The great polish
The whole Mikado has been revisited and polished using pylint as a guide.
Notable feature additions:
- added an XML merger (mikado.py util merge_blast)
- written an Abstract Class that now underlies both GtfLine and GffLine, leading to far less code duplication
- simplified most of the methods and reduced the size of most functions, e.g. in the compare procedure.
- added and tested phase calculation for CDS features
- created a new module for log utilities (currently a stub)
- added the possibility of specifying "good" class codes for alternative splicing events
- database names changed and simplified
WARNING: databases serialised with earlier versions of Mikado are NOT COMPATIBLE with 0.8.7 onward.