#!/opt/conda/conda-bld/vibrant_1586040355013/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/python
# Author: Kristopher Kieft, UW-Madison

# VIBRANT v1.2.1
# Virus Identification By iteRative ANnoTation
# Release date: March 13 2020

# Usage: $ python3 VIBRANT_run.py -i <input_file> [options]

############################### Imports  #######################################
import warnings
warnings.filterwarnings("ignore")
import sys
from Bio.SeqIO.FastaIO import SimpleFastaParser
from datetime import date
import datetime
import argparse
import subprocess
import math
import time
import logging
import pandas as pd
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import os
import sklearn
from sklearn.decomposition import PCA
import math
import matplotlib.patches as mpatches
from matplotlib.lines import Line2D

vibrant_path = str(os.getenv("VIBRANT_DATA_PATH"))
working_path = str(os.getcwd())

starting_time = time.time()
start_time = str(datetime.datetime.now().time()).rsplit(".",1)[0]

vibrant = argparse.ArgumentParser(description='Usage: VIBRANT_run.py -i <input_file> [options].\n VIBRANT identifies bacterial and archaeal viruses (phages) from assembled metagenomic scaffolds or whole genomes, including the excision of integrated proviruses. VIBRANT also performs curation of identified viral scaffolds, estimation of viral genome completeness and analysis of viral metabolic capabilities.')
vibrant.add_argument('--version', action='version', version='VIBRANT v1.2.1')

####### Required
vibrant.add_argument('-i', type=str, nargs=1, required=True, help='input fasta file')
####### Optional
vibrant.add_argument('-f', type=str, nargs=1, default='nucl', choices=['prot','nucl'], help='format of input [default="nucl"]')
vibrant.add_argument('-folder', type=str, nargs=1, default=str(working_path)+"/", help="path to deposit output folder and temporary files, will create if doesn't exist [default= working directory]")
vibrant.add_argument('-t', type=str, nargs=1, default='1', help='number of parallel VIBRANT runs, each occupies 1 CPU [default=1, max of 1 CPU per scaffold]')
vibrant.add_argument('-l', type=str, nargs=1, default='1000', help='length in basepairs to limit input sequences [default=1000, can increase but not decrease]')
vibrant.add_argument('-o', type=str, nargs=1, default='4', help='number of ORFs per scaffold to limit input sequences [default=4, can increase but not decrease]')
vibrant.add_argument('-virome', action='store_true', help='use this setting if dataset is known to be comprised mainly of viruses. More sensitive to viruses, less sensitive to false identifications [default=off]')
vibrant.add_argument('-no_plot', action='store_true', help='suppress the generation of summary plots [default=off]')
vibrant.add_argument('-d', type=str, nargs=1, default=str(vibrant_path) + '/databases/', help='path to original "databases" directory that contains .HMM files (if moved from default location)')
vibrant.add_argument('-m', type=str, nargs=1, default=str(vibrant_path) + '/files/', help='path to original "files" directory that contains .tsv and model files (if moved from default location)')

args = vibrant.parse_args()

if type(args.f) == str:
	format = args.f
else:
	format = "".join(args.f[0])
if args.folder == str(working_path)+'/':
	out_folder = args.folder
elif args.folder != str(working_path)+'/':
	out_folder = args.folder[0]
	if str(out_folder[-1]) != "/":
		out_folder += "/"
if args.virome == False:
	virome = ''
elif args.virome == True:
	virome = ' -virome'
suppress = args.no_plot

if str(args.d) == str(vibrant_path) + '/databases/':
	databases = str(args.d)
else:
	databases = str(args.d[0])
	if databases[-1] != '/':
		databases += '/'
if str(args.m) == str(vibrant_path) + '/files/':
	files = str(args.m)
else:
	files = str(args.m[0])
	if files[-1] != '/':
		files += '/'
if args.l == '1000':
	lim_low = args.l
if args.l != '1000':
	lim_low = args.l[0]
if args.t == '1':
	threads = int(args.t)
if args.t != '1':
	threads = int(args.t[0])
if args.o == '4':
	orf_low = args.o
if args.o != '4':
	orf_low = args.o[0]
try:
	filename = str(args.i[0].rsplit('/')[-1])
	filepath = str(args.i[0].rsplit('/')[0])
except Exception:
	filename = str(args.i[0])

base = str(filename.rsplit(".",1)[0])
if not os.path.exists(str(out_folder)):
	subprocess.run('mkdir ' + str(out_folder) + ' 2>/dev/null', shell=True)
	subprocess.run('mkdir ' + str(out_folder) + 'VIBRANT_' + base + ' 2>/dev/null', shell=True)
elif os.path.exists(str(out_folder)):
	subprocess.run('mkdir ' + str(out_folder) + 'VIBRANT_' + base + ' 2>/dev/null', shell=True)

logging.basicConfig(filename=str(out_folder)+'VIBRANT_log_run_' + base + '.log', level=logging.INFO, format='%(message)s')

try:
	if not os.path.exists(databases + 'KEGG_profiles_prokaryotes.HMM.h3f'):
		logging.info("VIBRANT error: could not identify KEGG HMM files in database directory. Please run VIBRANT_setup.py.")
		exit()
	if not os.path.exists(databases + 'Pfam-A_v32.HMM.h3f'):
		logging.info("VIBRANT error: could not identify Pfam HMM files in database directory. Please run VIBRANT_setup.py.")
		exit()
	if not os.path.exists(databases + 'VOGDB94_phage.HMM.h3f'):
		logging.info("VIBRANT error: could not identify VOG HMM files in database directory. Please run VIBRANT_setup.py.")
		exit()
	if not os.path.exists(files + 'VIBRANT_categories.tsv'):
		logging.info("VIBRANT error: could not identify VIBRANT_categories.tsv in files directory.")
		exit()
	if not os.path.exists(files + 'VIBRANT_AMGs.tsv'):
		logging.info("VIBRANT error: could not identify VIBRANT_AMGs.tsv in files directory.")
		exit()
	if not os.path.exists(files + 'VIBRANT_names.tsv'):
		logging.info("VIBRANT error: could not identify VIBRANT_names.tsv in files directory.")
		exit()
	if not os.path.exists(files + 'VIBRANT_machine_model.sav'):
		logging.info("VIBRANT error: could not identify VIBRANT_machine_model.sav in files directory.")
		exit()

	#######
	if int(orf_low) < 4 or int(lim_low) < 1000:
		logging.info("VIBRANT error: minimum ORFs is 4 and minimum sequence length is 1kb. These variables can only increase. Exiting." + "\n")
		exit()
	command = ' -f ' + str(format) + ' -d ' + str(databases) + ' -m ' + str(files) + ' -l ' + str(lim_low) + ' -o ' + str(orf_low) + str(virome)
	subprocess.run("echo '' > " + str(out_folder)+base + "_four-orf-count.txt", shell=True)

	#######
	if format == "prot":
		input_sequences = []
		with open(str(args.i[0]),'r') as infile:
			with open(str(out_folder)+str(base)+'.parallel-runs.txt', 'w') as outfile:
				for name, seq in SimpleFastaParser(infile):
					if " # " not in name:
						subprocess.run('rm ' + str(out_folder)+str(base)+'.parallel-runs* 2>/dev/null', shell=True)
						subprocess.run('rm ' + str(out_folder)+str(base)+'_four-orf-count.txt 2>/dev/null', shell=True)
						logging.info("VIBRANT Error: either the wrong format (-f) was set or proteins are not in Prodigal format. Check input file (-i) and format (-f).")
						logging.info("See example data file 'Microviridae_ctch16_MH552510.2.faa' for Prodigal format.")
						exit()
					protein = name.split(" # ",1)[0]
					genome = protein.rsplit("_",1)[0]
					input_sequences.append(genome)
					outfile.write(str(genome) + '\n')

		subprocess.run('cat ' + str(out_folder)+str(base)+'.parallel-runs.txt | uniq -d > ' + str(out_folder)+str(base)+'.parallel-runs.temp', shell=True)
		listing = 'wc -l ' + str(out_folder)+str(base)+'.parallel-runs.temp'
		listing_shell = subprocess.check_output(listing, shell=True)
		listing1 = str(listing_shell.strip()).split("'")[1]
		sequences = str(listing1.split("\\n")[0].split(" ",1)[0])

