prepare_database

#!/bin/bash
#database=$1
#organism=$2


for i in "$@"
do
case $i in
    -t=*|--gtype=*)
    GTYPE="${i#*=}"
    ;;

   -db=*|--database=*)
    database="${i#*=}"
    ;;
    -org=*|--organism=*)
    organism="${i#*=}"
    ;;
    -h*|--help)
    echo -e "\n\nprepare_database USAGE: \n\n./prepare_database -db=[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME|NCG] -org=[see,org_codes_help]\n\n==========\nOptions: ALL PARAMETERS MUST BE SPECIFIED\n==========\n\n[-db= | --database=]\tOptions:[GO_all|GO_BP|GO_MF|GO_CC|KEGG|REACTOME] \n\n[-org= | --organism=]\tOptions:[see,org_codes_help]\n\n";
exit 1;
    ;;
    *)
            # unknown option
    ;;
esac
done

DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )";
DT=`/bin/date`;

if [ $# -eq 0 ]; then
    echo -e "\n\nPlease use:\n\n./prepare_database -h \n\n(or)\n\n./prepare_database --help \n\n for help\n";
	exit 1;
fi

if [ -z $database ]; then
    echo "Error:Please specify one of these databses GO_all,GO_BP,GO_MF,GO_CC,KEGG,NCG,REACTOME";
	exit 1;
fi
if [ -z $organism ]; then

echo "Error:Please specify organism --organism. For KEGG and Geneontology use 'org_codes_help' folder comes with GeneSCF; For REACTOME and NCG use 'Hs'.";

exit 1;

fi



if [ $database == "GO_all" ] || [ $database == "GO_CC" ] || [ $database == "GO_MF" ] || [ $database == "GO_BP" ]; then

database="GO";

fi

if [ $database == "KEGG" ] || [ $database == "GO" ] || [ $database == "REACTOME" ]; then


sh ${DIR}/class/lib/db/update_${database}.sh ${organism} $DIR;

exit 1;
fi
if [ $database == "NCG" ]; then


echo -e "\nError: Database $database not supported. Please check the user manual for supported databases.\n";


else
echo -e "\nError: Database $database not supported. Please check the user manual for supported databases.\n";


exit 1;
fi