GitLab

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

Add beginnings of fetch_ancestor_chart(), which will return a simple
hash with some form of ancestor chart information for a term.

relationship types to consider, e.g. qw(is_a part_of).

Added specialied implementation of both fetch_by_dbID() and
fetch_by_dbID_list().

Renaming 'ontology_term' table into 'term'.

  Arg [1]   : Bio::EnsEMBL::OntologyTerm
              The GO term for which genes should be fetched.

  Example:  @genes = @{
              $gene_adaptor->fetch_all_by_GOTerm(
                $go_adaptor->fetch_by_accession('GO:0030326') ) };

  Description   : Retrieves a list of genes that are associated with
                  the given GO term, or with any of its descendent
                  GO terms.  The genes returned are in their native
                  coordinate system, i.e. in the coordinate system
                  in which they are stored in the database.  If
                  another coordinate system is required then the
                  Gene::transfer or Gene::transform method can be
                  used.

  Return type   : listref of Bio::EnsEMBL::Gene


(similarly for TranscriptAdaptor and TranslationAdaptor)

old behaviour restored after it was changed by whs / graef in january to not update the table.
option -update changed to -noupdate

description added for Uniprot_other