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

Reimplemented the dump_interpro method so that it dumps any xrefs, object_xrefs and go_xrefs that may be dependent on the interpro xrefs

Added ens-research:3309

The Registry will try to load the specified file (specified by argument
to the method load_all(), in the envrionment variable ENSEMBL_REGISTRY,
or the file '~/.ensembl_init', as before) as an ini-file.  If this fails
due to the file having the wrong format, the code reverts to the old
behaviour of using require() on the same file.

This is an example of a simple ini-file.  There is no check to see
that e.g. 'dbname' is actually present or to avoid calling the adaptor
initialization routines with unnecessary parameters (we trust the user
to get this right).  The correct adaptor is chosen by peeking at the
'group' setting.


; Simple Ensembl config file example

; The 'default' section is special and its settings will be implicit for
; all other sections in this file but may be overridden by individual           ; sections.  There should be no 'alias' settings in the 'default'
; section.

[default]
user    = anonymous
host    = ensembldb.ensembl.org
group   = Core

[the_human_db]
species = Human
dbname  = homo_sapiens_core_45_36g
alias   = mary
alias   = john

[the_mouse_db]
species = Mouse
dbname  = mus_musculus_core_45_36f
alias   = minnie
alias   = mickey

; Configuration ends here

The quotes are no longer necessary since the bind_param statement now explicitly specifies the type, removing the nasty MySQL casting issue that caused them to be added in the first place.

    cdna_start()
    cdna_end()

    cdna_coding_start()
    cdna_coding_end()

    coding_region_start()
    coding_region_end()

Changed POD from saying "in genomic coordinates" to say "in
slice-relative coordinates":

    coding_region_start()
    coding_region_end()

extra method for descriptions

Added evals to retrieval of hard-coded sources (wormbase, CCDS) so that the script does not crash if these are missing. Also added count_unmapped_reasons method for validation of the unmapped_reasons table in the target DB

file for the platypus xrefs

Added a unique index (species_id,taxonomy_id) to the species table. Duplicates cause duplicated xref errors later on

within the Sanger firewall.

added NOTE about fetching by primary accession not being bothered about what the external database is