You could write two programs. One takes what you have in the flatfile and inserts it into the database. The second does what you need to do out of the database.

Before you object, consider that it's effectively the same amount of work as what you're doing now. The difference is that it'll be much easier to work with data when it's in a database. (You'll have to figure out how to map back and forth between Perl and your flatfile, which is what the flatfile-to-database converter has to do anyway.)