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Bio::DB::Registry(3)  User Contributed Perl Documentation Bio::DB::Registry(3)

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>).

   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:

	 https://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08		  Bio::DB::Registry(3)

NAME | SYNOPSIS | DESCRIPTION | APPENDIX

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