	if format == "nucl":
		sequences = 0
		with open(str(args.i[0]),'r') as infile:
			with open(str(out_folder)+str(base)+'.parallel-runs.temp', 'w') as outfile:
				for name, seq in SimpleFastaParser(infile):
					outfile.write(str(name) + '\n')
					sequences += 1

	shuffle = 'sort -R ' + str(out_folder)+str(base)+'.parallel-runs.temp > ' + str(out_folder)+str(base)+'.parallel-runs.txt'
	s2 = subprocess.Popen(shuffle, shell=True)
	s2.wait()
	subprocess.Popen('rm ' + str(out_folder)+base + '.parallel-runs.temp', shell=True)
	time.sleep(0.1)

	lines = math.ceil(int(sequences)/int(threads))
	parallel = 'split -l ' + str(lines) + ' ' + str(out_folder)+str(base)+'.parallel-runs.txt' + ' ' + str(out_folder)+str(base)+'.parallel-runs_'
	subprocess.run(parallel, shell=True)
	time.sleep(0.1)

	move = 'for file in ' + str(out_folder)+str(base) + '.parallel-runs_*; do mv $file ${file}.txt; done'
	s1 = subprocess.Popen(move, shell=True)
	s1.wait()
	time.sleep(0.1)

	parallels = 'ls ' + str(out_folder)+str(base) + '.parallel-runs_*.txt'
	parallels_shell = subprocess.check_output(parallels, shell=True)
	parallels1 = str(parallels_shell.strip()).split("'")[1]
	parallels2 = parallels1.split("\\n")

	n = 0
	p_list = []
	while n < len(parallels2):
		if format == "nucl":
			execute = 'VIBRANT_extract_nucleotide.py ' + str(parallels2[n]) + " " + str(parallels2[n]).rsplit(".",1)[0] + ".fna " + str(args.i[0]) + " " + str(lim_low)
		elif format == "prot":
			execute = 'VIBRANT_extract_protein.py ' + str(parallels2[n]) + " " + str(parallels2[n]).rsplit(".",1)[0] + ".faa " + str(args.i[0])
		p = subprocess.Popen(execute, shell=True)
		p_list.append(p)
		n += 1

	for item in p_list:
		item.wait()
	time.sleep(0.1)

	if format == "nucl":
		try:
			listing = 'ls ' + str(out_folder)+str(base) + '.parallel-runs_*.fna 2>/dev/null'
			listing_shell = subprocess.check_output(listing, shell=True)
			listing1 = str(listing_shell.strip()).split("'")[1]
			listing2 = listing1.split("\\n")
		except Exception:
			subprocess.run('rm ' + str(out_folder)+str(base)+'.parallel-runs* 2>/dev/null', shell=True)
			subprocess.run('rm ' + str(out_folder)+str(base)+'_four-orf-count.txt 2>/dev/null', shell=True)
			logging.info('No phages found. There were either no scaffolds at least ' + str(lim_low) + 'bp or ' + str(orf_low) + ' ORFs (set minimum size), or the input file (-i) format (-f) was not FASTA nucleotide. Exiting.')
			exit()

	if format == "prot":
		try:
			listing = 'ls ' + str(out_folder)+str(base) + '.parallel-runs_*.faa  2>/dev/null'
			listing_shell = subprocess.check_output(listing, shell=True)
			listing1 = str(listing_shell.strip()).split("'")[1]
			listing2 = listing1.split("\\n")
		except Exception:
			subprocess.run('rm ' + str(out_folder)+str(base)+'.parallel-runs* 2>/dev/null', shell=True)
			subprocess.run('rm ' + str(out_folder)+str(base)+'_four-orf-count.txt 2>/dev/null', shell=True)
			logging.info("No phages found. There were either no scaffolds at least " + str(orf_low) + " ORFs (set minimum size) or VIBRANT never found any proteins. Verify input file (-i) format (-f) is FASTA protein. Exiting.")
			exit()

	remove = 'rm ' + str(out_folder)+str(base) + '.parallel-runs_*.txt'
	subprocess.run(remove, shell=True)
	time.sleep(0.1)

	n = 0
	p_list = []
	while n < len(listing2):
		execute = 'VIBRANT_annotation.py -x ' + str(out_folder) + ' -y ' + str(base) + ' -i ' + str(listing2[n]) + str(command)
		p = subprocess.Popen(execute, shell=True)
		p_list.append(p)
		n += 1

	for item in p_list:
		item.wait()
	time.sleep(0.1)

	try:
		grep = "grep -c '1' " + str(out_folder)+str(base) + "_four-orf-count.txt 2>/dev/null"
		grep_shell = subprocess.check_output(grep, shell=True)
		grep_out_count = str(grep_shell.strip()).split("'")[1]
		time.sleep(0.1)
	except Exception:
		logging.info('No phages found. There were no scaffolds at least ' + str(orf_low) + ' ORFs (set minimum size). Exiting.')
		subprocess.run('rm ' + str(out_folder)+str(base)+'.parallel-runs* 2>/dev/null', shell=True)
		subprocess.run('rm ' + str(out_folder)+str(base)+'_four-orf-count.txt 2>/dev/null', shell=True)
		exit()

	if format == "nucl":
		cat_combo_ffn = 'cat ' + str(out_folder)+base + '*parallel-runs*.phages_combined.ffn 1> ' + str(out_folder)+str(base) + '.phages_combined.ffn 2>/dev/null'
		subprocess.Popen(cat_combo_ffn, shell=True)
		cat_combo_fna = 'cat ' + str(out_folder)+base + '*parallel-runs*.phages_combined.fna 1> ' + str(out_folder)+str(base) + '.phages_combined.fna 2>/dev/null'
		subprocess.Popen(cat_combo_fna, shell=True)
		cat_lytic_ffn = 'cat ' + str(out_folder)+base + '*parallel-runs*.phages_lytic.ffn 1> ' + str(out_folder)+str(base) + '.phages_lytic.ffn 2>/dev/null'
		subprocess.Popen(cat_lytic_ffn, shell=True)
		cat_lytic_fna = 'cat ' + str(out_folder)+base + '*parallel-runs*.phages_lytic.fna 1> ' + str(out_folder)+str(base) + '.phages_lytic.fna 2>/dev/null'
		r1 = subprocess.Popen(cat_lytic_fna, shell=True)
		cat_lysogenic_ffn = 'cat ' + str(out_folder)+base + '*parallel-runs*.phages_lysogenic.ffn 1> ' + str(out_folder)+str(base) + '.phages_lysogenic.ffn 2>/dev/null'
		subprocess.Popen(cat_lysogenic_ffn, shell=True)
		cat_lysogenic_fna = 'cat ' + str(out_folder)+base + '*parallel-runs*.phages_lysogenic.fna 1> ' + str(out_folder)+str(base) + '.phages_lysogenic.fna 2>/dev/null'
		r2 = subprocess.Popen(cat_lysogenic_fna, shell=True)
		r1.wait()
		r2.wait()

	cat_combo_faa = 'cat ' + str(out_folder)+base + '*parallel-runs*.phages_combined.faa 1> ' + str(out_folder)+str(base) + '.phages_combined.faa 2>/dev/null'
	r3 = subprocess.Popen(cat_combo_faa, shell=True)
	cat_lytic_faa = 'cat ' + str(out_folder)+base + '*parallel-runs*.phages_lytic.faa 1> ' + str(out_folder)+str(base) + '.phages_lytic.faa 2>/dev/null'
	r4 = subprocess.Popen(cat_lytic_faa, shell=True)
	cat_lysogenic_faa = 'cat ' + str(out_folder)+base + '*parallel-runs*.phages_lysogenic.faa 1> ' + str(out_folder)+str(base) + '.phages_lysogenic.faa 2>/dev/null'
	r5 = subprocess.Popen(cat_lysogenic_faa, shell=True)
	r3.wait()
	r4.wait()
	r5.wait()
	time.sleep(0.1)

