Raw content of Bio::Das::ProServer::SourceAdaptor::Transport::efg_transport
<![CDATA[=head1 NAME
efg_transport.pm
=head1 DESCRIPTION
Transport module to retrieve REsult features from efg database
=head1 LICENCE
This code is distributed under an Apache style licence. Please see
/info/about/code_licence.html for details.
=head1 AUTHOR
Stefan Graf, Ensembl Functional Genomics
=head1 CONTACT
Please post comments/questions to the Ensembl development list
<ensembl-dev@ebi.ac.uk>
=cut
package Bio::Das::ProServer::SourceAdaptor::Transport::efg_transport;
#BEGIN {
# my ($eroot) = $ENV{'ENS_ROOT'} =~ m|([a-zA-Z0-9_/\.\-]+)|;
# my ($broot) = $ENV{'BIOPERL_HOME'} =~ m|([a-zA-Z0-9_/\.\-]+)|;
#
# unshift(@INC,"$eroot/ensembl/modules");
# unshift(@INC,"$broot");
#}
use strict;
use Data::Dumper;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Registry;
use Bio::Das::ProServer::SourceAdaptor::Transport::generic;
use vars qw(@ISA);
@ISA = qw(Bio::Das::ProServer::SourceAdaptor::Transport::generic);
sub adaptor {
my $self = shift;
unless($self->{'_adaptor'}) {
my $host = $self->config->{'host'} || 'localhost';
my $port = $self->config->{'port'} || '3306';
my $dbname = $self->config->{'dbname'};
my $username = $self->config->{'username'} || 'ensro';
my $password = $self->config->{'password'} || '';
my $species = $self->config->{'species'} || 'homo_sapiens';
my $data_version = $self->config->{'data_version'};
$self->{'_adaptor'} ||= Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new
(
-host => $host,
-user => $username,
-dbname => $dbname,
-species => $species,
-pass => $password,
-port => $port,
);
print Dumper $self->{'_adaptor'} if ($self->{'debug'});
return $self->{'_adaptor'};
}
}
sub chromosome_by_region {
my ($self, $chr, $start, $end) = @_;
my $slice = $self->adaptor->get_SliceAdaptor->fetch_by_region
(
'chromosome', $chr, $start, $end
);
return $slice;
}
sub disconnect {
my $self = shift;
return unless (exists $self->{'_adaptor'});
$self->{'_adaptor'}->disconnect();
delete $self->{'_adaptor'};
$self->{'debug'} and print STDERR "$self PERFORMED DBA DISCONNECT\n";
}
sub DESTROY {
my $self = shift;
$self->disconnect();
}
1;
]]>