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

Actually, rather don't include non-ref sequences for now. (The haplotypes don't have their own Chromosome summary page so these stats won't be displayed.)

warning() instead of throw() if analyiss description does not exist in analysis.description file

url for IPI for zfish corrected
add. url for zfish added

comment added for split_tscript etc