[ensembl-dev] Slow get_adaptor

[Genomeo Dev]

Thanks very much Magali and Andy.

With regard to the script,  fetch_all_by_stable_id_list() quietly fails on
gene ids which are no longer in Ensembl database. I have a set of genes
from Ensembl 73 which I obtained based on VEP 73. I still want to annotate
everything in this set with start, end and external names. I looked up by
fetch_by* in the Doxygen Perl Documentation but could not find a function
which recognises old ID genes. Do you know any function that solves that?

G.


On 8 January 2014 10:34, Andy Yates <ayates at ebi.ac.uk> wrote:

> Hi there,
>
> The blocking queries have been killed from the server so you should see a
> marked improvement in your code's performance. Script response time will be
> dependent on database load & your distance from the MySQL server. The
> figures Mag quoted are a best case where the database is located on the
> same network as the machine running the API script.
>
> Andy
>
> ------------
> Andrew Yates - Ensembl Support Coordinator
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> Tel: +44-(0)1223-492538
> Fax: +44-(0)1223-494468
> http://www.ensembl.org/
>
> On 8 Jan 2014, at 10:27, mag <mr6 at ebi.ac.uk> wrote:
>
> > Hi Genomeo,
> >
> > I am afraid we still have some heavy and long running queries slowing
> down our servers.
> > We are looking into it as we speak.
> >
> > I have tried running your code on a local server, for all the genes on
> chromosome 1.
> > This returns in less than a minute, with 5363 genes and 17531
> transcripts.
> > It would be a little bit slower from a remote server, but this gives you
> an idea of how fast the script should be running in normal conditions.
> >
> > The useast server seems a lot quieter, so I would recommend you try
> using that instead.
> > host => useastdb.ensembl.org, user => anonymous
> > (http://www.ensembl.org/info/data/mysql.html)
> >
> > Alternatively, if you are planning on using the databases regularly and
> have mysql installed locally, you can create your own local server.
> > The mysql dumps are available here:
> ftp://ftp.ensembl.org/pub/current_mysql/
> > And instructions on how to install it can be found here:
> http://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html
> >
> >
> > Hope that helps,
> > Magali
> >
> > On 08/01/2014 09:25, Genomeo Dev wrote:
> >> 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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>
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