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

Added transcribed_pseudogene to the pseudo code group

useful tool for getting info on the xref run taking place. Also will use this to rollback to variuos stages of the xref run. This is very much still in development

be recognised for horse.

ontology terms from it.

Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.

Currently knows how to get its own children/parent terms, and how to get
its own ancestors/descendants terms (all parents, all children).

Will be used in queries for genes, transcripts, and translations using
appropriate adaptors.

find_and_add_aliases() so that only one connection is used for this.
Bypasses the use of MetaContainer.

if output directory does not exist for ensembl dumpings of fasta files then status will be left as xref_fasta_dumped and the ensembl fatsa file not dumped. so check for xref_fasta_dumped too