	if format == "nucl":
		db_dict_circ = {}
		circular_list = []
		with open(str(out_folder)+str(base) + '.phages_lysogenic.fna', 'r') as lysogenic_phages:
			with open(str(out_folder)+str(base) + '.phages_lytic.fna', 'r') as lytic_phages:
				with open(str(out_folder)+'VIBRANT_complete_circular_' + base + '.tsv', 'w') as circular_phages:
					for name, seq in SimpleFastaParser(lysogenic_phages):
						save = seq
						if "fragment" not in name:
							seq = list(seq)
							seq_start = "".join(seq[0:20])
							n = int(len(seq))-900
							while n <= len(seq):
								seq_end = "".join(seq[n:n+20])
								if str(seq_start) == str(seq_end):
									circular_phages.write(str(name) + '\t' + 'lysogenic' + '\t' + 'complete circular' + '\n')
									db_dict_circ.update({name:save})
									circular_list.append(name)
									n += 900
								else:
									n += 1
					for item, sequence in SimpleFastaParser(lytic_phages):
						save = sequence
						sequence = list(sequence)
						sequence_start = "".join(sequence[0:20])
						n = int(len(sequence))-900
						while n <= len(sequence):
							sequence_end = "".join(sequence[n:n+20])
							if str(sequence_start) == str(sequence_end):
								circular_phages.write(str(item) + '\t' + 'lytic' + '\t' + 'complete circular' + '\n')
								db_dict_circ.update({item:save})
								circular_list.append(item)
								n += 900
							else:
								n += 1
		with open(str(out_folder)+base + '.phages_circular.fna', 'w') as circ_fna:
			for item in db_dict_circ.keys():
				circ_fna.write(">" + str(item) + "\n" + db_dict_circ[item] + "\n")
		with open(str(out_folder)+'VIBRANT_complete_circular_' + base + '.tsv', 'r') as circular:
			circular_database = circular.read().replace('\n','\t').split('\t')

	subprocess.run('rm ' + str(out_folder)+base + '*parallel-runs*phages_*.faa 2>/dev/null', shell=True)
	subprocess.Popen('rm ' + str(out_folder)+base + '*parallel-runs*phages_*.ffn 2>/dev/null', shell=True)
	subprocess.Popen('rm ' + str(out_folder)+base + '*parallel-runs*phages_*.fna 2>/dev/null', shell=True)

	if format == 'nucl':
		cat_ffn = 'cat ' + str(out_folder)+base + '.parallel-runs_*.ffn > ' + str(out_folder)+base + '.prodigal.ffn 2>/dev/null'
		subprocess.Popen(cat_ffn, shell=True)
		cat_faa = 'cat ' + str(out_folder)+base + '.parallel-runs_*.faa > ' + str(out_folder)+base + '.prodigal.faa 2>/dev/null'
		subprocess.Popen(cat_faa, shell=True)
	cat_annotations = 'cat '+str(out_folder)+'VIBRANT_annotations*' + base + '* > '+str(out_folder)+'temp_VIBRANT_annotations_' + str(base) + '.txt 2>/dev/null'
	p6 = subprocess.Popen(cat_annotations, shell=True)
	cat_results = 'cat '+str(out_folder)+'VIBRANT_results*' + base + '* > '+str(out_folder)+'temp_VIBRANT_results_' + str(base) + '.txt 2>/dev/null'
	p7 = subprocess.Popen(cat_results, shell=True)
	cat_norm = 'cat '+str(out_folder)+'VIBRANT_normalized*' + base + '* > '+str(out_folder)+'temp_VIBRANT_normalized_' + str(base) + '.txt 2>/dev/null'
	p12 = subprocess.Popen(cat_norm, shell=True)
	cat_amg = 'cat '+str(out_folder)+'VIBRANT_AMGs*' + base + '* 1> '+str(out_folder)+'temp_VIBRANT_AMGs_' + str(base) + '.txt 2>/dev/null'
	p10 = subprocess.Popen(cat_amg, shell=True)
	cat_gb = 'cat '+str(out_folder)+'VIBRANT_genbank_table*' + base + '* 1> '+str(out_folder)+'temp_VIBRANT_genbank_table_' + str(base) + '.txt 2>/dev/null'
	p11 = subprocess.Popen(cat_gb, shell=True)
	cat_machine = 'cat '+str(out_folder)+'temp_VIBRANT_machine.*' + base + '* 1> '+str(out_folder)+'temp2_VIBRANT_machine_' + str(base) + '.txt 2>/dev/null'
	p8 = subprocess.Popen(cat_machine, shell=True)
	rm_unmod = 'rm '+str(out_folder)+'unmodified_VIBRANT_results*' + base + '* 2>/dev/null'
	p9 = subprocess.Popen(rm_unmod, shell=True)
	cat_quality = 'cat ' + str(out_folder)+base + '*genome_quality.out 1> '+str(out_folder)+'temp_VIBRANT_genome_quality_' + base + '.tsv 2>/dev/null'
	y11 = subprocess.Popen(cat_quality, shell=True)
	cat_names = 'cat ' + str(out_folder)+base + '.parallel-runs_*.phages_combined.out 1> ' + str(out_folder)+base + '.phages_combined.txt 2>/dev/null'
	y12 = subprocess.Popen(cat_names, shell=True)
	y11.wait()
	y12.wait()
	p6.wait()
	p7.wait()
	p8.wait()
	p9.wait()
	p10.wait()
	p11.wait()
	p12.wait()
	time.sleep(0.1)
	header_quality = 'echo "scaffold\ttype\tQuality" | cat - ' + str(out_folder)+'temp_VIBRANT_genome_quality_' + base + '.tsv 1> ' + str(out_folder)+'VIBRANT_genome_quality_' + base + '.tsv 2>/dev/null'
	p7 = subprocess.Popen(header_quality, shell=True)
	p7.wait()
	time.sleep(0.1)

	if format == "nucl":
		subprocess.run('mv '+str(out_folder)+'VIBRANT_genome_quality_' + base + '.tsv ' +str(out_folder)+'temp_VIBRANT_genome_quality_' + base + '.tsv', shell=True)
		subprocess.run('cat '+str(out_folder)+'temp_VIBRANT_genome_quality_' + base + '.tsv '+str(out_folder)+ 'VIBRANT_complete_circular_' + base + '.tsv > '+str(out_folder)+'VIBRANT_genome_quality_' + base + '.tsv', shell=True)

	subprocess.Popen('rm '+str(out_folder)+'VIBRANT_annotations*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'VIBRANT_results*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'VIBRANT_normalized*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'VIBRANT_AMG*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'VIBRANT_genbank_table*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'temp_VIBRANT_machine.*' + base + '* 2>/dev/null', shell=True)

	header_anno = 'echo "protein\tscaffold\tKO\tAMG\tKO name\tKO evalue\tKO score\tKO v-score\tPfam\tPfam name\tPfam evalue\tPfam score\tPfam v-score\tVOG\tVOG name\tVOG evalue\tVOG score\tVOG v-score" | cat - ' + str(out_folder)+'temp_VIBRANT_annotations_' + str(base) + '.txt > ' + str(out_folder)+'VIBRANT_annotations_' + str(base) + '.tsv'
	p1 = subprocess.Popen(header_anno, shell=True)
	header_results ='echo "scaffold\ttotal genes\tall KEGG\tKEGG v-score\tall Pfam\tPfam v-score\tall VOG\tVOG v-score\tKEGG int-rep\tKEGG zero\tPfam int-rep\tPfam zero\tVOG redoxin\tVOG rec-tran\tVOG int\tVOG RnR\tVOG DNA\tKEGG restriction check\tKEGG toxin check\tVOG special\tannotation check\tp_v check\tp_k check\tk_v check\tk check\tp check\tv check\th check" | cat - ' + str(out_folder)+'temp_VIBRANT_results_' + str(base) + '.txt > ' + str(out_folder)+'VIBRANT_summary_results_' + str(base) + '.tsv'
	p2 = subprocess.Popen(header_results, shell=True)
	header_norm ='echo "scaffold\ttotal genes\tall KEGG\tKEGG v-score\tall Pfam\tPfam v-score\tall VOG\tVOG v-score\tKEGG int-rep\tKEGG zero\tPfam int-rep\tPfam zero\tVOG redoxin\tVOG rec-tran\tVOG int\tVOG RnR\tVOG DNA\tKEGG restriction check\tKEGG toxin check\tVOG special\tannotation check\tp_v check\tp_k check\tk_v check\tk check\tp check\tv check\th check" | cat - ' + str(out_folder)+'temp_VIBRANT_normalized_' + str(base) + '.txt > ' + str(out_folder)+'VIBRANT_summary_normalized_' + str(base) + '.tsv'
	p7 = subprocess.Popen(header_norm, shell=True)
	header_amg = 'echo "protein\tscaffold\tAMG KO\tAMG KO name\tPfam\tPfam name" | cat - ' + str(out_folder)+'temp_VIBRANT_AMGs_' + str(base) + '.txt 1> ' + str(out_folder)+'VIBRANT_AMG_individuals_' + str(base) + '.tsv 2>/dev/null'
	p4 = subprocess.Popen(header_amg, shell=True)
	header_gb = 'echo "protein\tscaffold\taccession\tname" | cat - ' + str(out_folder)+'temp_VIBRANT_genbank_table_' + str(base) + '.txt 1> ' + str(out_folder)+'VIBRANT_genbank_table_' + str(base) + '.tsv 2>/dev/null'
	p6 = subprocess.Popen(header_gb, shell=True)
	for1 = 'for f in ' + str(out_folder)+base + '*parse.txt; do sed "1d" $f > ${f%.*}.out; done'
	p3 = subprocess.Popen(for1, shell=True)
	header_machine = 'echo "scaffold\tprediction" | cat - ' + str(out_folder)+'temp2_VIBRANT_machine_' + str(base) + '.txt 1> ' + str(out_folder)+'VIBRANT_machine_' + str(base) + '.tsv 2>/dev/null'
	p5 = subprocess.Popen(header_machine, shell=True)
	if format == "nucl":
		for2 = 'for f in ' + str(out_folder)+base + '*parallel-runs*temp; do sed "1d" $f 1> ${f%.*}.temp.gff 2>/dev/null; done'
		subprocess.run(for2, shell=True)
	p1.wait()
	p2.wait()
	p3.wait()
	p4.wait()
	p5.wait()
	p6.wait()
	p7.wait()
	time.sleep(0.1)

