Your program could easily be re-written as a front-end to DBD::AnyData which would allow it to operate on FixedLength, XML, CSV (with any record and field separators, with alternate delimiters and escape characters, etc), and many other formats. This would not only allow you to use many other input formats, but you could also have an output flag that would allow you to dump the results to any of those formats or to any DBI database, not limited to SQLite as yours is. If all the user wants is the results of the query, with DBD::AnyData as a backend, everything would happen in memory without creating an intermediate database on disk as your script does.

If you want to submit a patch, I'd be glad to include it (with credit natch) in DBD::AnyData (I'm its author), or it could be a standalone. Either way, holler if you need AnyData to do something it doesn't currently.