fas')[0]
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### Gathers the sequences and categorizes them
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Euk_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'EUKARYOTIC'), key=lambda x: -int(len(x.seq)))
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Prok_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'PROKARYOTIC'), key=lambda x: -int(len(x.seq)))
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Und_Fasta = sorted((seq_rec for seq_rec in inFasta if CompDict[seq_rec.description][-1] == 'UNDETERMINED'), key=lambda x: -int(len(x.seq)))
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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)))
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### Writes out all of the categorized sequences
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with open(args.input_file.split('NorRNA')[0] + 'WTA_EPU.fasta', 'w') as epu:
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with open(BvE_output_base+'.Not_Bact.fasta','w+') as nb:
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for euk_seq in Euk_Fasta:
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nb.write('>' + euk_seq.description + '\n' + str(euk_seq.seq) + '\n')
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epu.write('>' + euk_seq.description + '_E' + '\n' + str(euk_seq.seq) + '\n')
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with open(BvE_output_base+'.Bact_Hit.fasta','w+') as pr:
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for prok_seq in Prok_Fasta:
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pr.write('>' + prok_seq.description + '\n' + str(prok_seq.seq) + '\n')
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epu.write('>' + prok_seq.description + '_P' + '\n' + str(prok_seq.seq) + '\n')
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||||||
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()
|
|
||||||
Loading…
x
Reference in New Issue
Block a user