GitLab

Added new option to method fetch_all which is include_lrg. By defualt lrg slices willl NOT be returned if this is not set (default is off) also since at present all lrg regions are non reference this flag must be set too to get the lrg regions.

added new method fetch_by_region_unique which returns the non duplicate regions. This is mainly for getting non duplicated regions like assembly patches or haplotype regions

(replacing splicing_event.type with a reference to attrib_type).

Not properly tested due to lack of data.

Added -species_suffix option to load_registry_from_db which adds the string passed to the end of the species name for all the databases on that server. e.g. -species_suffix => '_new'  so then to get the human core gene adaptor for this server you would use get_adaptor('human_new','core','gene')

make LRGSlice inherit from Slice as the lrg regions are now strored in the asembly differently so can now inherit

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..

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