	subprocess.Popen('rm '+str(out_folder)+'temp_VIBRANT_annotations*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'temp_VIBRANT_results*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'temp_VIBRANT_normalized*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'temp2_VIBRANT_machine*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'temp_VIBRANT_AMGs_*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'temp_VIBRANT_genbank_table_*' + base + '* 2>/dev/null', shell=True)
	subprocess.Popen('rm '+str(out_folder)+'temp_VIBRANT_genome_quality_' + base + '.tsv 2>/dev/null', shell=True)
	subprocess.Popen(['mkdir', str(out_folder)+'VIBRANT_HMM_tables_unformatted_'+base])
	subprocess.Popen(['mkdir', str(out_folder)+'VIBRANT_HMM_tables_parsed_'+base])
	subprocess.Popen(['mkdir', str(out_folder)+'VIBRANT_phages_'+base])
	subprocess.Popen(['mkdir', str(out_folder)+'VIBRANT_results_'+base])
	kegg_cat = 'cat ' + str(out_folder)+base + '*KEGG.hmmtbl.parse.out 1> ' + str(out_folder)+base + '.KEGG_hmmtbl_parse.txt 2>/dev/null'
	x1 = subprocess.Popen(kegg_cat, shell=True)
	kegg_table = 'cat ' + str(out_folder)+base + '*KEGG.hmmtbl 1> ' + str(out_folder)+base + '_unformatted_KEGG.hmmtbl 2>/dev/null'
	y1 = subprocess.Popen(kegg_table, shell=True)
	pfam_cat = 'cat ' + str(out_folder)+base + '*Pfam.hmmtbl.parse.out 1> ' + str(out_folder)+base + '.Pfam_hmmtbl_parse.txt 2>/dev/null'
	x2 = subprocess.Popen(pfam_cat, shell=True)
	pfam_table = 'cat ' + str(out_folder)+base + '*Pfam.hmmtbl 1> ' + str(out_folder)+base + '_unformatted_Pfam.hmmtbl 2>/dev/null'
	y2 = subprocess.Popen(pfam_table, shell=True)
	vog_cat = 'cat ' + str(out_folder)+base + '*VOG.hmmtbl.parse.out 1> ' + str(out_folder)+base + '.VOG_hmmtbl_parse.txt 2>/dev/null'
	x3 = subprocess.Popen(vog_cat, shell=True)
	vog_table = 'cat ' + str(out_folder)+base + '*VOG.hmmtbl 1> ' + str(out_folder)+base + '_unformatted_VOG.hmmtbl 2>/dev/null'
	y3 = subprocess.Popen(vog_table, shell=True)
	x1.wait()
	x2.wait()
	x3.wait()
	y1.wait()
	y2.wait()
	y3.wait()
	time.sleep(0.1)

	move_parse = 'mv ' + str(out_folder)+base + '*_hmmtbl_parse.txt ' + str(out_folder)+'VIBRANT_HMM_tables_parsed_'+base + ' 2>/dev/null'
	x6 = subprocess.Popen(move_parse, shell=True)
	move_table = 'mv ' + str(out_folder)+base + '*_unformatted_*.hmmtbl ' + str(out_folder)+'VIBRANT_HMM_tables_unformatted_'+base + ' 2>/dev/null'
	y6 = subprocess.Popen(move_table, shell=True)
	x6.wait()
	y6.wait()
	time.sleep(0.1)

	for2 = 'for f in '+str(out_folder)+'VIBRANT_HMM_tables_parsed_' + base + '/*.txt; do echo "protein\tid\tevalue\tscore" | cat - $f > ${f%.*}.tsv; done'
	z1 = subprocess.Popen(for2, shell=True)
	z1.wait()
	rm_parsed = 'rm '+str(out_folder)+'VIBRANT_HMM_tables_parsed_' + base + '/*.txt 2>/dev/null'
	z2 = subprocess.Popen(rm_parsed, shell=True)
	z2.wait()
	time.sleep(0.1)

	rm_faa = 'rm ' + str(out_folder)+base + '*parallel-runs*faa 2>/dev/null'
	rm_fna = 'rm ' + str(out_folder)+base + '*parallel-runs*fna 2>/dev/null'
	rm_ffn = 'rm ' + str(out_folder)+base + '*parallel-runs*ffn 2>/dev/null'
	rm_list = 'rm ' + str(out_folder)+base + '*parallel-runs_*txt 2>/dev/null'
	rm_names = 'rm ' + str(out_folder)+base + '*parallel-runs_*out 2>/dev/null'
	rm_temp = 'rm ' + str(out_folder)+base + '*parallel-runs_*temp 2>/dev/null'
	subprocess.Popen(rm_faa, shell=True)
	subprocess.Popen(rm_fna, shell=True)
	subprocess.Popen(rm_ffn, shell=True)
	subprocess.Popen(rm_list, shell=True)
	subprocess.Popen(rm_temp, shell=True)
	subprocess.Popen(rm_names, shell=True)

	if format == "nucl":
		cat1_faa = "cat " + str(out_folder)+base + ".prodigal.faa | sed 's/$~&/ /g' 1> " + str(out_folder)+base + ".temp.faa 2>/dev/null"
		cat2_faa = "cat " + str(out_folder)+base + ".temp.faa | sed 's/^@%/\"/g' 1> " + str(out_folder)+base + ".prodigal.faa 2>/dev/null"
		rm1 = 'rm ' + str(out_folder)+base + '.prodigal.faa 2>/dev/null'
		subprocess.run(cat1_faa, shell=True)
		subprocess.run(rm1, shell=True)
		subprocess.run(cat2_faa, shell=True)
		subprocess.run("rm " + str(out_folder)+base + ".temp.faa 2>/dev/null", shell=True)
		time.sleep(0.1)
		cat1_ffn = "cat " + str(out_folder)+base + ".prodigal.ffn | sed 's/$~&/ /g' 1> " + str(out_folder)+base + ".temp.ffn 2>/dev/null"
		cat2_ffn = "cat " + str(out_folder)+base + ".temp.ffn | sed 's/^@%/\"/g' 1> " + str(out_folder)+base + ".prodigal.ffn 2>/dev/null"
		cat_gff = "cat " + str(out_folder)+base + "*temp.gff 1> " + str(out_folder)+base + ".all.gff 2>/dev/null"
		c2 = subprocess.Popen(cat1_ffn, shell=True)
		c7 = subprocess.Popen(cat_gff, shell=True)
		c2.wait()
		c7.wait()
		time.sleep(0.1)
		cat1_gff = "cat " + str(out_folder)+base + ".all.gff | sed 's/$~&/ /g' 1> " + str(out_folder)+base + ".temp.gff 2>/dev/null"
		cat2_gff = "cat " + str(out_folder)+base + ".temp.gff | sed 's/^@%/\"/g' 1> " + str(out_folder)+base + ".all.gff 2>/dev/null"
		c10 = subprocess.Popen(cat1_gff, shell=True)
		c11 = subprocess.Popen(cat2_gff, shell=True)
		c10.wait()
		c11.wait()
		time.sleep(0.1)
		rm2 = 'rm ' + str(out_folder)+base + '.prodigal.ffn 2>/dev/null'
		rm3 = 'rm ' + str(out_folder)+base + '*temp.gff'
		c6 = subprocess.Popen(rm2, shell=True)
		c8 = subprocess.Popen(rm3, shell=True)
		c6.wait()
		c8.wait()
		c4 = subprocess.Popen(cat2_ffn, shell=True)
		header_gff = 'echo "##gff-version  3" | cat - ' + str(out_folder)+base + '.all.gff 1> ' + str(out_folder)+base + '.prodigal.gff 2>/dev/null'
		c9 = subprocess.Popen(header_gff, shell=True)
		c4.wait()
		c9.wait()
		subprocess.Popen("rm " + str(out_folder)+base + ".temp.ffn 2>/dev/null", shell=True)
		subprocess.Popen("rm " + str(out_folder)+base + ".all.gff 2>/dev/null", shell=True)

