feat: add support for reassigned Transcript Support Level

So far, only transcript with "TSL=1" were used, but based on the result of transcript sampler tool, TSL can be reassigned to 1, which caused an issue where the transcript was not correctly identified, i.e. instead of transcript_support_level "1", now transcript_support_level "1 (assigned to previous version 7)" will also be taken into account.

• Updated the text for the warning if TSL is not 1 or Annotation is missing
• Added setup.py
• Refactored cli.py and main.py to fit PEP8 style guide, removed "tqdm" package

merged