You appear to be doing a series of set operations. If you break down what your sets are and what operations you're needing, there are a number of modules that will allow you to easily, extensibly, and clearly operate over these sets

However, I'd recommend you use DBD::SQLite to throw the data into SQLite, then use it to query the db for the information you want.

An interesting reference I always seem to turn to in times of set operations in shell is, http://www.catonmat.net/blog/set-operations-in-unix-shell.