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Changes to allow ontology databases called ensemblgenome_ontology_60 in order to differentiate ourselves from the ensembl_ontology database

method from HEAD on the release 60 brnch.

ensembl-60'.

Sprout from master 2010-11-01 15:37:06 UTC Andreas Kusalananda Kähäri <ak4@sanger.ac.uk> 'Handle ASMPATCH and LRG genes.'
Delete:
    misc-scripts/protein_match/process_pmach.pl

Taking out the explicit passing of core DBAdaptors for multi-species funcgen adaptors as it was causing a core & funcgen connection to be held on the target server

make sure the cache stores the same case as the original sequence else it will look wierd (as if softmasked) if you get it again using the cache

analysis_description.

the other script (not sure this is going to be used here).

method.  This should be the type of the object, if it is known.  Using
this options speeds up searching for the species of the stable ID if we
end up having to do an exhaustive search.

Add --skip_tables and --only_tables (mutually exclusive) switches.
These both take a comma-delimited list of tables to include/exclude.

Modified code to get engine type from tables using SHOW TABLE STATUS
rather than querying the information_schema.

Minor formatting.

of the analysis descriptions.  Currently only flags wrongly capitalized
logic names and descriptions that are not available in the production
database.  Still in development.