#!/opt/conda/conda-bld/biocode_1660685443970/_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
# encoding: utf-8

## written by Nick Crawford
# taken from this post:
# http://www.ngcrawford.com/2012/03/28/interleave-paired-end-reads/

import gzip
import argparse

def interface():
	args = argparse.ArgumentParser(description="Interleave two FASTQ files")
	args.add_argument('-l', '--left-input',
		help='The first input file in fastq format.')

	args.add_argument('-r', '--right-input', 
		help='The first input file in fastq format.')

	args.add_argument('-o', '--output', 
		help='The output file in fastq format.')
	
	args = args.parse_args()
	return args


def process_reads(args):
	
	if args.left_input.endswith('.gz') or args.right_input.endswith('.gz'):

		left = gzip.open(args.left_input,'rb')
		right = gzip.open(args.right_input,'rb')
		fout = gzip.open(args.output,'wb')

	else:
		left = open(args.left_input,'rU')
		right = open(args.right_input,'rU')
		fout = open(args.output,'w')


	# USING A WHILE LOOP MAKE THIS SUPER FAST
	# Details here: 
	#   http://effbot.org/zone/readline-performance.htm
	
	while 1: 

		# process the first file
		left_line = left.readline()
		if not left_line: break
		fout.write(left_line)

		left_line = left.readline()
		fout.write(left_line)

		left_line = left.readline()
		fout.write(left_line)

		left_line = left.readline()
		fout.write(left_line)


		# process the second file
		right_line = right.readline()
		fout.write(right_line)

		right_line = right.readline()
		fout.write(right_line)

		right_line = right.readline()
		fout.write(right_line)

		right_line = right.readline()
		fout.write(right_line)

	left.close()
	right.close()
	fout.close()
	return 0

if __name__ == '__main__':
	args = interface()
	process_reads(args)
