Comment and rename code

Started providing docstrings to classes and functions based on the comments
present in the source code. Renamed several functions and variables, being
careful to ensure they are called in other files with the (new) correct name.

Removed the -n (number) option from mirscanTrainer.py.
Renaming of scripts

Renamed score_cut.py to fit in with the other script filenames and
mirscanExecute.py to mirscanScorer.py to better reflect its role.
Bugfixes (typo)
Finished documenting the source code for the main scripts

The main scripts (Trainer, Scorer and Cutter) have all functions documents with
doctrings, the name variables are sane and the layout of the code is more
rational.

mirscanModule.py is not ready, pending evaluation of the hairpin  criteria
feature objects. Functions below the file parsing methods are perhaps best
placed in a separate file since they are only used for the criteria rule files.