GitLab

supporting features and translation attributes are removed

version_check changed to only check when adaptors are instantiated or not at all if special file exists

Added coding_gene() and coding_transcript() methods to pull data from regulatory_factor_coding table.

Updated for regualtory_factor_transcript->regulatory_factor_coding schema change. Also added some data to allow testing of regulated_genes methods

Improved handling of parsing xrefs from local (i.e. not downloaded) files; these are now specified as e.g.

LOCAL:Anopheles_symbol/GeneName_translation_UniqID.txt

in populate_metadata.sql

Should remove need for nasty two-step process.

Changed local sources to have new LOCAL: convention so they can be dealt with more elegantly by BaseParser

>name|description

Now also loads xref descriptions

Modify gene description priority list so we get Anopheles_symbol descriptions in preference to anything else if they're there.

load_registry_from_db will now only load the databases that match the correct software version and not necessarily the latest versions