#!/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: processNCBIGenBank.py
### Author: Rauf Salamzade
### Kalan Lab
### UW Madison, Department of Medical Microbiology and Immunology

# BSD 3-Clause License
#
# Copyright (c) 2021, Kalan-Lab
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import os
import sys
import argparse
from Bio import SeqIO
from Bio.Seq import Seq
import gzip
from zol import util

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

	Process NCBI Genbanks to create proteome + genbanks with specific locus tag.

	""", formatter_class=argparse.RawTextHelpFormatter)

	parser.add_argument('-i', '--input_ncbi_genbank', help='Path to genomic assembly in GenBank format.', required=True)
	parser.add_argument('-g', '--genbank_outdir',
						help='Path to output directory where genbank file should be written. Should already be created!',
						required=True)
	parser.add_argument('-p', '--proteome_outdir',
						help='Path to output directory where proteome file should be written. Should already be created!',
						required=True)
	parser.add_argument('-n', '--name_mapping_outdir',
						help='Path to output directory where gene old-to-new mapping text files should be written. 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=None, required=False)

	args = parser.parse_args()
	return args


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

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

	input_genbank_file = os.path.abspath(myargs.input_ncbi_genbank)
	gbk_outdir = os.path.abspath(myargs.genbank_outdir) + '/'
	pro_outdir = os.path.abspath(myargs.proteome_outdir) + '/'
	map_outdir = os.path.abspath(myargs.name_mapping_outdir) + '/'

	try:
		assert (util.is_genbank(input_genbank_file))
	except:
		raise RuntimeError('Issue with input Genbank file from NCBI.')

	outdirs = [gbk_outdir, pro_outdir, map_outdir]
	for outdir in outdirs:
		if not os.path.isdir(outdir):
			sys.stderr.write("Output directory %s does not exist! Please create and retry program." % outdir)

	"""
	PARSE OPTIONAL INPUTS
	"""

	sample_name = myargs.sample_name
	locus_tag = myargs.locus_tag

	"""
	START WORKFLOW
	"""

	# Step 1: Process NCBI Genbank and (re)create genbank/proteome with updated locus tags.
	try:
		gbk_outfile = gbk_outdir + sample_name + '.gbk'
		pro_outfile = pro_outdir + sample_name + '.faa'
		map_outfile = map_outdir + sample_name + '.txt'

		gbk_outfile_handle = open(gbk_outfile, 'w')
		pro_outfile_handle = open(pro_outfile, 'w')
		map_outfile_handle = open(map_outfile, 'w')

		locus_tag_iterator = 1
		oigf = None
		if input_genbank_file.endswith('.gz'):
			oigf = gzip.open(input_genbank_file, 'rt')
		else:
			oigf = open(input_genbank_file)
		for rec in SeqIO.parse(oigf, 'genbank'):
			for feature in rec.features:
				if feature.type == "CDS":
					all_starts = []
					all_ends = []
					all_directions = []
					all_coords = []
					if 'order' in str(feature.location):
						raise RuntimeError(
							'Currently order is not allowed for CDS features in Genbanks. Please consider removing sample %s from analysis and trying again.' % sample_name)
					if not 'join' in str(feature.location):
						start = min([int(x.strip('>').strip('<')) for x in
									 str(feature.location)[1:].split(']')[0].split(':')]) + 1
						end = max(
							[int(x.strip('>').strip('<')) for x in str(feature.location)[1:].split(']')[0].split(':')])
						direction = str(feature.location).split('(')[1].split(')')[0]
						all_starts.append(start);
						all_ends.append(end);
						all_directions.append(direction)
						all_coords.append([start, end, direction])
					else:
						all_starts = []
						all_ends = []
						all_directions = []
						for exon_coord in str(feature.location)[5:-1].split(', '):
							start = min(
								[int(x.strip('>').strip('<')) for x in exon_coord[1:].split(']')[0].split(':')]) + 1
							end = max([int(x.strip('>').strip('<')) for x in exon_coord[1:].split(']')[0].split(':')])
							direction = exon_coord.split('(')[1].split(')')[0]
							all_starts.append(start);
							all_ends.append(end);
							all_directions.append(direction)
							all_coords.append([start, end, direction])
					assert (len(set(all_directions)) == 1)
					start = min(all_starts)
					end = max(all_ends)
					direction = all_directions[0]
					old_locus_tag = 'NA'
					prot_seq = ''
					try:
						old_locus_tag = feature.qualifiers.get('locus_tag')[0]
					except:
						pass
					try:
						prot_seq = str(feature.qualifiers.get('translation')[0]).replace('*', '')
					except:
						raise RuntimeError(
							"Currently only full Genbanks with translations available for each CDS is accepted.")
						nucl_seq = str(rec.seq)[start - 1:end]
						if direction == '-':
							nucl_seq = str(Seq(nucl_seq).reverse_complement())
						prot_seq = Seq(nucl_seq).translate()
						feature.qualifiers['translation'] = prot_seq
					# sys.stderr.write('CDS with locus tag %s does not have translation available, generating translation.\n' % old_locus_tag)

					new_locus_tag = None
					try:
						new_locus_tag = feature.qualifiers.get('locus_tags')[0]
					except:
						pass
					if locus_tag != None or new_locus_tag == None:
						if locus_tag == None:
							sys.stderr.write('Using AAAA as locus tag because non-provided by user or GenBank for CDS.\n')
							locus_tag = 'AAAA'
						new_locus_tag = locus_tag + '_'
						if locus_tag_iterator < 10:
							new_locus_tag += '00000' + str(locus_tag_iterator)
						elif locus_tag_iterator < 100:
							new_locus_tag += '0000' + str(locus_tag_iterator)
						elif locus_tag_iterator < 1000:
							new_locus_tag += '000' + str(locus_tag_iterator)
						elif locus_tag_iterator < 10000:
							new_locus_tag += '00' + str(locus_tag_iterator)
						elif locus_tag_iterator < 100000:
							new_locus_tag += '0' + str(locus_tag_iterator)
						else:
							new_locus_tag += str(locus_tag_iterator)
						locus_tag_iterator += 1
						feature.qualifiers['locus_tag'] = new_locus_tag
					pro_outfile_handle.write('>' + str(new_locus_tag) + ' ' + rec.id + ' ' + str(start) + ' ' + str(end) + ' ' + str(direction) + '\n' + prot_seq + '\n')
					map_outfile_handle.write(str(old_locus_tag) + '\t' + str(new_locus_tag) + '\n')
			SeqIO.write(rec, gbk_outfile_handle, 'genbank')
		oigf.close()
		gbk_outfile_handle.close()
		pro_outfile_handle.close()
		map_outfile_handle.close()
	except:
		raise RuntimeError("Issue processing NCBI Genbank file.")

if __name__ == '__main__':
	processAndReformatNCBIGenbanks()