Raw content of Bio::EnsEMBL::ExternalData::GO::GOAdaptor
<![CDATA[#
# BioPerl module for Bio::EnsEMBL::ExternalData::GO::GOAdaptor
#
# Cared for by Tony Cox <avc@sanger.ac.uk>
#
# Copyright EnsEMBL
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
HaplotypeAdaptor - DESCRIPTION of Object
GO database interface.
=head1 SYNOPSIS
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::ExternalData::GO::GOAdaptor;
$hapdb = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
-user => 'ensro',
-dbname => 'haplotype_5_28',
-host => 'ecs3d',
-driver => 'mysql',
);
my $go_adtor = Bio::EnsEMBL::ExternalData::GO::GOAdaptor->new($godb);
my $term = $go_adtor->get_term({acc=>"GO:0005509"});
printf
"GO term; name=%s GO ID=%s\n\n",
$term->name(), $term->public_acc();
### You can add the GOAdaptor as an 'external adaptor' to the 'main'
### Ensembl database object, then use it as:
$ensdb = Bio::EnsEMBL::DBSQL::DBAdaptor->new( ... );
$ensdb->add_ExternalAdaptor('go', $go_adtor);
# then later on, elsewhere:
$go_adtor = $ensdb->get_ExternalAdaptor('go');
# also available:
$ensdb->list_ExternalAdaptors();
$ensdb->remove_ExternalAdaptor('go');
=head1 DESCRIPTION
This module is an entry point into a GO database.
The objects can only be read from the database, not written. (They are
loaded ussing a separate perl script).
For more info, see GO::AppHandle.pm
=head1 CONTACT
Tony Cox <avc@sanger.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::ExternalData::GO::GOAdaptor;
use vars qw(@ISA $AUTOLOAD);
use strict;
# Object preamble - inherits from Bio::Root::Object
use Bio::Root::Object;
use DBI;
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
use Bio::DBLinkContainerI;
use Bio::Annotation::DBLink;
use GO::AppHandle;
use Bio::EnsEMBL::Root;
use Bio::EnsEMBL::Registry;
my $reg = "Bio::EnsEMBL::Registry";
@ISA = qw(Bio::EnsEMBL::Root GO::AppHandle);
sub new {
my($class,@args) = @_;
my $group = "go";
my $self = {};
bless $self, $class;
my ($db,$user,$pass,$host,$port,$driver,$species) =
rearrange([qw(
DBNAME
USER
PASS
HOST
PORT
DRIVER
SPECIES
)],@args);
if(!defined($species)){
$species = "MULTI";
}
if(defined($reg->get_alias($species,"no throw"))){
my $adap = $reg->get_DBAdaptor($species,$group);
if(defined($adap)){
return $adap;
}
}
if( ! $driver ) {
$driver = 'mysql';
}
if( ! $host ) {
$host = 'localhost';
}
if (! $port ) {
$port = 3306;
}
if(! $pass ) { $pass =''; }
my $dbh ; eval { $dbh= GO::AppHandle->connect(-dbname=>$db,-dbhost=>"$host:$port",-dbuser=>$user,($pass?(-dbauth=>$pass):())); };
throw("Could not connect to database $db user $user as a locator ($@)") unless $dbh;
$self->_db_handle($dbh);
$self->dbname($db);
$self->port($port);
$self->host($host);
$self->driver($driver);
$self->group($group);
$self->species($species);
$reg->add_DBAdaptor($species, $group, $self);
return $self; # success - we hope!
}
sub db{
my $self = shift;
return $self;
}
sub port {
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_port} = $arg );
return $self->{_port};
}
sub species {
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_species} = $arg );
return $self->{_species};
}
sub group {
my ($self, $arg) = @_;
(defined $arg) &&
($self->{_group} = $arg );
return $self->{_group};
}
sub dbname {
my ($self, $arg ) = @_;
( defined $arg ) &&
( $self->{_dbname} = $arg );
$self->{_dbname};
}
sub driver {
my($self, $arg ) = @_;
(defined $arg) &&
($self->{_driver} = $arg );
return $self->{_driver};
}
sub host {
my ($self, $arg ) = @_;
( defined $arg ) &&
( $self->{_host} = $arg );
$self->{_host};
}
# evil....
sub AUTOLOAD {
my $self = shift;
my @args = @_;
(my $function = $AUTOLOAD) =~ s/.*:://;
#print STDERR "Autoloading: $function via ", $self->_db_handle, "\n";
my $return;
eval {
no strict 'vars';
$return = $self->_db_handle->$function(@args);
};
return $return;
}
# retrieve a GO accession using an accession ID (GO::NNNNNNN)
sub fetch_GO_by_accession {
my ($self,$value) = @_;
my $term = $self->_db_handle->get_term({acc=>$value});
}
# set/get handle on ensembl database
sub _ensdb {
my ($self,$value) = @_;
if( defined $value) {$self->{'_ensdb'} = $value;}
return $self->{'_ensdb'};
}
# get/set handle on GO adaptor
sub adaptor {
my ($self,$value) = @_;
if( defined $value) {
$self->{'_adaptor'} = $value;
}
return $self->{'_adaptor'};
}
# set/get handle on GO database
sub _db_handle {
my ($self,$value) = @_;
if( defined $value) {$self->{'_db_handle'} = $value;}
return $self->{'_db_handle'};
}
sub DESTROY {
my ($self) = @_;
if( $self->{'_db_handle'} ) {
$self->{'_db_handle'}->disconnect;
$self->{'_db_handle'} = undef;
}
}
1;
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