# Last updated 8/18/2017
# Authors: Xyrus Maurer-Alcala

# This script is intended to identify and isolate SSU/LSU sequences by BLASTn-ing
# all length-filtered assembled transcripts against a reference database. It then
# writes these sequences into a separate file, removing them from the remainder
# of the sequences that will go forwards for gene family assignment. This script
# should be in Part 1 of the EukPhylo pipeline using the script wrapper.py.

# You must run Script 1a before this step. Optionally, you may also have run Script 1b.
# Before running this script, ensure that you have a properly formatted rRNA reference
# BLAST database in the Databases/db_BvsE/SSULSUdb folder; it is relatively narrow in scope 
# and could be easily replaced or updated to better capture a user's target taxa

#Dependencies
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)

###########################################################################################
###-------------------------------- 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)
 	 	
	clean_up(args)
 
	next_script(args)

main()