[source UniProt::protein_id] and [source Uniprot::EMBL]

Modified medaka to download EMBL and protein_id.

change to subroutine transcript_display+xref_sources so that it now return the list to use and also a hash of those to ignore if they match the regular expression given

Don't project if a GO term with the same accession, but IEA evidence code, exists, as this will lead to duplicates when the projected term has its evidence code changed to IEA after projection

fetch_all_by_external_name() in GeneAdaptor.pm, TranscriptAdaptor.pm,
and in TranslationAdaptor.pm.

This will limit the returned genes, transcripts, or translations, to
those that originates from the named external database.

This also means adding the optional argument to
list_gene_ids_by_extids(), list_transcript_ids_by_extids(),
list_translation_ids_by_extids(), and to _type_by_external_id() in
DBEntryAdaptor.pm.

The matching is done on 'db_name' in the 'external_db' table with LIKE
and an appended '%' to the given $external_db_name.

ficex Go to use ALL tax ids for a particular species (anonpholese fix but useful if more species get strains)

Also keep help text below 80 chars/line.

Added ability to project (apparent)one2many orthologs as well. Multiple targets are labeled "1 of 2", "2 of 2" etc

new code to work out the cmp seq regions that have multuple assemblys. This is now stored in the seq_region_attrib table

    Allow aliases to also be specified in the 'default' section, but
    require that there must also be a 'species' setting in the same
    section.  Aliases will never be installed if there is no 'speices'
    setting in the current section.  The 'species' section may be
    inherited from the 'default' section.

    Example:

    [default]
    host    = db.example.com
    user    = anonymous
    species = Human
    alias   = H_Sapiens
    alias   = Homo_Sapiens
    alias   = Me

    [my_core_db]
    group   = core
    dbname  = homo_sapiens_core_45_36g

    [my_estgene_db]
    group   = estgene
    dbname  = homo_sapiens_estgene_29_35b

  - allow mismatches
  - fixes to cope with changes to ConversionSupport->sort_chromosomes()
  - allow most scripts (with the exception of load_alternative_assembly.pl) to
    use source and target dbs on different hosts
  - various other improvements