[ensembl-dev] Slow get_adaptor

[Andy Yates]

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
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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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