Bio::DB::BioSQL::OBDA
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.
bioperl-l@bio.perl.org
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
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 :
