[ensembl-dev] Best way to collect probesets (excluding all exon arrays)?

Alexander Pico apico at gladstone.ucsf.edu
Tue May 24 18:14:07 BST 2011

Looks like a known problem. The API code has the following comment notes:

Funcgen/DBSQL/ResultFeatureAdaptor.pm: line 1259
 #Not straight forward without creating tmp table

In version 60, the note in this area stated:
 #This join between sr and pf is causing the slow down.  Need to select
right join for this.
 #just do two separate queries for now.

Indeed, the tmp table triggered by the join is still causing a slow down.
Let us know if you come up with any workarounds or solutions to this tmp
table issue. Thanks!
 - Alex

On 5/23/11 6:28 PM, "Alexander Pico" <apico at gladstone.ucsf.edu> wrote:

> Hi,
> I'm looking for a better way to get probe features. I'm currently using
> 'fetch_all_by_linked_transcript_Gene()', but for species with all exon
> arrays, this can take days...
> Other than going in and deleting probesets from the funcgen databases (local
> copies), how can I get around processing certain arrays, like the all exon
> arrays, and just collect everything else?
> Here's my current code snippet:
> my $probe_adaptor = $registry->get_adaptor($species, "funcgen",
> "ProbeFeature");
> my $probe_features =
> $probe_adaptor->fetch_all_by_linked_transcript_Gene($gene);
> foreach my $pf (@$probe_features) {
>     // do stuff
> }
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