	with open(str(out_folder)+'VIBRANT_summary_results_'+base+'.tsv') as results:
		out_phages = -1
		for line in results:
			out_phages += 1

	remove_run1 = str('rm ' + str(out_folder)+base + '.parallel-runs*hmmtbl 2>/dev/null')
	subprocess.Popen(remove_run1, shell=True)
	remove_run2 = str('rm ' + str(out_folder)+base + '.parallel-runs*hmmtbl.parse* 2>/dev/null')
	subprocess.Popen(remove_run2, shell=True)

	genbank_database = []
	master_coords = []
	with open(str(out_folder)+base + '.phages_combined.faa', 'r') as fasta:
		with open(str(out_folder)+'VIBRANT_integrated_prophage_coordinates_' + base + '.tsv', 'w') as coord_file:
			coord_file.write("scaffold\tfragment\tprotein start\tprotein stop\tprotein length\tnucleotide start\tnucleotide stop\tnucleotide length\n")
			for name, seq in SimpleFastaParser(fasta):
				sequence = ''
				if len(seq) > 44:
					sequence += str(seq[0:44])+"\n"
					for group in range(44,len(seq),58):
						sequence += '					 ' + str(seq[group:group+58]) + '\n'
					sequence = sequence.rstrip("\n")
				elif len(seq) <= 44:
					sequence = seq
				protein = str(name.split("\t")[0])
				genome = str(protein.rsplit("_",1)[0])
				location = str(name.split("\t")[1])
				strand = str(name.split("\t")[2])
				accession = str(name.split("\t")[3])
				name_split = str(name.split("\t")[4])
				genbank_database.extend((protein,genome,location,strand,accession,name_split,str(sequence)))
				#
				if "_fragment_" in name:
					rename = name.split("\t",1)[0]
					coords = name.split("\t",2)[1]
					master_coords.append(str(rename.rsplit("_",1)[0]))
					master_coords.append(str(coords.split("..")[0])[1:])
					master_coords.append(str(coords.split("..")[1])[0:-1])
					master_coords.append(str(rename.rsplit("_",1)[1]))
			master_coords.append('')
			genbank_database.extend(('',''))

			n = 0
			first = True
			while master_coords[n] != '':
				if master_coords[n] == master_coords[n+4]:
					if first == True:
						start = master_coords[n+1]
						prot = master_coords[n+3]
					first = False
				else:
					coord_file.write(str(master_coords[n]).rsplit("_",2)[0] + "\t" + str(master_coords[n]) + "\t" + str(prot) + "\t" + str(master_coords[n+3]) + "\t" + str(int(master_coords[n+3])-int(prot)+1) + "\t" + str(start) + "\t" + str(master_coords[n+2]) + "\t" + str(int(master_coords[n+2])-int(start)+1) + "\n")
					first = True
				n += 4

	if format == "nucl":
		length_database = {}
		sequence_database = {}
		length_list = []
		db_dict_circ = {}
		with open(str(out_folder)+base + '.phages_combined.fna', 'r') as fasta:
			for name, seq in SimpleFastaParser(fasta):
				length_database.update({name:len(seq)})
				length_list.append(int(len(seq)))
				n = 0
				count = 0
				i = 61
				spaces_database = '			   '
				sequence = '		 1 '
				for group in range(0,len(seq),10):
					sequence += str(seq[group:group+10]) + ' '
					count += 1
					if count == 6:
						length = list(str(i))
						size = 9-len(length)
						spaces = str(spaces_database[0:size+1])
						sequence += '\n' + str(spaces) + str(i) + ' '
						i += 60
						count = 0
				sequence_database.update({name:sequence})
				db_dict_circ.update({name:seq})

		with open(str(out_folder)+base + '.phages_combined.temp.gbk', 'w') as genbank:
			n = 1
			check = False
			while n < len(genbank_database)-1:
				if check == False:
					start_site = int(str(genbank_database[n+1][1:-1]).split(".",1)[0])-1
					if str(genbank_database[n]) in circular_database:
						form = "circular"
					else:
						form = "linear"
					genbank.write('//\nLOCUS	   ' + str(genbank_database[n]) + '				 ' + str(length_database[genbank_database[n]]) + ' bp	DNA	 ' + str(form) + '   VRL ' + str(date.today()) + '\nDEFINITION  ' + str(genbank_database[n]) + '.\nFEATURES			 Location/Qualifiers\n	 source		  /organism="' + str(genbank_database[n]) + '"\n')
					check = True
				if "fragment" in str(genbank_database[n]):
					if check == True:
						location_A = int(str(genbank_database[n+1][1:-1]).split("..")[0])-start_site
						location_B = int(str(genbank_database[n+1][1:-1]).split("..")[1])-start_site
						location = str(location_A) + ".." + str(location_B)
						if str(genbank_database[n+2]) == "-1":
							if str(genbank_database[n]) == str(genbank_database[n+7]):
								genbank.write('	 CDS			 complement(' + str(location) + ')' + '\n					 /locus_tag="' + str(genbank_database[n-1]) + '"\n					 /protein_id="' + str(genbank_database[n+3]) + '"\n					 /product="' + str(genbank_database[n+4]) + '"\n					 /translation="' + str(genbank_database[n+5]) + '"\n')
							if str(genbank_database[n]) != str(genbank_database[n+7]):
								genbank.write('	 CDS			 complement(' + str(location) + ')' + '\n					 /locus_tag="' + str(genbank_database[n-1]) + '"\n					 /protein_id="' + str(genbank_database[n+3]) + '"\n					 /product="' + str(genbank_database[n+4]) + '"\n					 /translation="' + str(genbank_database[n+5]) + '"\n')
								genbank.write('ORIGIN\n' + str(sequence_database[genbank_database[n]]) + '\n')
								check = False
								start_site = 0
						elif str(genbank_database[n+2]) == "1":
							if str(genbank_database[n]) == str(genbank_database[n+7]):
								genbank.write('	 CDS			 ' + str(location) + '\n					 /locus_tag="' + str(genbank_database[n-1]) + '"\n					 /protein_id="' + str(genbank_database[n+3]) + '"\n					 /product="' + str(genbank_database[n+4]) + '"\n					 /translation="' + str(genbank_database[n+5]) + '"\n')
							if str(genbank_database[n]) != str(genbank_database[n+7]):
								genbank.write('	 CDS			 ' + str(location) + '\n					 /locus_tag="' + str(genbank_database[n-1]) + '"\n					 /protein_id="' + str(genbank_database[n+3]) + '"\n					 /product="' + str(genbank_database[n+4]) + '"\n					 /translation="' + str(genbank_database[n+5]) + '"\n')
								genbank.write('ORIGIN\n' + str(sequence_database[genbank_database[n]]) + '\n')
								check = False
								start_site = 0
				elif "fragment" not in str(genbank_database[n]):
					if check == True:
						if str(genbank_database[n+2]) == "-1":
							if str(genbank_database[n]) == str(genbank_database[n+7]):
								genbank.write('	 CDS			 complement' + str(genbank_database[n+1]) + '\n					 /locus_tag="' + str(genbank_database[n-1]) + '"\n					 /protein_id="' + str(genbank_database[n+3]) + '"\n					 /product="' + str(genbank_database[n+4]) + '"\n					 /translation="' + str(genbank_database[n+5]) + '"\n')
							if str(genbank_database[n]) != str(genbank_database[n+7]):
								genbank.write('	 CDS			 complement' + str(genbank_database[n+1]) + '\n					 /locus_tag="' + str(genbank_database[n-1]) + '"\n					 /protein_id="' + str(genbank_database[n+3]) + '"\n					 /product="' + str(genbank_database[n+4]) + '"\n					 /translation="' + str(genbank_database[n+5]) + '"\n')
								genbank.write('ORIGIN\n' + str(sequence_database[genbank_database[n]]) + '\n')
								check = False
						elif str(genbank_database[n+2]) == "1":
							if str(genbank_database[n]) == str(genbank_database[n+7]):
								genbank.write('	 CDS			 ' + str(genbank_database[n+1][1:-1]) + '\n					 /locus_tag="' + str(genbank_database[n-1]) + '"\n					 /protein_id="' + str(genbank_database[n+3]) + '"\n					 /product="' + str(genbank_database[n+4]) + '"\n					 /translation="' + str(genbank_database[n+5]) + '"\n')
							if str(genbank_database[n]) != str(genbank_database[n+7]):
								genbank.write('	 CDS			 ' + str(genbank_database[n+1][1:-1]) + '\n					 /locus_tag="' + str(genbank_database[n-1]) + '"\n					 /protein_id="' + str(genbank_database[n+3]) + '"\n					 /product="' + str(genbank_database[n+4]) + '"\n					 /translation="' + str(genbank_database[n+5]) + '"\n')
								genbank.write('ORIGIN\n' + str(sequence_database[genbank_database[n]]) + '\n')
								check = False
				n += 7


