#!/opt/conda/conda-bld/zol_1718245333928/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/python

### Program: runProdigalAndMakeProperGenbank.py
### Author: Rauf Salamzade
### Kalan Lab
### UW Madison, Department of Medical Microbiology and Immunology

# BSD 3-Clause License
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# Copyright (c) 2021, Kalan-Lab
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import os
import sys
import argparse
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
from collections import defaultdict
from zol import util
import subprocess
from operator import itemgetter

def create_parser():
	""" Parse arguments """
	parser = argparse.ArgumentParser(description="""
	Program: runProdigalAndMakeProperGenbank.py
	Author: Rauf Salamzade
	Affiliation: Kalan Lab, UW Madison, Department of Medical Microbiology and Immunology

	Program to run prodigal gene calling and then create a genbank file with CDS features. Final genome-wide predicted 
	proteomes + genbank will be edited to have locus tags provided with the "-l" option. 
	
	11/17/2022 - can now use pyrodigal instead of progial.
	""", formatter_class=argparse.RawTextHelpFormatter)

	parser.add_argument('-i', '--input_genomic_fasta', help='Path to genomic assembly in FASTA or GenBank (needed for Eukaryotes) format.', required=True)
	parser.add_argument('-o', '--output_directory', help='Path to output directory. Should already be created!', required=True)
	parser.add_argument('-s', '--sample_name', help='Sample name', default='Sample', required=False)
	parser.add_argument('-l', '--locus_tag', help='Locus tag', default='AAA', required=False)
	parser.add_argument('-gcm', '--gene_calling_method', help='Method to use for gene calling. Options are: pyrodigal, prodigal,\nor prodigal-gv. [Default is pyrodigal].', required=False, default='pyrodigal')
	parser.add_argument('-m', '--meta_mode', action='store_true', help='Use meta mode instead of single for pyrodigal/prodigal. Automatically turned on if prodigal-gv is requested.', default=False, required=False)

	args = parser.parse_args()
	return args

def prodigalAndReformat():
	"""
	Void function which runs primary workflow for program.
	"""

	"""
	PARSE REQUIRED INPUTS
	"""
	myargs = create_parser()

	input_genomic_fasta_file = os.path.abspath(myargs.input_genomic_fasta)
	outdir = os.path.abspath(myargs.output_directory) + '/'
	gene_calling_method = (myargs.gene_calling_method).lower()
	meta_mode = myargs.meta_mode

	try:
		assert(os.path.isfile(input_genomic_fasta_file))
	except:
		raise RuntimeError('Issue with input genomic assembly file path.')

	if not os.path.isdir(outdir):
		sys.stderr.write("Output directory does not exist! Please create and retry program.")

	"""
	PARSE OPTIONAL INPUTS
	"""

	sample_name = myargs.sample_name
	locus_tag = myargs.locus_tag

	"""
	START WORKFLOW
	"""

	# check if uncompression needed
	try:
		if input_genomic_fasta_file.endswith('.gz'):
			os.system('cp %s %s' % (input_genomic_fasta_file, outdir))
			updated_genomic_fasta_file = outdir + input_genomic_fasta_file.split('/')[-1].split('.gz')[0]
			os.system('gunzip %s' % (updated_genomic_fasta_file + '.gz'))
			input_genomic_fasta_file = updated_genomic_fasta_file
		assert(util.is_fasta(input_genomic_fasta_file))
	except:
		raise RuntimeError('Input genomic assembly does not appear to be in FASTA format.')

