setupDatabases.sh

#!/bin/bash

#rm gdb.config 2> /dev/null

DATE_WITH_TIME=`date "+%Y%m%d-%H%M%S"`

mv gdb.config gdb.config.$DATE_WITH_TIME

find . -depth -name '*.zip' -exec /usr/bin/unzip -n {} \; -delete

wget -q https://raw.githubusercontent.com/bridgedb/BridgeDb/master/dbbuilder/src/org/bridgedb/extract/SpeciesList -O SpeciesList

while IFS=$'\t' read -r -a myArray
do
 #echo "a ${myArray[0]}"
 #echo "b ${myArray[1]}"
 echo "c ${myArray[4]}"

 path=`pwd`
 file=`ls | grep "^${myArray[4]}_Derby_"`
 if [ ${#file} -ge 1 ]; then
   #echo $path
   echo -e "file $file"
   #echo -e "${myArray[2]}\n"
   echo -e "${myArray[0]}\t$path/$file" >> gdb.config
 fi

done < SpeciesList

#metabolites (automate)

file=`ls | grep "metabolites_"`

if [ ${#file} -ge 1 ]; then
   echo -e "*	$path/$file" >> gdb.config
fi

#interactions (automate)
file=`ls | grep "interactions_"`

if [ ${#file} -ge 1 ]; then
   echo -e "*	$path/$file" >> gdb.config
fi