[ensembl-dev] Slow get_adaptor

[mr6 at ebi.ac.uk]

Hi Genomeo,

I don't think there is anything massively wrong with the code you are using.

Looking at our mysql server, it is currently under heavy load, which would
explain slow response time.

Please let us know if the problem persists.


Regards,
Magali

> Hi all,
>
> I am finding this code very slow. I am using Ensembl VM 74:
>
> $gene_adaptor = Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
> "gene" );
>
> my $genes =
> $gene_adaptor->fetch_all_by_stable_id_list(["ENSG00000249352","ENSG00000109576"]);
>
> while ( my $gene = shift @{$genes} ) {
> my $gstring = feature2string($gene);
> print "$gstring\n";
> my $transcripts = $gene->get_all_Transcripts();
> while ( my $transcript = shift @{$transcripts} ) {
> my $tstring = feature2string($transcript);
> print "\t$tstring\n";
> }
> }
>
> I suspect the first line is the problem. Any advice on how I can run this
> faster? especially for a large set of genes?
>
> Thanks,
>
> Genomeo
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