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  1. 02 Dec, 2010 1 commit
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  13. 06 May, 2010 1 commit
    • Andreas Kusalananda Kähäri's avatar
      Added new 'species' argument to load_registry_from_db(): · 4b3a1051
      Andreas Kusalananda Kähäri authored
      Arg [SPECIES]:  (optional) string
                      By default, all databases that are found on the server
                      and that corresponds to the correct release are probed
                      for aliases etc.  For some people, depending on where
                      they are in the world, this might be a slow operation.
                      With the '-species' argument, one may reduce the startup
                      time by restricting the set of databases that are probed
                      to those of a particular species.
      
                      Note that the latin name of the species is required,
                      e.g., 'homo sapiens', 'gallus gallus', 'callithrix
                      jacchus' etc.  It may be the whole species name, or only
                      the first part of the name, e.g. 'homo', 'gallus', or
                      'callithrix'.  This will be used in matching against the
                      name of the databases.
      4b3a1051
  14. 04 May, 2010 1 commit
  15. 14 Apr, 2010 1 commit
  16. 16 Mar, 2010 1 commit
  17. 03 Feb, 2010 1 commit
  18. 02 Feb, 2010 1 commit
  19. 26 Jan, 2010 2 commits
  20. 04 Dec, 2009 2 commits
  21. 02 Dec, 2009 4 commits
  22. 25 Nov, 2009 2 commits
  23. 17 Nov, 2009 2 commits
    • Andreas Kusalananda Kähäri's avatar
      Add to documentation of get_species_and_object_type(): · 5be7a5e3
      Andreas Kusalananda Kähäri authored
        NOTE: No validation is done to see if the stable ID actually exists.
      5be7a5e3
    • Andreas Kusalananda Kähäri's avatar
      Rewrite of get_species_and_object_type(): · 43ea3ea9
      Andreas Kusalananda Kähäri authored
        Description:  Get the species name, object type (gene, transcript,
                      translation, or exon etc.), and database type for a
                      stable ID.
      
        Arg[1]     :  String
                      The stable ID to find species and object type for.
      
        Example    :  my ( $species, $object_type, $db_type ) =
                        $registry->get_species_and_object_type('ENST00000326632');
      
        Return type:  Array consisting of the species name, object type,
                      and database type.  The array may be empty if no
                      match is found.
      
        Exceptions :  none
        Status     :  At Risk.
      43ea3ea9
  24. 13 Nov, 2009 1 commit
  25. 07 Oct, 2009 1 commit
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  27. 12 Aug, 2009 1 commit
  28. 11 Aug, 2009 1 commit
  29. 10 Aug, 2009 1 commit
    • Andreas Kusalananda Kähäri's avatar
      Move programmatic alias creation into find_and_add_aliases(). · ba447552
      Andreas Kusalananda Kähäri authored
      # Some aliases are added programatically.
      # 1) The "species_name"
      # 2) The "species name"
      # 3) The "sname" (1+last part)
      # 4) The "snam" (1+3 letters)
      # 5) The "spenam" (3+3 letters)
      
      # Others are read from the meta table.
      # 6) Any species.alias
      # 7) The species.taxonomy_id
      # 8) The assembly.name
      # 9) The species.common_name (if it exists)
      ba447552