How do people write ripping tools?

[ÿZEROLIGHT]

I'm trying to write a program for ripping sprite tiles directly from the .rom file, without having to go through a program like Desmume and deal with the complications and limitations it presents. I'm trying figure out how people interpret the game files so they can write algorithms to open or rip them.

It's a...complicated process  .

Here's what I think they do:

People find what byte order the file uses, and do trial and error to figure out the header. After they successfully detect the header, they then define the type of filestream it is.
Some filestreams are made by the game authors themselves, so if it is encrypted or compressed may make it very difficult to interpret. 
The reason why some file types are made by the companies themselves is mainly for protecting their content, hence copyright. But we don't really do that, we just want to use them for art or fan-animations.
Anyway, you have to make the program interpret the data in a specific way so it reads it just like how the rom's code does, which means ignoring the file header, or extracting different segments of it if it's an archived one. (which means multiple headers are in it)