GitLab

support will be available once a schema patch has been committed and
databases have been patched...

databases in Registry.

not really a general purpose method but quite specific to what the web
team will want to do later.

Add subclass of StableIdGenerator::EnsemblGeneric to do Anopheles gambiae stable ID incrementation and verification.

Entry added for Tgut_symbols. These are the gene symbols assigned to Taeniopygia guttata (zebra finch) genes by Dave Burt.

  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose ancestor terms should be fetched.

  Description   : Given a child ontology term, returns a hash
                  structure containing its ancestor terms, up to and
                  including any root term.  In GO, relations of the
                  type 'is_a' and 'part_of' are included, but not
                  'regulates' etc.

  Example       : my %chart =
                    %{ $ot_adaptor->fetch_ancestor_chart($term) };

  Return type   : A reference to a hash structure like this:

    {
      'GO:XXXXXXX' => {
        'term' =>           # ref to Bio::EnsEMBL::OntologyTerm object
        'is_a'    => [...], # listref of Bio::EnsEMBL::OntologyTerm
        'part_of' => [...], # listref of Bio::EnsEMBL::OntologyTerm
      },
      'GO:YYYYYYY' => {
        # Similarly for all ancestors,
        # and including the query term itself.
      }
    }

new test code to calculate display xrefs using the xref database and SQL only. So much, much faster as just simple sql instead of gettin gall genes, then all transcripts then all dbentries. Caveat though is that all the xrefs have to be in the xref database and cannot be used to an update mode. i.e. just adding one particular source.  Can only be used whan adding ALL sources possible.

use object_xref_id to join dependent xref to object_xref and not xref_id as this is more unique. Interpro GOs do not have dependent_xrefs so GOs need to be processed slightly differently by doing a left join instead