	with open(str(files)+'VIBRANT_names.tsv', 'r') as names:
		names = names.read().replace('\n','\t').split('\t')
		names_dict = {}
		n = 0
		while n < len(names):
			names_dict.update({names[n]:names[n+1]})
			n += 2

	with open(str(files)+'VIBRANT_KEGG_pathways_summary.tsv', 'r') as summary:
		with open(str(out_folder)+'VIBRANT_AMG_individuals_' + str(base) + '.tsv', 'r') as annotations:
			with open(str(out_folder)+'VIBRANT_AMG_counts_' + str(base) + '.tsv', 'w') as count_file:
				with open(str(out_folder)+'VIBRANT_AMG_pathways_' + str(base) + '.tsv', 'w') as path_file:
					count_file.write('AMG count\tAMG KO\tAMG KO name\n')
					summary = summary.read().replace('\n','\t').split('\t')
					annotations = pd.read_csv(annotations, sep='\t', header=0)
					annotations = pd.DataFrame(annotations)
					temp_anno = list(annotations['AMG KO'])
					kegg_anno = []
					count_dict = {}
					for item in temp_anno:
						if str(item).startswith('K'):
							kegg_anno.append(item)
					kegg_set = list(set(kegg_anno))
					for item in kegg_set:
						count = kegg_anno.count(item)
						count_dict.update({str(item):str(count)})
						count_file.write(str(count) + "\t" + str(item) + "\t" + str(names_dict[item]) + "\n")

					n = 4
					sum_count = 0
					present = []
					path_file.write("KEGG Entry\tMetabolism\tPathway\tTotal AMGs\tPresent AMG KOs\n")
					while n < len(summary):
						KOs = summary[n+3].split("~")
						for item in KOs:
							if item in count_dict.keys():
								sum_count += int(count_dict[item])
								present.append(item)
						if sum_count > 0:
							path_file.write(str(summary[n]) + "\t" + str(summary[n+1]) + "\t" + str(summary[n+2]) + "\t" + str(sum_count) + "\t" + str(",".join(present)) + "\n")
						sum_count = 0
						present = []
						n += 4

	sed_gb = 'sed "1d" ' + str(out_folder)+base + '.phages_combined.temp.gbk 1> ' + str(out_folder)+base + '.phages_combined.gbk 2>/dev/null'
	y12 = subprocess.Popen(sed_gb, shell=True)
	y12.wait()
	subprocess.run('rm ' + str(out_folder)+base + '.phages_combined.temp.gbk 2>/dev/null',shell=True)


	####### Visualization
	if suppress == False and int(out_phages) > 0:
		plt.figure()
		carbohydrate = ['map00010', 'map00020', 'map00030', 'map00040', 'map00051', 'map00052', 'map00053', 'map00500', 'map00520', 'map00620', 'map00630', 'map00640', 'map00650', 'map00660', 'map00562']
		energy = ['map00190', 'map00195', 'map00196', 'map00710', 'map00720', 'map00680', 'map00910', 'map00920']
		lipid = ['map00061', 'map00062', 'map00071', 'map00072', 'map00073', 'map00100', 'map00120', 'map00121', 'map00140', 'map00561', 'map00564', 'map00565', 'map00600', 'map00590', 'map00591', 'map00592', 'map01040']
		nucleotide = ['map00230', 'map00240']
		amino = ['map00250', 'map00260', 'map00270', 'map00280', 'map00290', 'map00300', 'map00310', 'map00220', 'map00330', 'map00340', 'map00350', 'map00360', 'map00380', 'map00400', 'map00410', 'map00430', 'map00440', 'map00450', 'map00460', 'map00471', 'map00472', 'map00473', 'map00480']
		glycan = ['map00510', 'map00513', 'map00512', 'map00515', 'map00514', 'map00532', 'map00534', 'map00533', 'map00531', 'map00563', 'map00601', 'map00603', 'map00604', 'map00540', 'map00550', 'map00511', 'map00571', 'map00572']
		cofactor = ['map00730', 'map00740', 'map00750', 'map00760', 'map00770', 'map00780', 'map00785', 'map00790', 'map00670', 'map00830', 'map00860', 'map00130']
		terpenoid = ['map00900', 'map00902', 'map00909', 'map00904', 'map00906', 'map00905', 'map00981', 'map00908', 'map00903', 'map00281', 'map01052', 'map00522', 'map01051', 'map01059', 'map01056', 'map01057', 'map00253', 'map00523', 'map01054', 'map01053', 'map01055']
		secondary = ['map00940', 'map00945', 'map00941', 'map00944', 'map00942', 'map00943', 'map00901', 'map00403', 'map00950', 'map00960', 'map01058', 'map00232', 'map00965', 'map00966', 'map00402', 'map00311', 'map00332', 'map00261', 'map00331', 'map00521', 'map00524', 'map00525', 'map00231', 'map00401', 'map00404', 'map00405', 'map00333', 'map00254', 'map00998', 'map00999']
		aromatic = ['map00362', 'map00627', 'map00364', 'map00625', 'map00361', 'map00623', 'map00622', 'map00633', 'map00642', 'map00643', 'map00791', 'map00930', 'map00363', 'map00621', 'map00626', 'map00624', 'map00365', 'map00984', 'map00980', 'map00982', 'map00983']
		relay = ['map04122']

		with open(str(out_folder)+'VIBRANT_AMG_pathways_' + str(base) + '.tsv', 'r') as pathways:
			pathways = pathways.read().replace('\n','\t').split('\t')
			if len(pathways) > 6:
				carbohydrate_count = 0
				energy_count = 0
				lipid_count = 0
				nucleotide_count = 0
				amino_count = 0
				glycan_count = 0
				cofactor_count = 0
				terpenoid_count = 0
				secondary_count = 0
				aromatic_count = 0
				relay_count = 0

				n = 5
				while n < len(pathways):
					if str(pathways[n]) in carbohydrate:
						carbohydrate_count += int(pathways[n+3])
					elif str(pathways[n]) in energy:
						energy_count += int(pathways[n+3])
					elif str(pathways[n]) in lipid:
						lipid_count += int(pathways[n+3])
					elif str(pathways[n]) in nucleotide:
						nucleotide_count += int(pathways[n+3])
					elif str(pathways[n]) in amino:
						amino_count += int(pathways[n+3])
					elif str(pathways[n]) in glycan:
						glycan_count += int(pathways[n+3])
					elif str(pathways[n]) in cofactor:
						cofactor_count += int(pathways[n+3])
					elif str(pathways[n]) in terpenoid:
						terpenoid_count += int(pathways[n+3])
					elif str(pathways[n]) in secondary:
						secondary_count += int(pathways[n+3])
					elif str(pathways[n]) in aromatic:
						aromatic_count += int(pathways[n+3])
					elif str(pathways[n]) in relay:
						relay_count += int(pathways[n+3])
					n += 5

