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<p>Hello Jon,</p>
<p>The code base hasn't changed significantly transitioning from
E!108 to E!109, TBH.</p>
<p>I tried (sort of) your code below, and I could get some IDs back
from the API.</p>
<p>Possible differences between our code do not seem enough to
explain why you are not retrieving any data:<br>
</p>
<ul>
<li>Used "ensembldb.ensembl.org" host</li>
<li>Focussed on region chr18 between 49481681 and 49492479</li>
<li>returned the first 5 IDs</li>
</ul>
<p>As additional note, I would check</p>
<ol>
<li>you are not connecting to our former US West mirror (which
should not be the case)</li>
<li>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</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.</p>
<p>Hope this helps</p>
<p>Cheers,</p>
<p>Stefano<br>
</p>
<div class="moz-cite-prefix">On 13/02/2023 14:40, Williams, Jonathan
(RTH) OUH wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20230213124330.C89BD62BCA4_3EA3072B@hh-mx3.ebi.ac.uk">
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<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>
</div>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
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</pre>
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