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<p>Dear Rokhaya,<br>
<br>
The <b>homo_sapiens_merged_vep_95_GRCh37.tar </b>file you
downloaded is what we call a VEP cache file and is not mean to be
read/parsed outside VEP<b>. </b>Therefore we don't have a README
file at the moment.<b><br>
</b>This file helps to speed up local installation of VEP,
whithout the need to access remotely to the Ensembl databases, nor
the REST API.</p>
<p>If you want to run VEP locally instead of using our REST API, you
can find some documentation about the VEP installation here: <a
moz-do-not-send="true"
href="https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html">https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html</a><b><br>
</b></p>
<p>And documentation about the VEP cache here: <a
moz-do-not-send="true"
href="https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache">https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache</a><b><br>
</b></p>
<p>If you struggle to install VEP, we also have a Docker image
available: <a moz-do-not-send="true"
href="https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#docker">https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#docker</a><b>.<br>
</b></p>
<p>Best regards,<b><br>
</b></p>
<pre class="moz-signature" cols="72">Laurent</pre>
<div class="moz-cite-prefix">On 26/03/2019 13:42, Rokhaya BA wrote:<br>
</div>
<blockquote type="cite"
cite="mid:4874280b-b7f9-c659-1256-a96242fc6776@univ-nantes.fr">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<p>Dear Mark,</p>
<p>Thank you very much for your answer. I tried to reduce my
request according to the service rate limit. Unfortunately, 15
requests per second did not increase considerably my runtime, I
need to submit hundreds of variants per second.</p>
<p>Anyway, I downloaded your "<b><i>homo_sapiens_merged_vep_95_GRCh37.tar</i></b>"
file and then tried to retrieve SIFT/Polyphen scores and
predictions locally. However, the file is a little bit tricky
for me and does not provide any readme. <br>
</p>
<p>Is there any documentation that can help to understand the file
directories or where I can obtain information I need
(SIFT/Polyphen scores and predictions)?</p>
<p>I am really grateful for your help.</p>
<p>Best regards,</p>
<p>Rokhaya BA</p>
<p>PhD Student in Bioinformatics </p>
<div class="moz-cite-prefix">Le 21/03/2019 à 12:19, Mark McDowall
a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:c9b186b9-1179-c900-209b-cabf70002d9b@ebi.ac.uk">Hi
Rokhaya, <br>
<br>
A 429 error highlights that you are hitting the rate limit for a
client to the service: <br>
<br>
<a class="moz-txt-link-freetext"
href="https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Response-Codes"
moz-do-not-send="true">https://github.com/Ensembl/ensembl-rest/wiki/HTTP-Response-Codes</a>
<br>
<br>
Have a look at the following documentation for the defined rate
limits for the service: <br>
<br>
<a class="moz-txt-link-freetext"
href="https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits"
moz-do-not-send="true">https://github.com/Ensembl/ensembl-rest/wiki/Rate-Limits</a>
<br>
<br>
You'll need to throttle your code by monitoring the headers to
avoid getting the 503 errors <br>
<br>
Hope this helps, <br>
<br>
Mark <br>
<br>
On 21/03/2019 11:02, Rokhaya BA wrote: <br>
<blockquote type="cite">Hello, <br>
<br>
I am a PhD student in bioinformatics within the CRTI in
Nantes, France. <br>
<br>
I am developing Ferret (<a class="moz-txt-link-freetext"
href="http://limousophie35.github.io/Ferret/"
moz-do-not-send="true">http://limousophie35.github.io/Ferret/</a>),
a Java application designed to retrieve annotations from the
VEP REST API using variants id (rsid). This application
submits a https request and extract the sift/polyphen scores
and predictions from the JSON output. <br>
<br>
However, VEP server usually shut down my requests after some
iterations. Please see below some examples of errors returned
by the app: <br>
<br>
/Server returned HTTP response code: 429 for URL:
<a class="moz-txt-link-freetext"
href="https://rest.ensembl.org/vep/human/id/rs41282276?content-type=application/json/"
moz-do-not-send="true">https://rest.ensembl.org/vep/human/id/rs41282276?content-type=application/json/</a><br>
<br>
/Server returned HTTP response code: 503 for URL:
<a class="moz-txt-link-freetext"
href="https://rest.ensembl.org/vep/human/id/rs543148494?content-type=application/json/"
moz-do-not-send="true">https://rest.ensembl.org/vep/human/id/rs543148494?content-type=application/json/</a><br>
<br>
In practice, I use threads to speed up my runtime. Then, the
application submits many requests in a short amount of time. <br>
<br>
I wanted to know if there is any way to solve this issue? <br>
<br>
Thank you very much for your help. <br>
<br>
Best regards, <br>
<br>
Rokhaya BA <br>
<br>
PhD Student in Bioinformatics <br>
<br>
<br>
<br>
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</blockquote>
<br>
</blockquote>
<br>
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