[ensembl-dev] database access
Dan Staines
dstaines at ebi.ac.uk
Thu Mar 14 15:42:32 GMT 2013
On 03/14/2013 02:49 PM, Gary Duncan wrote:
> here it is
Thanks - however, without the requisite input files etc. its hard to
test properly, but the work of getting the registry loaded, and then
getting the DBAdaptor and GeneAdaptor works fine, as does running
through all protein_coding genes and executing your code to get introns
(takes about 2-3 mins to run for me):
#Load all DBs from Ensembl Genomes
Bio::EnsEMBL::Registry->load_registry_from_db(
-HOST => 'mysql.ebi.ac.uk',
-PORT => 4157,
-USER => 'anonymous',
-verbose => 1
);
#Get the adaptors once
my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor('Dictyostelium
discoideum', 'core');
my $gene_adaptor = $dba->get_GeneAdaptor();
my @data;
for my $gene (@{$gene_adaptor->fetch_all_by_biotype('protein_coding')}) {
foreach my $transcript (@{$gene->get_all_Transcripts()}) {
print $transcript->stable_id(), "\n";
foreach my $intron (@{$transcript->get_all_Introns}) {
print $intron->seq_region_start.' - '.$intron->seq_region_end.' -
'.$intron->seq. "\n";
#Store into a temporary array
push(@data, [
$transcript->stable_id(),
$intron->seq_region_start(),
$intron->seq_region_end(),
$intron->seq()
]);
}
}
}
What version of the Ensembl API are you using? I used the current public
branch (branch-ensembl-70) and all is fine (could be a bit faster to
load the registry with branch-ensemblgenomes-17-70 but its a matter of
~10s vs ~5s initial startup).
Dan.
--
Dan Staines, PhD Ensembl Genomes Technical Coordinator
EMBL-EBI Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
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