GitLab

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.

#
# Title:
#   Extend the object_type_idx index of the object_xref table.
#
# Description:
#   Add the 'analysis_id' to the end of the object_type_idx index in the
#   object_xref table so that we may allow for object_xref entries that
#   only differ in analysis_id.

#
# Title:
#   Replace splicing_event.type with splicing_event.attrib_type_id
#
# Description:
#   The 'type' enumeration in the splicing_event table is too terse.
#   Replace it with a reference to a proper attrib_type.

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')

#
# Title:
#   Modify the assembly_exception.exc_type enumeration.
#
# Description:
#   Add 'PATCH_FIX' and 'PATCH_NOVEL' to the assembly_exception.exc_type
#   enumeration.

assembly_exception table.

to flush index data to file before copying.

Add new flag:

  --noopt           (Optional)
                    Skip the optimization step.  The database tables are
                    optimized (as with "OPTIMIZE TABLE") to flush the
                    index data onto disk.  This may be a time consuming
                    operation for very large tables.  The --noopt flag
                    disables the optimization.

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

Get sequence using mfetch as fasta file has fasta of the pathced region and not of the contigs that make up this region

many changes but the most important is to only add seq_region mapping if the seq_region_ids are different

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.