[Annotation tools] Revamp and simplify annotation tools

## Type of Issue

Select the type of issue:
- [ ] Bug report (to report a bug)
- [ ] Feature request (to request an additional feature)
- [ ] Tracker (I am just using this as a tracker)
- [x] Refactor request
- [ ] Documentation Ask

## Description

There're a lot of subprocess calls in annotation tools. This version (although is a working one) needs some revamp and simplification in order to make it more understandable and reusable.

Now is low priority but is a nice-to-have thing.