	# Step 1: Run Prodigal (if needed)
	og_prod_pred_prot_file = outdir + sample_name + '.original_predicted_proteome'
	prodigal_cmd = []
	if gene_calling_method == 'pyrodigal':
		prodigal_cmd = ['pyrodigal', '-i', input_genomic_fasta_file, '-a', og_prod_pred_prot_file]
	elif gene_calling_method == 'prodigal':
		prodigal_cmd = ['prodigal', '-i', input_genomic_fasta_file, '-a', og_prod_pred_prot_file]
	elif gene_calling_method == 'prodigal-gv':
		prodigal_cmd = ['prodigal-gv', '-p', 'meta', '-i', input_genomic_fasta_file, '-a', og_prod_pred_prot_file]
	else:
		sys.stderr.write('The gene-calling method selected is not a valid option. Has to be either: prodigal, pyrodigal, or prodigal-gv.\n')
		sys.exit(1)

	if meta_mode and not gene_calling_method == 'prodigal-gv':
		prodigal_cmd += ['-p', 'meta']

	subprocess.call(' '.join(prodigal_cmd), shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, executable='/bin/bash')
	try:
		assert(os.path.isfile(og_prod_pred_prot_file))
	except:
		raise RuntimeError("Prodigal did not run until the end.")

	# Step 2: Process Prodigal predicted proteome and create polished version with locus tags
	pc_prod_pred_prot_file = outdir + sample_name + '.faa'
	pc_prod_pred_prot_handle = open(pc_prod_pred_prot_file, 'w')
	scaffold_prots = defaultdict(list)
	prot_sequences = {}
	prot_locations = {}
	with open(og_prod_pred_prot_file) as ooppf:
		for i, rec in enumerate(SeqIO.parse(ooppf, 'fasta')):
			if (i+1) < 10:
				pid = '00000'+str(i+1)
			elif (i+1) < 100:
				pid = '0000'+str(i+1)
			elif (i+1) < 1000:
				pid = '000'+str(i+1)
			elif (i+1) < 10000:
				pid = '00'+str(i+1)
			elif (i+1) < 100000:
				pid = '0'+str(i+1)
			else:
				pid = str(i+1)
			new_prot_id = locus_tag + '_' + pid
			scaffold = '_'.join(rec.id.split('_')[:-1])
			start = int(rec.description.split(' # ')[1])
			end = int(rec.description.split(' # ')[2])
			direction = int(rec.description.split(' # ')[3])
			scaffold_prots[scaffold].append([new_prot_id, start])
			prot_locations[new_prot_id] = [scaffold, start, end, direction]
			prot_sequences[new_prot_id] = str(rec.seq)
			dir_str = '+'
			if direction == -1: dir_str = '-'
			pc_prod_pred_prot_handle.write('>' + new_prot_id + ' ' + scaffold + ' ' + str(start) + ' ' + str(end) + ' ' + dir_str + '\n' + str(rec.seq) + '\n')
	pc_prod_pred_prot_handle.close()

	print(scaffold_prots.keys())

	# Step 3: Process Prodigal predicted genbank and create polished version with locus tags and protein + nucleotide
	# sequences
	pc_prod_genbank_file = outdir + sample_name + '.gbk'
	pc_prod_genbank_handle = open(pc_prod_genbank_file, 'w')
	with open(input_genomic_fasta_file) as oigff:
		for fasta_rec in SeqIO.parse(oigff, 'fasta'):
			seq = fasta_rec.seq
			record = SeqRecord(seq, id=fasta_rec.id, name=fasta_rec.id, description='')
			record.annotations['molecule_type'] = 'DNA'
			feature_list = []
			for prot in sorted(scaffold_prots[fasta_rec.id], key=itemgetter(1)):
				pstart = prot_locations[prot[0]][1]
				pend = prot_locations[prot[0]][2]
				pstrand = prot_locations[prot[0]][3]
				feature = SeqFeature(FeatureLocation(start=pstart-1, end=pend, strand=pstrand), type='CDS')
				feature.qualifiers['locus_tag'] = prot[0]
				feature.qualifiers['translation'] = prot_sequences[prot[0]].rstrip('*')
				feature_list.append(feature)
			record.features = feature_list
			SeqIO.write(record, pc_prod_genbank_handle, 'genbank')
	pc_prod_genbank_handle.close()

if __name__ == '__main__':
	prodigalAndReformat()
