Raw content of Bio::Das::ProServer::SourceAdaptor::Transport::efg_transport =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;