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

  Initialize the merged registry with whatever is in the registry at
  that point.  Suggested by Andy Yates (thanks!).

needed but can be useful so keeping a record of it.

* If there is only one protein_coding transcript in a gene, use it as
  the canonical transcript but make sure it doesn't have internal stops.

* If a seq_region_name is given, zero set the canonical_transcript_id
  and canonical_annotation, otherwise zero set all
  canonical_transcript_ids.

Added minimal doc.

processed_transcript', if gene biotype is protein_coding.

The TranslationAdaptor now has a fetch_all_by_Transcript() method with
which it's possible to get all translations for a transcript.

The fetch_by_Transcript() method now uses the new
canonical_translation_id field in the transcript table to get the
canonical transcript.

For species without alternative initiation (all Core speaces today), the
semantics and the results are the same as before.

Using the API from now on, without patch_56_57_e.sql applied, will
result in SQL errors.

The TranscriptAdaptor now knows how to store the canonical translation ID.

results anyway).

command line arguments standardized to the ones used in the genebuild scripts ( dbhost dbname dbport ... )