#!/bin/bash
######################################################################################################
# author nselem84@gmail.com
# _________________________________________________________________________________________________
# usage
# ./run_corason -h   
#	shows help menu
#  
# ./run_evomining <queryEnzyme> <gbks_directory> <referenceBGC> <genomicVicinitySize>
#  queryEnzyme			Fasta file with aminoacid sequence of the query enzyme  
#
#  gbks_directory 		Directory with genomes or BGCs in gbk format  
#
#  referenceBGC			File name of a gbk file that contains a BGC or genome 
#				where the query enzyme belong.
#
#  genomicVicinitySize 		Optional, size of the genomic contexts. Default 20 genes (10 at each side)
#
#   __________________________________________________________________________________________________
#
#  docker run --volume --volume --volume nselem/corason -g -q queryEnzyme -s -o
#
#  QUERY_FILE   query enzyme   
#  INPUT_FILE   reference cluster (relative path)
#  GENOME_DIR   Genome gbks directory 
# 
#
#  Pendientes  
#  Dentro del docker llamar GENOME al GENOME_DIR
#  Convertir de gbk a rast format
#  poner ".query al enzyme file"
#  Tomar el nombre del reference file 
#  
#
########################################################################################################

if [[ $# -eq 0 ||  $1 == "-h" ||  $1 == "--help" ]]; then
	docker run \
	--detach=false \
	--rm \
	nselem/corason corason.pl\
    	$@
else
	set -o errexit
	set -o nounset

	function realpath() {
    	echo $(readlink -f $1 2>/dev/null || python -c "import sys; import os; print(os.path.realpath(os.path.expanduser(sys.argv[1])))" $1)
	}

	# handle input query file (Only one enzyme in fasta)
	if [[ ! -f ${1} ]]; then echo "File $1 does not exists"; exit ;fi
	readonly QUERY_FILE=$(basename $1)
	readonly QUERY_DIR=$(dirname $(realpath $1))
#	echo "input query file: ${QUERY_FILE}"
#	echo "input query dir: ${QUERY_DIR}"
	shift

	# handle genomic database
	if [[ ! -d ${1} ]]; then echo "Directory $1 does not exists";exit;fi
	readonly GENOME_DIR=$(realpath $1)
#	echo "input gbk dir: ${GENOME_DIR}"
	shift

	# handle input file where the query belongs (genome file in BGCs)
	if [[ ! -f ${1} ]]; then echo "File $1 does not exists";exit;fi
	readonly INPUT_FILE=$(basename $1)
	readonly INPUT_DIR=$(dirname $(realpath $1))
#	echo "input special cluster dir: ${INPUT_DIR}/${INPUT_FILE}"
	if [[ ${INPUT_DIR} != ${GENOME_DIR} ]]; then 
		echo "${INPUT_FILE} must be located in ${GENOME_DIR}"
		echo "The program will exit now, please move ${INPUT_FILE} to ${GENOME_DIR}"
		exit
	fi
	shift

	OUTPUT_DIR=${PWD}
	# Links within the container
	readonly CONTAINER_SRC_DIR=/usr/src/CORASON
	readonly CONTAINER_DST_DIR=/home/output


	#if [ ${INPUT_FILE} ${OUTPUT_FILE} ]; then
	if [ ! -z ${INPUT_FILE} ] ; then
		echo "corason is now running"
		echo docker run --volume ${QUERY_DIR}/${QUERY_FILE}:${CONTAINER_DST_DIR}/${QUERY_FILE}:ro --volume ${INPUT_DIR}:${CONTAINER_DST_DIR}/CORASON_GENOMES:ro --volume ${OUTPUT_DIR}:${CONTAINER_DST_DIR}:rw --detach=false --rm nselem/corason corason.pl -g -q ${QUERY_FILE} -s ${INPUT_FILE} $@

	fi
fi