Bio::DB::Registry - Access to the Open Bio Database Access registry scheme
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");
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.org/howtos/OBDA_HOWTO.html>).
Please direct usage questions or support issues to the mailing list:
[email protected]
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.
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:
https://github.com/bioperl/bioperl-live/issues
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
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
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
Title : services
Usage : my @available = $registry->services();
Function: returns list of possible services
Returns : list of strings
Args : none
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
Title : _make_private_registry
Usage :
Function: Make private registry in file in $HOME
Returns : Path to private registry file
Args : None