Hi Nicole,
The issue here is that DBEntryAdaptor serves a dual purpose; the first is as you've previously used is to retrieve Xrefs from an Ensembl object. This is indicated by the ensembl_id and ensembl_object_type keys in the resulting object hash (from the join between xref and object_xref). However when you go in by source you are asking for all instances in the xref table without the join to object_xref. That's why you do not get the ensembl_id key in the hash. The API does not support the fetching of DBEntries linked to all Genes by a source.
Your available options are
1). Loop through all Genes and use fetch_all_by_Gene (as you said very expensive)
2). Use BioMart which has already de-normalised the entries and so will be very quick
3). Write and execute custom SQL against the database
We will consider if it is possible to perform this kind of query using the API but I cannot guarantee when (and if) it will be completed by.
Best regards,
Andy
Andrew Yates Ensembl Core Software Project Leader
EMBL-EBI Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensembl.org/
On 1 Mar 2013, at 21:34, Nicole Washington <nlwashington at lbl.gov> wrote:
> Hi,
>
> I want to fetch all DBEntries by a given source, say EntrezGene, and then locally make a gene-based hash of the entries. My reason is that repeated queries of fetch_all_by_Gene is a very expensive operation time-wise, particularly when needing to fetch for all genes in a genome.
>
> In order to to this, I need the ensembl ids linked to the DBEntry. However, the objects I get from a fetch_all_by_Source don't seem to be delivering this info.
>
> I'm using r70 of the ensembl API.
>
> Here's a bit of my code:
>
> my $dbentries_by_source = {};
> my %dbentries_by_ensembl_id = {};
>
>
> print STDOUT "Fetching xrefs...\n";
> my $xref_count=0;
>
> foreach my $xref (@xrefs_to_fetch) {
> my $dbes = $dbentry_adaptor->fetch_all_by_source($xref);
> print STDOUT @$dbes . " found. Sorting...";
> $dbentries_by_source->{$xref} = $dbes;
> foreach my $dbe (@$dbes) {
> print STDOUT $dbe->ensembl_id() . ", ";
> if (!defined ($dbentries_by_ensembl_id{$dbe->ensembl_id()})) {
> @{$dbentries_by_ensembl_id{$dbe->ensembl_id()}} = ();
> print "c"; #feedback for making reference hash
> }
> push(@{$dbentries_by_ensembl_id{$dbe->ensembl_id()}},$dbe);
> print "r"; #feedback for adding an reference element
> }
>
> Below you'll find what the Dumper of the first object returned is...you'll notice that there's no "ensembl_id" key-value pair in the DBEntry object.
>
> Am I going about this the wrong way? Any hints? Thanks in advance...
>
> Nicole
>
> $VAR1 = bless( {
> 'priority' => '250',
> 'adaptor' => bless( {
> '_is_multispecies' => '',
> 'db' => bless( {
> 'seq_region_cache' => bless( {
> 'id_cache' => {
> '27527' => [
> '27527',
> '5',
> '2',
> '180915260'
> ],
> '27526' => [
> '27526',
> '19',
> '2',
> '59128983'
> ],
> '27525' => [
> '27525',
> '10',
> '2',
> '135534747'
> ],
> '27524' => [
> '27524',
> '4',
> '2',
> '191154276'
> ],
> '27523' => [
> '27523',
> '8',
> '2',
> '146364022'
> ],
> '27522' => [
> '27522',
> '20',
> '2',
> '63025520'
> ],
> '27521' => [
> '27521',
> '15',
> '2',
> '102531392'
> ],
> '27520' => [
> '27520',
> '14',
> '2',
> '107349540'
> ],
> '27519' => [
> '27519',
> '12',
> '2',
> '133851895'
> ],
> '27518' => [
> '27518',
> '9',
> '2',
> '141213431'
> ],
> '27517' => [
> '27517',
> '3',
> '2',
> '198022430'
> ],
> '27515' => [
> '27515',
> '6',
> '2',
> '171115067'
> ],
> '27514' => [
> '27514',
> '16',
> '2',
> '90354753'
> ],
> '27513' => [
> '27513',
> '13',
> '2',
> '115169878'
> ],
> '27512' => [
> '27512',
> '18',
> '2',
> '78077248'
> ],
> '27511' => [
> '27511',
> '1',
> '2',
> '249250621'
> ],
> '27510' => [
> '27510',
> '22',
> '2',
> '51304566'
> ],
> '27509' => [
> '27509',
> '17',
> '2',
> '81195210'
> ],
> '27508' => [
> '27508',
> '2',
> '2',
> '243199373'
> ],
> '27507' => [
> '27507',
> 'Y',
> '2',
> '59373566'
> ],
> '27516' => [
> '27516',
> 'X',
> '2',
> '155270560'
> ],
> '27506' => [
> '27506',
> '7',
> '2',
> '159138663'
> ],
> '27505' => [
> '27505',
> '21',
> '2',
> '48129895'
> ],
> '27504' => [
> '27504',
> '11',
> '2',
> '135006516'
> ],
> '100965601' => [
> '100965601',
> 'MT',
> '2',
> '16569'
> ]
> },
> 'name_cache' => {
> '5:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27527'},
> '19:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27526'},
> '10:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27525'},
> '4:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27524'},
> '8:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27523'},
> '20:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27522'},
> '15:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27521'},
> '14:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27520'},
> '12:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27519'},
> '9:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27518'},
> '3:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27517'},
> 'X:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27516'},
> '6:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27515'},
> '16:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27514'},
> '13:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27513'},
> '18:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27512'},
> '1:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27511'},
> '22:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27510'},
> '17:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27509'},
> '2:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27508'},
> '7:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27506'},
> '21:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27505'},
> '11:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27504'},
> 'MT:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'100965601'},
> 'Y:2' => $VAR1->{'adaptor'}{'db'}{'seq_region_cache'}{'id_cache'}{'27507'}
> }
> }, 'Bio::EnsEMBL::Utils::SeqRegionCache' ),
> '_is_multispecies' => '',
> '_dbc' => bless( {
> '_username' => 'anonymous',
> 'connected86253' => 1,
> '_timeout' => 0,
> '_host' => 'ensembldb.ensembl.org',
> '_port' => '5306',
> '_query_count' => 10,
> '_driver' => 'mysql',
> '_dbname' => 'homo_sapiens_core_70_37',
> 'db_handle86253' => bless( {}, 'DBI::db' )
> }, 'Bio::EnsEMBL::DBSQL::DBConnection' ),
> '_species' => 'homo_sapiens',
> '_group' => 'core',
> '_species_id' => 1
> }, 'Bio::EnsEMBL::DBSQL::DBAdaptor' ),
> 'dbc' => $VAR1->{'adaptor'}{'db'}{'_dbc'},
> 'species_id' => 1
> }, 'Bio::EnsEMBL::DBSQL::DBEntryAdaptor' ),
> 'display_id' => 'A1BG',
> 'primary_id' => '1',
> 'version' => '0',
> 'description' => 'alpha-1-B glycoprotein',
> 'dbname' => 'EntrezGene',
> 'dbID' => '936659',
> 'synonyms' => [
> 'A1B'
> ],
> 'info_text' => '',
> 'info_type' => 'DEPENDENT',
> 'type' => 'MISC',
> 'db_display_name' => 'EntrezGene'
> }, 'Bio::EnsEMBL::DBEntry' );
>
>
>
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