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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>
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<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>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="mso-fareast-language:EN-GB">From:</span></b><span lang="EN-US" style="mso-fareast-language:EN-GB"> Dev <dev-bounces@ensembl.org>
<b>On Behalf Of </b>Stefano Giorgetti<br>
<b>Sent:</b> 13 February 2023 16:03<br>
<b>To:</b> dev@ensembl.org<br>
<b>Subject:</b> Re: [ensembl-dev] Changes to COSMIC data storage in ensembl API?<o:p></o:p></span></p>
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<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 start="1" type="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>
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<p class="MsoNormal">On 13/02/2023 14:40, Williams, Jonathan (RTH) OUH wrote:<o:p></o:p></p>
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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>
<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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