[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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