Commit a08b56ee authored by Magali Ruffier's avatar Magali Ruffier
Browse files

supports different dbtype

parent 80f69c74
......@@ -11,16 +11,17 @@ use Bio::EnsEMBL::DensityType;
use Bio::EnsEMBL::DensityFeature;
## Default run method
## For a given species, generates the required density features in the core database
# default run method
# For a given databases of dbtype, flags exons which are constitutive
sub run {
my ($self) = @_;
my $species = $self->param('species');
my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, 'core');
my $dbtype = $self->param('dbtype');
my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $dbtype);
my $helper = $dba->dbc()->sql_helper();
my $ga = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'Gene');
my $ga = Bio::EnsEMBL::Registry->get_adaptor($species, $dbtype, 'Gene');
my $slices = Bio::EnsEMBL::Registry->get_adaptor($species, 'core', 'slice')->fetch_all('toplevel');
my $slices = Bio::EnsEMBL::Registry->get_adaptor($species, $dbtype, 'slice')->fetch_all('toplevel');
my @gene_dbIDs = sort { $a <=> $b } @{ $ga->list_dbIDs() };
my $bin = scalar(@gene_dbIDs)/1000;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment