GitLab

table.

changed parsers as curated_trascriptParserhas now replaced HGNC_curated_transcriptParser and MGI_curated_transcriptParser

curated_transcriptParser now replaces HGNC and MGI variants as it was basically the same code in both

Added Aspergillus_fumigatus A1163 species, updated niger species entry, added SGD_GENE and SGD_TRANSCRIPT sources

data from the attrib_type table.

than 'species.alias'.  Bug found by Andy Yates.

Also, some reformatting.

Also merged two sets of similar INSERTs.

#
# Title:
#   Add new 'schema_type' meta key.
#
# Description:
#   All Ensembl databases with a 'meta' table should have a
#   'schema_type' key in them.  For Core datbases, the corresponding
#   value should be 'core'.

meta table with value 'ontology'.

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.

#
# 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.