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Summary

efg_transport.pm

Package variables

Included modules

Inherit

Bio::Das::ProServer::SourceAdaptor::Transport::generic

Synopsis

No synopsis!

Description

Transport module to retrieve REsult features from efg database

Methods

Methods description

None available.

Methods code

sub DESTROY {

  my $self = shift;
  $self->disconnect();
}

1;

}

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";

}

General documentation

This code is distributed under an Apache style licence. Please see
/info/about/code_licence.html for details.

Stefan Graf, Ensembl Functional Genomics

Please post comments/questions to the Ensembl development list
<ensembl-dev@ebi.ac.uk>