Fix variable name in error message
Standardise on function name sys_exit not stop_err

This will match my other scripts here:
https://github.com/peterjc/picobio

$ sed -i "s/stop_err/sys_exit/g" tools/*/*.py

I also fixed a typo in tools/protein_analysis/promoter2.py
Fix variable name in assert message
Fixed error handling in mira4_bait.py (there is no manifest)
Fixed two error messages
Fix inconsistent variable name