If you want to empty the tables of a database you are going to, at some point, use the facilities provided by the database designers to do so. This may be a command line script to drop tables or a program that uses the database API to do it programatically. Short of deleting all of the database files on the system there isn't much of an alternative.
What kind of database? MySQL has a command line utility that allows you to execute database commands from a shell script. For instance, to delete all the rows in a table called bartable, in a database called dbfoo:
mysql dbfoo -e 'delete from bartable'
Of course, you'll need to have a .my.cnf file with login credentials for that database OR provide the username and password to the mysql command (mysql -uuser -ppass dbfoo ...).