[ENSCORESW-475] fixing the dbentry return to prioritise genes, transcripts and translations found on reference slices

Added a method that lists the species in available databases. Ancestral_ are ignored, and the list is filtered to a group type, defaulting to core dbs. Testcase is less than perfect, because the test db has so few species in it.

Swapped the count_by_slice_constraint constraint triggers, as they were the wrong way round. Test suite was passing by luck. Rewrote adjoining comments.

Inverted the sense of the SQL limit flags. It was re-enabling them every loop, and not disabling them ever. ENSCORESW-459

[ENSCORESW-461]. Improved messaging when db doesn't match. Skip db (do not die) if schema version < oldest option

Added:
- patch_71_72b.sql to Ensembl Production (create meta table)
- patch_71_72c.sql to Ontology (add schema_version)

Updated Ontology patch_71_72b.sql to insert patch meta entry

Modified queries to match Variation schema changes. The sample table was removed, and the information was pushed into population and individual tables.

skip transcripts that have a ribosomal_frameshift as well as those having the specific '_rib_frameshift' attribute

[ENSCORESW-457]. Better documentation for the associated xref tables. Passed onto regulation as well

[ENSCORESW-395]. Addition of -eg and -ue options to get people to ping different database servers for ensembl genomes and useast respectively. Also allow users to specify the species used.

first, test all the cases and add seq_region_mapping entries when necessary
then, update the mapping_set table
prevents us from skipping a species where a previous run might have failed

[ENSCORESW-448]. new overlap algorithm and better test cases. supports overlaps when you do not want to normalise WRT the backing slice

[ENSCORESW-445]. Fixes an issue with transformed and transfered transcripts. Attribute arrays are shallowed copied so attributes meant for the transformed object go back into the parent object. This causes more issues when you start to do multiple transformations from the same transcript. Regression test case added

There are some circumstances where exon coordinate recalculation is not the right thing to do and the user has them correctly set out (ori spanning transcription models). Rather than tie this directly into the coordinate recalculations we are allowing skipping this procedure. It is up to the user to do the right thing if using this module. It also does not alter any existing functionality

was giving it an exon mapping list where a transcript mapping list was required

[ENSCORESW-438]. Fixed API when someone can specify a _rna_edit where the substring length was not equal to the substituting string length

better testing of meta_coord and the container object. Now testing if updates work to existing data sets