This module is meant to be used a part of the OBDA system, e.g.:
use Bio::DB::Registry; my $registry = Bio::DB::Registry->new; my $db = $registry->get_database('biosql'); my $seq = $db->get_Seq_by_acc('P41932');
This module connects code that uses OBDA to the bioperl-db package and the underlying BioSQL database.
The Open Biological Database Access (OBDA) system was designed so that one could use the same application code to access data from multiple database types by simply changing a few lines in a configuration file. See http://www.bioperl.org/wiki/HOWTO:OBDA for more information.
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
Please direct usage questions or support issues to the mailing list:
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:
Email bosborne at alum.mit.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new_from_registry Usage : Function: Create a database object that can be used by OBDA Returns : Args : Hash containing connection parameters read from an OBDA registry file
Title : get_Seq_by_id Usage : $seq = $db->get_Seq_by_id(12345) Function: Example : Returns : One or more Sequence objects Args : An identifier
Title : get_Seq_by_acc Usage : $seq = $db->get_Seq_by_acc('A12345') Function: Example : Returns : One or more Sequence objects Args : An accession number
Title : get_Seq_by_version Usage : $seq = $db->get_Seq_by_version('A12345.3') Function: Example : Returns : One or more Sequence objects Args : A versioned accession number
Title : _db Usage : Function: Get or set the BioDB object Example : Returns : Args :