mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-27 21:40:24 +08:00
Delete PTL1/Transcriptomes/Scripts/2a_remove_rRNA.py
This commit is contained in:
Auden Cote-L'Heureux
GitHub
parent
3e01100304
commit
b6f439e7d6
@ -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()
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
Loading…
x
Reference in New Issue
Block a user