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.

Tried to keep the format of the script the same and just add in the extra rows needed. The script should now do:

1. Set the canonical transcript to be the one with the longest CCDS translation
2. If no CCDS, set the canonical transcript to be the merged transcript with the longest translation
3. If no merged, set the canonical transcript to be the one with the longest translation
4. If no coding transcripts, choose the longest noncoding merged transcript
5. If no merged transcripts, choose the longest noncoding transcript

database, prefix each SQL line with the string "#HEADS_UP!#" to avoid
unnecessary suffering.

when the primary key exists in both database table and master table
(didn't do this before).

look for entries that are the same (sans private key) and report these
in the output and SQL.