Minor: refactoring, small changes.

Moved some imports around; minor changes to some docstrings etc.

Refactored add_gene_annotation to use _get_gene_annotation_dict so it's
easier for other classes to re-use.

Extended Insertion_position.__cmp__ to return -1 when the other object
is a different type.
Further updates for v5.3 chlamy genome - old

(This was actually done a while ago, I forgot to commit.)
Minor fixes to metadata parsing.

Fixed errors I got on some real data with partially unknown metadata -
the number of returned things from get_info_from_metadata_files wasn't
always the same, or type didn't match in a += operation.
BIG update to Carette data processing!

This was done over a long period.