GitLab

Regular expressions expanded to allow for 0-9 in the second portion of a database name. Original patch only allowed this in the first scan of names. Passed by Andreas

  We know that fetch_all_by_Transcript() (on a TranslationAdaptor) will
  return a list of translations, where the first one will always be the
  canonical translation (if there is one).  Make use of this fact to
  make the routine slightly quicker.

  * Use fetch_all_by_Transcript() rather than translation() on the
    transcript to get the canonical translation (and any alternative
    translations).

  * ... then store the translation and any alternative translations.

Solves a problem stopping genebuilders from copying genes from one
database to another.

  * Correct documentation.
  * Use fetch_by_Transcript() to get canonical translation.
  * Modify SQL not to get canonical translation.

get_all_alternative_translations().

  * In the _list_dbIDs() method: Wrap the execute() in an eval() and
    throw() if it fails.

  * In the generic_fetch() method: For multi-species databases, make
    sure we're using the correct SQL table aliases for the seq_region
    and coord_system tables..

perl rather than relying on the script to be executable.

like "aspergillus_fumigatusa1163_core_5_58_1a"
(containing integers as part of the second part
of their names).

Added check to make sure that only the causative allele is evaluated when a variation has more than two alleles