—
—
—
—
—
—

              
# $Id: OBDA.pm,v 1.3 2006/10/03 12:49:41 bosborne Exp $
#
# BioPerl module for Bio::DB::BioSQL::OBDA
#
# Copyright Brian Osborne
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
HideShow 53 lines of Pod
=head1 NAME
Bio::DB::BioSQL::OBDA
=head1 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 = $db->get_Seq_by_acc('P41932');
=head1 DESCRIPTION
This module connects code that uses OBDA to the bioperl-db package
and the underlying BioSQL database.
The Open Biological Database Access (OBDA) system was designed so that one 
could use the same application code to access data from multiple database 
types by simply changing a few lines in a configuration file. See
L<http://www.bioperl.org/wiki/HOWTO:OBDA> for more information.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
  bioperl-l@bio.perl.org
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the web:
  http://bugzilla.open-bio.org
=head1 AUTHOR - Brian Osborne
Email bosborne at alum.mit.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal 
methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::BioSQL::OBDA;
use strict;
use Bio::DB::Query::BioQuery;
use Bio::DB::BioDB;
use base qw(Bio::Root::Root Bio::DB::RandomAccessI);
HideShow 11 lines of Pod
=head2 new_from_registry
 Title   : new_from_registry
 Usage   : 
 Function: Create a database object that can be used by OBDA
 Returns : 
 Args    : Hash containing connection parameters read from an OBDA
           registry file
=cut
sub new_from_registry {
   my ($class, %conf) = @_;
        my $self = $class->SUPER::new();
        my ($host,$port) = split ":", $conf{'location'};
        my $db = Bio::DB::BioDB->new(-database => 'biosql',
                                                                                  -host     => $host,
                                                                                  -port     => $port,
                                                                                  -dbname   => $conf{'dbname'},
                                                                                  -driver   => $conf{'driver'},
                                                                                  -user     => $conf{'user'},
                                                                                  -pass     => $conf{'passwd'} );
        $self->_db($db);
        $self;
}
HideShow 13 lines of Pod
=head1 Methods inherited from Bio::DB::RandomAccessI
=head2 get_Seq_by_id
 Title   : get_Seq_by_id
 Usage   : $seq = $db->get_Seq_by_id(12345)
 Function:
 Example :
 Returns : One or more Sequence objects
 Args    : An identifier
=cut
sub get_Seq_by_id {
   my ($self,$id) = @_;
        my $db = $self->_db;
        my @seqs = ();
        $self->throw("No identifier given") unless $id;
        my $query = Bio::DB::Query::BioQuery->new(
                  -datacollections => ['Bio::SeqI seq'],
             -where => ["seq.primary_id = $id"]);
        my $seq_adaptor = $db->get_object_adaptor('Bio::SeqI');
        my $result = $seq_adaptor->find_by_query($query);
        for my $seq ($result->next_object) {
                push @seqs,$seq;
        }
        return wantarray ? @seqs : $seqs[0];
}
HideShow 11 lines of Pod
=head2 get_Seq_by_acc
 Title   : get_Seq_by_acc
 Usage   : $seq = $db->get_Seq_by_acc('A12345')
 Function:
 Example :
 Returns : One or more Sequence objects
 Args    : An accession number
=cut
sub get_Seq_by_acc {
   my ($self,$acc) = @_;
        my $db = $self->_db;
        my @seqs = ();
        $self->throw("No accession given") unless $acc;
        my $query = Bio::DB::Query::BioQuery->new(
     -datacollections => ['Bio::SeqI seq'],
          -where => ["seq.accession_number = '$acc'"]);
        my $seq_adaptor = $db->get_object_adaptor('Bio::SeqI');
        my $result = $seq_adaptor->find_by_query($query);
        for my $seq ($result->next_object) {
                push @seqs,$seq;
        }
        return wantarray ? @seqs : $seqs[0];
}
HideShow 11 lines of Pod
=head2 get_Seq_by_version
 Title   : get_Seq_by_version
 Usage   : $seq = $db->get_Seq_by_version('A12345.3')
 Function:
 Example :
 Returns : One or more Sequence objects
 Args    : A versioned accession number
=cut
sub get_Seq_by_version {
   my ($self,$vacc) = @_;
        my $db = $self->_db;
        my @seqs = ();
        my ($acc,$ver) = split /\./, $vacc; # split on period
        $self->throw("Must supply a versioned accession: <accession>.<version>")
          unless ($acc && $ver);
        my $query = Bio::DB::Query::BioQuery->new(
     -datacollections => ['Bio::SeqI seq'],
          -where => ["seq.accession_number = '$acc'",
                                         "seq.version = $ver"]);
        my $seq_adaptor = $db->get_object_adaptor('Bio::SeqI');
        my $result = $seq_adaptor->find_by_query($query);
        for my $seq ($result->next_object) {
                push @seqs,$seq;
        }
        return wantarray ? @seqs : $seqs[0];
}
HideShow 13 lines of Pod
=head1 Private methods
=head2 _db
 Title   : _db
 Usage   : 
 Function: Get or set the BioDB object
 Example :
 Returns : 
 Args    : 
=cut
sub _db {
        my ($self,$db) = @_;
        $self->{_db} = $db if ($db);
        $self->{_db};
}
1;
__END__