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<p>Hellp Jon,</p>
<p>It's quite strange, indeed!</p>
<p>Do you "hardcode" anything w.r.t. Ensembl release, perhaps?<br>
(I am blundering in the dark ... not sure what's happening here)</p>
<p>S<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 13/02/2023 16:13, Williams, Jonathan
(RTH) OUH wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20230213161629.237851181AA_3EA625DB@hh-mx4.ebi.ac.uk">
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<p class="MsoNormal">Hello Stefano, <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks for the speedy reply. Connecting via
“ensembldb.ensembl.org”, is this still correct?
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Will adapt code to restrict to COSMIC – the
performance increase will be useful. I don’t think it’s a
region related issue; matching regions before and after
January 2023 returned COSV IDs previously and no longer do
now, a separate query to look up gene names using the same
declared slice still performs quite happily. Very strange!
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Jon<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span
style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#999999;mso-fareast-language:EN-GB">Jonathan
Williams DClinSci PhD FRCPath<br>
Principal Clinical Scientist (HSS Registered) | NGS Core
and Cancer Genetics</span></b><span
style="font-size:12.0pt;font-family:"Times New
Roman",serif;color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="mso-fareast-language:EN-GB" lang="EN-US">From:</span></b><span
style="mso-fareast-language:EN-GB" lang="EN-US"> Dev
<a class="moz-txt-link-rfc2396E" href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a>
<b>On Behalf Of </b>Stefano Giorgetti<br>
<b>Sent:</b> 13 February 2023 16:03<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a><br>
<b>Subject:</b> Re: [ensembl-dev] Changes to COSMIC data
storage in ensembl API?<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p>Hello Jon,<span style="mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p>The code base hasn't changed significantly transitioning from
E!108 to E!109, TBH.<o:p></o:p></p>
<p>I tried (sort of) your code below, and I could get some IDs
back from the API.<o:p></o:p></p>
<p>Possible differences between our code do not seem enough to
explain why you are not retrieving any data:<o:p></o:p></p>
<ul type="disc">
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0
level1 lfo1">
Used "ensembldb.ensembl.org" host<o:p></o:p></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0
level1 lfo1">
Focussed on region chr18 between 49481681 and 49492479<o:p></o:p></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0
level1 lfo1">
returned the first 5 IDs<o:p></o:p></li>
</ul>
<p>As additional note, I would check<o:p></o:p></p>
<ol type="1" start="1">
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1
level1 lfo2">
you are not connecting to our former US West mirror (which
should not be the case)<o:p></o:p></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1
level1 lfo2">
you may want to use
"$slice->get_all_somatic_VariationFeatures_by_source('COSMIC')"
instead of "get_all_somatic_VariationFeatures()"<br>
I am getting 6-fold increase in performance ... if you are
interested only in COSMIC variants, of course<o:p></o:p></li>
</ol>
<p>Is it maybe region-specific issue?<br>
Feel free to share the regions you are interested in, should
you want me to double check.<o:p></o:p></p>
<p>Hope this helps<o:p></o:p></p>
<p>Cheers,<o:p></o:p></p>
<p>Stefano<o:p></o:p></p>
<div>
<p class="MsoNormal">On 13/02/2023 14:40, Williams, Jonathan
(RTH) OUH wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hello All, <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">As part of a pipeline, I’ve been using
the following code snippet to grab COSMIC variant IDs from
specific regions of the human genome – this all worked
wonderfully until the beginning of February this year and
I’m wondering if the code base has changed with the most
recent ensembl release? Any advice on how to do this now,
bearing in mind I am definitely a bit of a Bioinformatics
amateur?<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">my $slice_adaptor =
$registry->get_adaptor('Human', 'Core', 'Slice');<o:p></o:p></p>
<p class="MsoNormal">my $slice =
$slice_adaptor->fetch_by_region($coords);<o:p></o:p></p>
<p class="MsoNormal">my $vs =
$slice->get_all_somatic_VariationFeatures();<o:p></o:p></p>
<p class="MsoNormal">my @variants = @{$vs};<o:p></o:p></p>
<p class="MsoNormal">foreach (@variants){<o:p></o:p></p>
<p class="MsoNormal"> my $name = $_->name();<o:p></o:p></p>
<p class="MsoNormal"> push (@variant_list,
$name);<o:p></o:p></p>
<p class="MsoNormal">};<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">When this was working the end result was
pushing of COSV IDs into the final @variant_list array which
I was then able to print against regions in a final report.
This array now ends up empty so either the “->name()”
parameter or something to do with COSMIC data storage
amongst the “get_all_somatic_VariationFeatures” dataset may
have been altered…<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Jon Williams <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB"><br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
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<pre class="moz-signature" cols="72">--
—
Stefano Giorgetti
Ensembl Infrastructure Team Leader, EMBL-EBI
<a class="moz-txt-link-abbreviated" href="mailto:sgiorgetti@ebi.ac.uk">sgiorgetti@ebi.ac.uk</a></pre>
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