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

some addition data for platypus

added entry for platypus olfactory recpetors

as per email from Glenn on the core list (won't be in release 45 as it
was not declared, but is likely to be in release 46).

as per email from Glenn on the core list (won't be in release 45 as it
was not declared, but is likely to be in release 46).

  implementation
- added fetch_associated_archived()
- removed deprecated methods

From the code:

# This parser will read Direct Xrefs from a simple tab-delimited file.
# The columns of the file should be the following:
#
# 1)    Accession ID
# 2)    Ensembl ID
# 3)    Type (one of 'transcript', 'gene', or 'translation',
#       will default to 'gene')
# 4)    Display label (will default to the Accession ID in column 1)
# 5)    Description (will default to the empty string)
# 6)    Version (will default to '1')
#
# Columns 1 and 2 are obligatory.

Only clear old registry configuration if we have a configuration file
name and if that file exists.

- rewrote fetch_by_stable_id*() methods to look up current versions of stable
  IDs in *_stable_id tables
- new method lookup_current() to assist the former (also replaces
  _lookup_version())
- new method add_all_current_to_history() to implement this behaviour for
  StableIdHistoryTree

- new methods to get properties of current db:
  - get_current_release()
  - get_current_assembly()

- fixed _resolve_type() to copy with non Ensembl-style stable IDs (e.g.
  Anopheles)

- removed deprecated methods

  - get_latest_StableIdEvent(): find latest Event in tree for a given stable ID
  - getters/setters for current db properties:
    - current_release()
    - current_assembly()
    - current_dbname()
  - is_incomplete(): flag to indicate incomplete trees

  - current_version(): retrieves current version of stable ID from db
  - is_current(): test if this is the current version
  - get_latest_incarnation(): get latest incarnation of stable ID from db
  - is_latest(): test if this is the latest version

- version() no longer lazy-loaded (now always set by adaptor)

- removed deprecated methods

as filled paragraphs.  Long lines shortened.  Spelling.

Make Vega transcript data URI a glob pattern.

directory before ls'ing.

Listings of subdirectories with 'ls' on FTP servers may return only
filenames *or* whole file paths.  This probably depends on the FTP
server software being used, but it makes relying on getting the whole
path back a bit silly.

all files are unchanged.

    The fetch_files() method returns a list of files, including
    directories where they can be found, so don't go prefixing them with
    $dir again silly.

All files are now treated as local, except for those configured as
'mysql:' URIs in the configuration file.

specific) file Seg_xrefs.txt of the IMGT/LIGM_DB and IMGT/GENE_DB
sources would clash.  Put the two files in subfolders.  Split the
sources.

--cleanup is specified on the command line.