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Fixed bug that showed up on Y chromosome and problem with not deleting entries when no analysis description was present, see release 58 notes for more details.

Arg [SPECIES]:  (optional) string
                By default, all databases that are found on the server
                and that corresponds to the correct release are probed
                for aliases etc.  For some people, depending on where
                they are in the world, this might be a slow operation.
                With the '-species' argument, one may reduce the startup
                time by restricting the set of databases that are probed
                to those of a particular species.

                Note that the latin name of the species is required,
                e.g., 'homo sapiens', 'gallus gallus', 'callithrix
                jacchus' etc.  It may be the whole species name, or only
                the first part of the name, e.g. 'homo', 'gallus', or
                'callithrix'.  This will be used in matching against the
                name of the databases.

fixes for LRGSlices and new methods to find nearest gene to a feature (this will change greatly as this is a very simple case)

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