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Bio::DB::Registry.3pm

NAME

Bio::DB::Registry - Access to the Open Bio Database Access registry scheme

SYNOPSIS

     use Bio::DB::Registry();
 
     $registry = Bio::DB::Registry->new();
 
     @available_services = $registry->services;
 
     $db = $registry->get_database('embl');
     # $db is a Bio::DB::SeqI implementing class
 
     $seq = $db->get_Seq_by_acc("J02231");
 
 

DESCRIPTION

This module provides access to the Open Bio Database Access (OBDA) scheme, which provides a single cross-language and cross-platform specification of how to get to databases. These databases may be accessible through the Web, they may be BioSQL databases, or they may be local, indexed flatfile databases.

If the user or system administrator has not installed the default init file, seqdatabase.ini, in /etc/bioinformatics or ${HOME}/.bioinformatics then creating the first Registry object copies the default settings from the www.open-bio.org. The Registry object will attempt to store these settings in a new file, ${HOME}/.bioinformatics/seqdatabase.ini.

Users can specify one or more custom locations for the init file by setting $OBDA_SEARCH_PATH to those directories, where multiple directories should be separated by ';'.

Please see the OBDA Access HOWTO for more information (http://bioperl.open-bio.org/wiki/HOWTO:OBDA <http://bioperl.open-bio.org/wiki/HOWTO:OBDA>).

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

_load_registry

  Title   : _load_registry
  Usage   :
  Function: Looks for seqdatabase.ini files in the expected locations and
            in the directories specified by $OBDA_SEARCH_PATH. If no files
            are found download a default file from www.open-bio.org
  Returns : nothing
  Args    : none
 
 

get_database

  Title   : get_database
  Usage   : my $db = $registry->get_database($dbname);
  Function: Retrieve a Database object which implements Bio::DB::SeqI interface
  Returns : Bio::DB::SeqI object
  Args    : string describing the name of the database
 
 

services

  Title   : services
  Usage   : my @available = $registry->services();
  Function: returns list of possible services
  Returns : list of strings
  Args    : none
 
 

_get_ini_files

  Title   : _get_ini_files
  Usage   : my @files = $self->_get_ini_files
  Function: To find all the seqdatabase.ini files
  Returns : list of seqdatabase.ini paths
  Args    : None
 
 

_make_private_registry

  Title   : _make_private_registry
  Usage   :
  Function: Make private registry in file in $HOME
  Returns : Path to private registry file
  Args    : None