# Last updated Sept 2023
# Authors: Xyrus Maurer-Alcala and Auden Cote-L'Heureux

# This script classifies assembled transcripts into gene families by
# similarity-searching using Diamond against a reference database of
# gene families. We provide the Hook database on the GitHub, but this
# may be replaced with a custom reference database by REPLACING the
# .dmnd and .fasta files in the Databases/db_OG folder. This script
# is intended to be run as part of the EukPhylo Part 1 pipeline using
# the script wrapper.py.
								

import argparse, os, sys, re
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','-g', action='store',
	help=color.BOLD+color.GREEN+"Path to fasta file with Hook sequences"+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

	ogdb_count = 0
	for file in os.listdir(args.databases + '/db_OG'):
		if file.endswith('.dmnd'):
			ogdb_count += 1

	if ogdb_count == 0:
		print (color.BOLD+color.RED+'\nError:'+color.END+color.BOLD+' Cannot find the '\
		'Diamond formatted '+color.ORANGE+'Gene Family databases!\n\n'+color.END+color.BOLD+\
		'Ensure that they 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
	elif ogdb_count > 1:
		print('\nMultiple OG databases found. Please only provide 1 database in the db_OG folder.\n')
		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/'
	db = [file for file in os.listdir(args.databases + '/db_OG') if file.endswith('.dmnd')][0]

	print (color.BOLD + '\n\n"BLAST"-ing against OG database using DIAMOND: ' + color.DARKCYAN + db + color.END + '\n\n')
			
	OG_diamond_cmd = diamond_path + ' blastx -q ' + args.input_file + ' -d ' + args.databases + '/db_OG/' + db + ' --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 = { }
	for line in keep:
		try:
			og_number = re.split('OG.{1}_', line.split('\t')[1])[1][:6]
			og_prefix = line.split('\t')[1].split(og_number)[-2][-4:]
			og = og_prefix + og_number

			keep_dict.update({ re.split('_OG.{1}_', line.split('\t')[0])[0]  : re.split('_OG.{1}_', line.split('\t')[0])[0] + '_' + og_prefix + line.split('\t')[1].split('_')[-1] })
		except IndexError:
			pass

	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)

##########################################################################################
###--------------------- 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)

	clean_up(args)

	next_script(args)

main()