				dataframe = pd.DataFrame({"AMG Metabolism Category": ['carbohydrates', 'energy metabolism', 'lipids', 'nucleotides', 'amino acids', 'glycan', 'cofactors/vitamins', 'terpenoids/polyketides', 'secondary metabolites', 'aromatic compounds', 'sulfur relay'], "Number of AMGs": [carbohydrate_count, energy_count, lipid_count, nucleotide_count, amino_count, glycan_count, cofactor_count, terpenoid_count, secondary_count, aromatic_count, relay_count]})
				figure = sns.barplot(x="AMG Metabolism Category", y="Number of AMGs", data=dataframe, palette=sns.color_palette("pastel"), edgecolor=sns.color_palette("bright"))
				sns.set(style="white")
				plt.ylim(0, None)
				plt.xticks(rotation=90)
				plt.tight_layout()
				plt.savefig(str(out_folder)+'VIBRANT_figure_pathways_' + str(base) + '.pdf', format='pdf')

	if suppress == False and int(out_phages) > 0:
		plt.figure()
		sns.set(style="white")
		with open(str(out_folder)+'VIBRANT_genome_quality_' + base + '.tsv', 'r') as qual_file:
			data_frame = pd.read_csv(qual_file, sep='\t', header=0)
			data_frame = pd.DataFrame(data_frame)
			qualities = data_frame['Quality'].tolist()
			lowqual = qualities.count("low quality draft")
			mediumqual = qualities.count("medium quality draft")
			highqual = qualities.count("high quality draft")
			if format == 'nucl':
				circqual = qualities.count("complete circular")
				data = [lowqual,  mediumqual, highqual, circqual]
				names = ['low quality\n(' + str(data[0]) + ')', 'medium quality\n(' + str(data[1]) + ')', 'high quality\n(' + str(data[2]) + ')', 'circular\n(' + str(data[3]) + ')']
			if format == 'prot':
				data = [lowqual,  mediumqual, highqual]
				names = ['low quality\n(' + str(data[0]) + ')', 'medium quality\n(' + str(data[1]) + ')', 'high quality\n(' + str(data[2]) + ')']
			qual_fig = sns.barplot(x=names, y=data, alpha=0.6, palette=sns.color_palette("pastel"), edgecolor=sns.color_palette("bright"))
			plt.ylabel('Count')
			plt.tight_layout()
			plt.savefig(str(out_folder)+'VIBRANT_figure_quality_' + str(base) + '.pdf', format='pdf')


	if suppress == False and format == "nucl" and int(out_phages) > 0:
		plt.figure()
		size = int(len(length_list)*0.1+1)
		if len(length_list) <= 10:
			size = int(len(length_list))
		if len(length_list) > 10 and len(length_list) <= 50:
			size = int(len(length_list)/2)
		if size > 50:
			size = 50
		if size < 1:
			size = 1
		sns.set(style="white")
		figure = sns.distplot(length_list, bins=size, kde=False, rug=False, color='green')
		plt.xlabel("Scaffold size")
		plt.ylabel("Count")
		plt.tight_layout()
		plt.savefig(str(out_folder)+'VIBRANT_figure_sizes_' + str(base) + '.pdf', format='pdf')

	if suppress == False:
		if int(sequences) >= 10:
			plt.figure()
			proportions = [int(sequences),int(grep_out_count),int(out_phages)]
			names = ["total sequences\n"+str(sequences), "correct size\n"+str(grep_out_count), "total phages\n"+str(out_phages)]
			sns.set(style="white", font_scale=0.75)
			chart = sns.color_palette('Blues', 3)
			fig, figure = plt.subplots()
			for n, p in enumerate(proportions):
				circle = plt.Circle((1, p), radius=p, facecolor=chart[n], edgecolor="black")
				figure.add_artist(circle)
				if n == 0:
					figure.text(p+(p/3), p*1.25, names[n], color=chart[n], horizontalalignment='center')
					save = float(p)
				if n == 1:
					figure.text(save+(save/3), save, names[n], color=chart[n], horizontalalignment='center')
				if n == 2:
					figure.text(save+(save/3), save*0.75, names[n], color=chart[n], horizontalalignment='center')
			figure.set_xlim(-int(sequences)-(save*0.1), int(sequences)+(save*0.1))
			figure.set_ylim(-(save*0.1), 2*int(sequences)+(save*0.1))
			figure.set_aspect('equal')
			plt.tight_layout()
			figure.set_xticks([])
			figure.set_yticks([])
			sns.despine(fig=None, top=True, right=True, left=True, bottom=True, offset=None, trim=True)
			plt.savefig(str(out_folder)+'VIBRANT_figure_phages_' + str(base) + '.pdf', format='pdf')



	if suppress == False and int(out_phages) > 2:
		plt.figure()
		lifestyle_list = []
		quality_list = []
		circ_list = []
		label_list = []
		with open(str(out_folder)+'VIBRANT_genome_quality_' + base + '.tsv', 'r') as qual_file:
			qual_file = qual_file.read().replace("\n","\t").split("\t")
			x = 3
			lq = 0
			hq = 0
			mq = 0
			circ = 0
			lin = 0
			lyt = 0
			lyso = 0

			try:
				cl = len(circular_list)
			except Exception:
				cl = 0
			while x < len(qual_file)-1-(cl*3):
				if str(qual_file[x+2]) == 'low quality draft':
					quality_list.append((0.9,0,0.1,0.5))
					label_list.append('low quality draft')
					lq += 1
				elif str(qual_file[x+2]) == 'medium quality draft':
					quality_list.append((0,0.2,0.9,0.5))
					label_list.append('medium quality draft')
					mq += 1
				elif str(qual_file[x+2]) == 'high quality draft':
					quality_list.append((0.2,0.9,0,0.5))
					label_list.append('high quality draft')
					hq += 1
				if format == 'nucl':
					if str(qual_file[x]) in circular_list:
						circ_list.append('dotted')
						circ += 1
					else:
						circ_list.append('solid')
						lin += 1
				if str(qual_file[x+1]) == 'lytic':
					lifestyle_list.append((0,0,0,1))
					lyt += 1
				elif str(qual_file[x+1]) == 'lysogenic':
					lifestyle_list.append((0.85,0.85,0.85,1))
					lyso += 1
				x += 3

		annotations = pd.read_csv(str(out_folder)+'VIBRANT_summary_normalized_'+base+'.tsv', sep='\t', header=0)
		anno = pd.DataFrame(annotations, columns=['total genes', 'all KEGG' , 'KEGG v-score' , 'all Pfam' , 'Pfam v-score' , 'all VOG' , 'VOG v-score' , 'KEGG int-rep' , 'KEGG zero' , 'Pfam int-rep' , 'Pfam zero' , 'VOG redoxin' , 'VOG rec-tran' , 'VOG int' , 'VOG RnR' , 'VOG DNA' , 'KEGG restriction check', 'KEGG toxin check', 'VOG special', 'annotation check' , 'p_v check' , 'p_k check' , 'k_v check' , 'k check' , 'p check' , 'v check' , 'h check'])

		size_list = anno['total genes'].tolist()
		size_list = [10**i for i in size_list]

		anno[['scaffold']] = annotations[['scaffold']]
		anno_cols = anno.drop(['scaffold', 'total genes'], axis='columns')

		pca = PCA(n_components=2)
		principalComponents = pca.fit_transform(anno_cols)
		principalDf = pd.DataFrame(data = principalComponents, columns = ['principal component 1', 'principal component 2'])
		finalDf = pd.concat([principalDf, anno[['scaffold']]], axis = 1)
		coordsDf = pd.concat([principalDf, anno[['scaffold']]], axis = 1)
		coordsDf.to_csv(str(out_folder)+'VIBRANT_figure_PCA_' + str(base) + '.tsv', index=False, sep="\t")
		x_list = principalDf['principal component 1'].tolist()
		y_list = principalDf['principal component 2'].tolist()
		indicesToKeep = finalDf['scaffold']
		fig, ax = plt.subplots()
		plt.style.use('seaborn-white')
		ax.set_xlabel('Principal Component 1', fontsize = 15)
		ax.set_ylabel('Principal Component 2', fontsize = 15)

