Add "_synonym" to database name for cross reference lines that are generated from external_synonyms (previously they were indistinguishable).

Note that Uniprot, EMBL etc are still "merged" so that Uniprot/SWISSPROT and Uniprot/TREMBL become Uniprot.

Also fixed bug that was causing EntrezGene to be changed to ENSEMBLGene

Always de-reference the value got from get_mapping_path().
Found by Magali.

distribution.

database in GFF format (STDOUT).

Added code to delete names/GO terms if the -delete_only option is specified. Added code to check whether
-registryconf is submitted as a string from the submit_projections.pl script or as a file on the command
line.

translation ID, and ALWAYS update it to the correct translation ID
later, after storing the translation.

Avoids problems (the canonical_translation_id being duplicated) when
transferring transcripts with translations from another database.

Amonida found this.

  Fix store() so that the canonical_translation_id in the transcript
  table is updated if the translation gets a new dbID when it is stored.

a) added unused_priority to the order list as this now contains the number of times that trancript name was used and is need to make sure that the gene name is the same as the transcripts. b) make sure there is a description else we get a ton of warning regarding undefined vars

For offical naming take the gene name of the most comman transcript name. Also remove any version numbers from the transcripts

commented out the finding the best gene match as we only need the best transcript match. Having both confuses Biomart anyway