Bio::DB::Registry(3) User Contributed Perl Documentation Bio::DB::Registry(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::DB::Registry(3)
