[ensembl-dev] Slow get_adaptor

[mag]

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 <mailto: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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