NAME

Bio::DB::BioSQL::OBDA

SYNOPSIS

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');

DESCRIPTION

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.

FEEDBACK

Mailing Lists

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

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://redmine.open-bio.org/projects/bioperl

AUTHOR - Brian Osborne

Email bosborne at alum.mit.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new_from_registry

 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

Methods inherited from Bio::DB::RandomAccessI

get_Seq_by_id

 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id(12345)
 Function:
 Example :
 Returns : One or more Sequence objects
 Args    : An identifier

get_Seq_by_acc

 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

get_Seq_by_version

 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

Private methods

_db

 Title   : _db
 Usage   : 
 Function: Get or set the BioDB object
 Example :
 Returns : 
 Args    : 

cpanm Bio::BioEntry

perl -MCPAN -e shell
install Bio::BioEntry