		if format == "nucl":
			plot = ax.scatter(x_list, y_list, s = size_list, marker = 'h', c = quality_list, label=label_list, edgecolors=lifestyle_list, linestyle=circ_list, linewidth=0.4)
		if format == "prot":
			plot = ax.scatter(x_list, y_list, s = size_list, marker = 'h', c = quality_list, label=label_list, edgecolors=lifestyle_list, linewidth=0.4)

		a = mpatches.Patch(color=(0.9,0,0.1,0.5), label='low quality ('+str(lq)+')')
		b = mpatches.Patch(color=(0,0.2,0.9,0.5), label='medium quality ('+str(mq)+')')
		c = mpatches.Patch(color=(0.2,0.9,0,0.5), label='high quality ('+str(hq)+')')
		legend1 = plt.legend(handles=[a,b,c], title='Scaffold quality', bbox_to_anchor=(1.0, 0.9), loc='upper left', borderaxespad=0)
		ax.add_artist(legend1)

		a = mpatches.Patch(color=(0,0,0,1), label='lytic ('+str(lyt)+')')
		b = mpatches.Patch(color=(0.85,0.85,0.85,1), label='lysogenic ('+str(lyso)+')')
		legend3 = plt.legend(handles=[a,b], title='Outline color', bbox_to_anchor=(1.0, 0.6), loc='center left', borderaxespad=0)
		ax.add_artist(legend3)

		lines = [Line2D([0], [0], color="darkgray", marker='h',markersize=3, markerfacecolor="darkgray", label='10', alpha=0.6, markeredgecolor='white', markeredgewidth='1', lw=0), Line2D([0], [0], color="darkgray", marker='h',markersize=6, markerfacecolor="darkgray", label='25', alpha=0.6, markeredgecolor='white', lw=0), Line2D([0], [0], color="darkgray", marker='h',markersize=8.2, markerfacecolor="darkgray", label='50', alpha=0.6, markeredgecolor='white', lw=0), Line2D([0], [0], color="darkgray", marker='h',markersize=9.7,markerfacecolor="darkgray", label='75', alpha=0.6, markeredgecolor='white', lw=0)]
		legend2 = plt.legend(handles=lines, title='Size (ORFs)', bbox_to_anchor=(1.0, 0.25), loc='upper left', borderaxespad=0)
		ax.add_artist(legend2)

		if format == "nucl":
			legend4 = [Line2D([0], [0], color='black', lw=2, label='circular ('+str(circ)+')', linestyle='dotted'), Line2D([0], [0], lw=2, color='black', label='linear ('+str(lin)+')')]
			ax.legend(handles=legend4, loc='center left', bbox_to_anchor=(1.0, 0.4), borderaxespad=0, title='Outline style')

		fig.set_size_inches(12, 8)
		plt.savefig(str(out_folder)+'VIBRANT_figure_PCA_' + str(base) + '.pdf', format='pdf', bbox_inches='tight')

	if suppress == False:
		subprocess.run('mkdir '+str(out_folder)+'VIBRANT_figures_'+base, shell=True)

	subprocess.run("rm " + str(out_folder)+base + "_four-orf-count.txt 2>/dev/null", shell=True)
	subprocess.run("rm " + str(out_folder)+base + "*parallel-runs* 2>/dev/null", shell=True)
	move_phages = 'mv ' + str(out_folder)+base + '.phages_* ' + str(out_folder)+'VIBRANT_phages_'+base + ' 2>/dev/null'
	move_run4 = str('mv '+str(out_folder)+'VIBRANT*' + base + '.tsv ' + str(out_folder)+'VIBRANT_results_' +base + ' 2>/dev/null')
	move_figs = str('mv '+str(out_folder)+'VIBRANT_figure_*' + base + '.pdf ' + str(out_folder)+'VIBRANT_figures_' +base + ' 2>/dev/null')
	y8 = subprocess.Popen(move_run4, shell=True)
	y7 = subprocess.Popen(move_phages, shell=True)
	y9 = subprocess.Popen(move_figs, shell=True)
	y7.wait()
	y8.wait()
	y9.wait()
	time.sleep(0.1)
	#
	#
	#
	note = ''
	if str(sklearn.__version__) != '0.21.3':
		if int(str(sklearn.__version__).split(".")[1]) > 21 or int(str(sklearn.__version__).split(".")[2]) > 3:
			note = 'CAUTION: running a version of Scikit-Learn higher than v0.21.3 may cause issues. With pip you can update by running "pip install --upgrade scikit-learn==0.21.3".'
		elif int(str(sklearn.__version__).split(".")[1]) < 21 or int(str(sklearn.__version__).split(".")[2]) < 3:
			note = 'CAUTION: running a version of Scikit-Learn lower than v0.21.3 will likely cause issues. With pip you can update by running "pip install --upgrade scikit-learn==0.21.3".'
	if str(np.version.version) != '1.17.0':
		if int(str(np.version.version).split(".")[0]) < 1 or int(str(np.version.version).split(".")[1]) < 17:
			note = 'CAUTION: running a version of Numpy lower than v1.17.0 will likely cause issues. With pip you can update by running "pip install --upgrade numpy==1.17.0".'

	log_command = sys.argv
	logging.info("Command:  " + str(" ".join(log_command)))
	logging.info("Date:     " + str(date.today()))
	logging.info("Start:    " + str(start_time))
	logging.info("End:      " + str(datetime.datetime.now().time()).rsplit(".",1)[0])
	logging.info("Runtime:  " + str(round((time.time() - float(starting_time))/60,1)) + " minutes")
	logging.info("Program:  VIBRANT v1.2.1")
	logging.info("\n")
	logging.info(str(sequences) + " scaffolds were read in.")
	if format == "nucl":
		logging.info(str(grep_out_count) + " scaffolds met minimum requirements: at least " + str(lim_low) + "bp and " + str(orf_low) + " ORFs.")
	if format == "prot":
		logging.info(str(grep_out_count) + " scaffolds met the minimum requirement: at least " + str(orf_low) + " ORFs.")
	logging.info(str(out_phages) + " putative phages were identified.")
	logging.info("\n")
	logging.info(str(note))
	logging.info('                                                               ##')
	logging.info('                                                             ##  ##')
	logging.info('                                                           ##      ##')
	logging.info('######   ##  ##     ##     #######   ######    #####       ##      ##')
	logging.info('##  ##   ##  ##   ##  ##   ##        ##       ##             ##  ##')
	logging.info('######   ######   ######   ##  ###   ######    ###             ##')
	logging.info('##       ##  ##   ##  ##   ##   ##   ##           ##           ##')
	logging.info('##       ##  ##   ##  ##   #######   ######   #####            ##')
	logging.info('                                                            #  ##  #')
	logging.info('                                                           # # ## # #')
	logging.info('                                                          #   #  #   #')
	logging.info('                                                         #            #')
	logging.info("\n")
	#
	#
	#
	if format == "nucl":
		subprocess.run('mv ' + str(out_folder)+base + '.prodigal.ffn ' + str(out_folder) + 'VIBRANT_' + base +' 2>/dev/null', shell=True)
		subprocess.run('mv ' + str(out_folder)+base + '.prodigal.gff ' + str(out_folder) + 'VIBRANT_' + base +' 2>/dev/null', shell=True)
		subprocess.run('mv ' + str(out_folder)+base + '.prodigal.faa ' + str(out_folder) + 'VIBRANT_' + base +' 2>/dev/null', shell=True)
	if format == "prot":
		subprocess.run('rm ' + str(out_folder)+base + '.phages_combined.gbk 2>/dev/null', shell=True)
	subprocess.run('mv '+str(out_folder)+'VIBRANT*' + base + ' ' + str(out_folder) + 'VIBRANT_' + base +' 2>/dev/null', shell=True)
	subprocess.run('mv '+str(out_folder)+'VIBRANT*' + base + '.log ' + str(out_folder) + 'VIBRANT_' + base +' 2>/dev/null', shell=True)
	time.sleep(0.1)
	#
	#
	#
except Exception as e:
	logging.exception(e)
