[ensembl-dev] Slow get_adaptor

Genomeo Dev genomeodev at gmail.com
Wed Jan 8 09:25:56 GMT 2014


Hi,

This morning it is getting even slower - takes minutes to just run the code
for two genes.

Do you have any advice on how I can run it for 5000 genes within a
reasonable time?

G.


On 7 January 2014 19:26, <mr6 at ebi.ac.uk> wrote:

> 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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> >
>
>
>
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