<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
Hi Genomeo,<br>
<br>
Unfortunately, if a gene id is no longer in the Ensembl database, it
is because we were unable to find a gene in the newer release that
would map accurately enough to the old model.<br>
This can be because the gene was completely removed, or because its
structure has changed so massively (add a dozen transcripts or a
5000bp UTR) that it does not bear enough resemblance any more.<br>
This is more common in human because of the continuous integration
of manual annotation.<br>
<br>
The rest server archive endpoint (
<meta charset="utf-8">
<a class="moz-txt-link-freetext" href="http://beta.rest.ensembl.org/archive/id/ENSG00000101321?content-type=application/json">http://beta.rest.ensembl.org/archive/id/ENSG00000101321?content-type=application/json</a>)
can help you find out when a given ID was last seen.<br>
If that ID was not mapped in the latest release, it can sadly not
provide you with much more information.<br>
<br>
To recognise old gene ids, you need to use the old database version
in which these genes were last seen.<br>
Given your set was generated on release 73, you can use the 73 API
version which will automatically use the 73 data.<br>
<br>
<br>
Regards,<br>
Magali<br>
<br>
<div class="moz-cite-prefix">On 08/01/2014 11:31, Genomeo Dev wrote:<br>
</div>
<blockquote
cite="mid:CAKry3c3gpDoJ0Aammcb_Tn4oFw9a+eYUp3vRmj_31+T7iM0KMA@mail.gmail.com"
type="cite">
<div dir="ltr">Thanks very much Magali and Andy.
<div><br>
</div>
<div>With regard to the script, <span
style="font-size:13px;font-family:arial,sans-serif">fetch_all_by_</span><font
face="arial, sans-serif">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?</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">G.</font></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 8 January 2014 10:34, Andy Yates <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:ayates@ebi.ac.uk" target="_blank">ayates@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 there,<br>
<br>
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.<br>
<br>
Andy<br>
<br>
------------<br>
Andrew Yates - Ensembl Support Coordinator<br>
European Bioinformatics Institute (EMBL-EBI)<br>
European Molecular Biology Laboratory<br>
Wellcome Trust Genome Campus<br>
Hinxton<br>
Cambridge CB10 1SD<br>
Tel: <a moz-do-not-send="true"
href="tel:%2B44-%280%291223-492538" value="+441223492538">+44-(0)1223-492538</a><br>
Fax: <a moz-do-not-send="true"
href="tel:%2B44-%280%291223-494468" value="+441223494468">+44-(0)1223-494468</a><br>
<a moz-do-not-send="true" href="http://www.ensembl.org/"
target="_blank">http://www.ensembl.org/</a><br>
<div class="HOEnZb">
<div class="h5"><br>
On 8 Jan 2014, at 10:27, mag <<a
moz-do-not-send="true" href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>>
wrote:<br>
<br>
> 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 => <a moz-do-not-send="true"
href="http://useastdb.ensembl.org" target="_blank">useastdb.ensembl.org</a>,
user => anonymous<br>
> (<a moz-do-not-send="true"
href="http://www.ensembl.org/info/data/mysql.html"
target="_blank">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
moz-do-not-send="true"
href="ftp://ftp.ensembl.org/pub/current_mysql/"
target="_blank">ftp://ftp.ensembl.org/pub/current_mysql/</a><br>
> And instructions on how to install it can be found
here: <a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html"
target="_blank">http://www.ensembl.org/info/docs/webcode/mirror/install/ensembl-data.html</a><br>
><br>
><br>
> Hope that helps,<br>
> Magali<br>
><br>
> On 08/01/2014 09:25, Genomeo Dev wrote:<br>
>> Hi,<br>
>><br>
>> This morning it is getting even slower - takes
minutes to just run the code for two genes.<br>
>><br>
>> Do you have any advice on how I can run it for
5000 genes within a reasonable time?<br>
>><br>
>> G.<br>
>><br>
>><br>
>> On 7 January 2014 19:26, <<a
moz-do-not-send="true" href="mailto:mr6@ebi.ac.uk">mr6@ebi.ac.uk</a>>
wrote:<br>
>> 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>
>><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>
>> >
_______________________________________________<br>
>> > Dev mailing list <a
moz-do-not-send="true" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
>> > Posting guidelines and
subscribe/unsubscribe info:<br>
>> > <a moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev"
target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
>> > Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
>> ><br>
>><br>
>><br>
>><br>
><br>
> _______________________________________________<br>
> Dev mailing list <a moz-do-not-send="true"
href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info:
<a moz-do-not-send="true"
href="http://lists.ensembl.org/mailman/listinfo/dev"
target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
> Ensembl Blog: <a moz-do-not-send="true"
href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</body>
</html>