For running a program on a scheduled basis such as every n minutes, you should use a scheduling program. Most likely your operating system already comes with one: on Unix it would be cron, on Windows it would be the Task Scheduler etc. There's not much point in making this part of your program itself, generally speaking.

The main part of your question I don't think I can help you with. If you can attach a small sample of what your data file actually looks like, that would help.