Remove unused imports

[sebastian-luna-valero]

Used autoflake to automatically remove unused imports:
https://github.com/myint/autoflake

Commands:

autoflake --remove-all-unused-imports -i -r cgat/CGAT/
autoflake --remove-all-unused-imports -i -r cgat/doc/
autoflake --remove-all-unused-imports -i -r cgat/tests/

This will help to create a (smaller) conda environment for code portability.

[sebastian-luna-valero]

The main goal of this PR was to reduce the number of conda dependencies. However, the total number of dependencies did not decreased at all after refactoring the code.

In addition to that, here is a text from the autoflake page that concerns me:

By default, autoflake only removes unused imports for modules that are part of the standard library. (Other modules may have side effects that make them unsafe to remove automatically.)

Although the tests on travis pass, I have not had time to test the code fully with Jenkins. Therefore, please leave the PR open until I can do that.

[sebastian-luna-valero]

Jenkins tests are currently passing with on this branch, so will merge to master.