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Hi Genomeo,<br>
<br>
I am afraid we still have some heavy and long running queries
slowing down our servers.<br>
We are looking into it as we speak.<br>
<br>
I have tried running your code on a local server, for all the genes
on chromosome 1.<br>
This returns in less than a minute, with 5363 genes and 17531
transcripts.<br>
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.<br>
<br>
The useast server seems a lot quieter, so I would recommend you try
using that instead.<br>
host => useastdb.ensembl.org, user => anonymous<br>
(<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/data/mysql.html">http://www.ensembl.org/info/data/mysql.html</a>)<br>
<br>
Alternatively, if you are planning on using the databases regularly
and have mysql installed locally, you can create your own local
server.<br>
The mysql dumps are available here:
<a class="moz-txt-link-freetext" href="ftp://ftp.ensembl.org/pub/current_mysql/">ftp://ftp.ensembl.org/pub/current_mysql/</a><br>
And instructions on how to install it can be found here:
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html">http://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html</a><br>
<br>
<br>
Hope that helps,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 08/01/2014 09:25, Genomeo Dev wrote:<br>
</div>
<blockquote
cite="mid:CAKry3c3NvKJdp-uYt0MPEDnU1Y8G-b8OCh3MX+qTDCbgDuan_w@mail.gmail.com"
type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>This morning it is getting even slower - takes minutes to
just run the code for two genes.</div>
<div><br>
</div>
<div>Do you have any advice on how I can run it for 5000 genes
within a reasonable time?</div>
<div><br>
</div>
<div>G.</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 7 January 2014 19:26, <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi
Genomeo,<br>
<br>
I don't think there is anything massively wrong with the
code you are using.<br>
<br>
Looking at our mysql server, it is currently under heavy
load, which would<br>
explain slow response time.<br>
<br>
Please let us know if the problem persists.<br>
<br>
<br>
Regards,<br>
Magali<br>
<div>
<div class="h5"><br>
> Hi all,<br>
><br>
> I am finding this code very slow. I am using
Ensembl VM 74:<br>
><br>
> $gene_adaptor =
Bio::EnsEMBL::Registry->get_adaptor( "human", "core",<br>
> "gene" );<br>
><br>
> my $genes =<br>
>
$gene_adaptor->fetch_all_by_stable_id_list(["ENSG00000249352","ENSG00000109576"]);<br>
><br>
> while ( my $gene = shift @{$genes} ) {<br>
> my $gstring = feature2string($gene);<br>
> print "$gstring\n";<br>
> my $transcripts = $gene->get_all_Transcripts();<br>
> while ( my $transcript = shift @{$transcripts} ) {<br>
> my $tstring = feature2string($transcript);<br>
> print "\t$tstring\n";<br>
> }<br>
> }<br>
><br>
> I suspect the first line is the problem. Any advice
on how I can run this<br>
> faster? especially for a large set of genes?<br>
><br>
> Thanks,<br>
><br>
> Genomeo<br>
</div>
</div>
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><br>
<br>
<br>
</blockquote>
</div>
<br>
</div>
</blockquote>
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