update_ReactomeDB

#!/bin/bash

bin=`cd $(dirname $0);pwd`
date="`date +%Y%m%d`"
current_version=`ls $bin/database/basic/reactome/`

usage() 
{ 
    echo -e "\e[1;33m
This is a program for GO database update for AllEnricher.
It will download the up to date gene2go, obo and goa files. 
The new build database will be named in \"GO+current date\".

\e[1;31m[Exsits DB version]:
$current_version
[To update new DB version]:
    Reactome$date
[To update new DB path]:
    $bin/database/basic/reactome/Reactome$date

\e[1;33m[Usage]: `basename $0`
    
    -h|help	Print this help information." 
    exit 1 
} 

while getopts 'h' opt; 
do	
    case ${opt} in
        h|help)
            usage
            exit 1;;
        ?)
            usage
	    exit 1
    esac
done

versionfile="$bin/database/basic/reactome/Reactome$date";

# tips
echo -e "\e[1;33m
This is a program for GO database update for AllEnricher.
It will download the up to date gene2go, obo and goa files. 
The new build database will be named in \"GO+current date\".

\e[1;31m[Exsits DB version]:
    $current_version
[To update new DB version]:
    Reactome$date
[To update new DB path]:
    $bin/database/basic/reactome/Reactome$date\n"


#mkdir -p $versionfile
cd $bin/database/basic/reactome/
if [ "$current_version" != "Reactome$date" ]
then
    mv $current_version Reactome$date
fi

cd $versionfile
echo -e "\e[1;33m|----Downloading gene_info from NCBI..."$(tput sgr0)
wget -c ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

echo -e "\e[1;33m|----Downloading All levels of the pathway hierarchy (NCBI2Reactome) ..."$(tput sgr0)
wget -c https://reactome.org/download/current/NCBI2Reactome_All_Levels.txt
gzip -f NCBI2Reactome_All_Levels.txt

#echo -e "\e[1;33m|----Downloading Complete List of Pathways (Reactome-Pathways-species) ..."$(tput sgr0)
#wget -c https://reactome.org/download/current/ReactomePathways.txt

#echo -e "\e[1;33m|----Downloading Pathways hierarchy relationship (parent <- child) ..."$(tput sgr0)
#wget -c https://reactome.org/download/current/ReactomePathwaysRelation.txt

echo -e "\e[1;33m----|AllEnricher Reactome database update done!!!\n\nNew version path:\n$versionfile" $(tput sgr0)

#if [ "$current_version" != GO$date ];then
#    read -n1 -p "Delete the old version to save storage? [Y|N]" answer
#    echo
#    case $answer in
#        y|Y) 
#            rm -rf $bin/database/basic/reactome/$current_version && echo Done.;;
#        N|n) 
#            echo ok
#            exit 1;;
#    esac
#fi