<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Ramiro,<div class=""><br class=""></div><div class="">Thanks for the follow-up. Here are couple of thoughts on your queries:</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Q8) This is more of a generic and larger request which could potentially lead to re-looking at most of the end-points. e.g.: Going by REST standards, a correct http code needs to be sent with each response. So this might be looked at a later stage.</div><div class="">Q7) There are couple of options to get this data:</div><div class=""><br class=""></div><div class="">- Using REST endpoint: <font face="Slack-Lato, appleLogo, sans-serif" class=""><span style="box-sizing: inherit; color: rgba(var(--sk_highlight,18,100,163),1); font-size: 15px; font-variant-ligatures: common-ligatures; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class=""><a href="http://rest.ensembl.org/info/assembly/homo_sapiens?content-type=application/json" class="">http://rest.ensembl.org/info/assembly/homo_sapiens?content-type=application/json</a></span></font></div><div class="">The top_level_region key has a list of coord_system which needs to be made unique</div><div class=""><br class=""></div><div class="">- Use Perl API:</div><div class="">Refer to the script given under ‘Coordinate Systems & Slices’ over here : <a href="https://www.ebi.ac.uk/training/online/sites/ebi.ac.uk.training.online/files/u1218/Core3.pdf" class="">https://www.ebi.ac.uk/training/online/sites/ebi.ac.uk.training.online/files/u1218/Core3.pdf</a></div><div class=""><br class=""></div><div style="orphans: 2; widows: 2;" class="">- Use the read only connection to the database and get it from '<font color="#1d1c1d" face="Slack-Lato, appleLogo, sans-serif" class=""><span style="caret-color: rgb(29, 28, 29); font-size: 15px; background-color: rgb(248, 248, 248);" class="">coord_system' table</span></font></div><div class=""><br class=""></div><div class="">Thanks,</div><div class="">Ameya</div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 24 Sep 2019, at 10:18, Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com" class="">ramiro.magno@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Devs,<br class=""><div class=""><br class=""></div><div class="">When can I expect an update on these questions (Q7 and Q8)?</div><div class=""><br class=""></div><div class="">Thanks a lot!</div><div class=""><br class=""></div><div class="">Cheers, RM</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 13 Sep 2019 at 17:53, Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com" class="">ramiro.magno@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr" class="">Thank you Brandon for the information!<br class=""></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, 13 Sep 2019 at 17:38, Brandon Walts <<a href="mailto:bwalts@ebi.ac.uk" target="_blank" class="">bwalts@ebi.ac.uk</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class=""><p class="">Hi Ramiro</p><p class="">Apologies for the delay. We have some answers for you now, and
more will be forthcoming:</p><p class="">Q1: This endpoint should work for most species. I have seen the
errors that sometimes arise, and we think suspect (but have not
confirmed) that there may be a bug in the TranscriptMapper that
supports this in the underlying Perl API. We will look into this
further.</p><p class="">Q2: No, but this is a good suggestion and we will look into
possibly implementing this.</p><p class="">Q3: Yes, only transcript IDs are valid for this endpoint.</p><p class="">Q4 and Q5: For the first part of your question, basically yes.
Gap represents a gap in the sequence. We will look into whether
setting the "overrun" to a gap is the desired behaviour, or
whether there may be a better way to return a result for a query
that goes beyond the end of a transcript.</p><p class="">Best<br class="">
-Brandon<br class="">
</p>
<div class="gmail-m_-6185895876161707102gmail-m_-4241928598382362686moz-cite-prefix">On 10/09/2019 14:21, Ramiro Magno
wrote:<br class="">
</div>
<blockquote type="cite" class="">
<div dir="ltr" class="">Hi Devs,<br class="">
<div class=""><br class="">
</div>
<div class="">I have a few questions about the endpoint
"map/cdna/:id/:region".</div>
<div class=""><br class="">
</div>
<div class="">Q1: How can I find what species work with this endpoint?</div>
<div class=""><br class="">
</div>
</div>
</blockquote>
<blockquote type="cite" class="">
<div dir="ltr" class="">
<div class="">Q2: Is there a way of specifying the "range" parameter so
that it starts at 1 and goes till the end of the cDNA
sequence? E.g., 1..end?</div>
<div class=""><br class="">
</div>
</div>
</blockquote>
<blockquote type="cite" class="">
<div dir="ltr" class="">
<div class="">Q3: In the doc, the description of the "id" parameter reads
"An Ensembl stable ID". But only transcript ids are valid
choices, correct? For example, making the nonsensical query
with a gene id gives back a not so tidy error: <a href="https://rest.ensembl.org/map/cdna/ENSG00000115263/1..1000?content-type=application/json;include_original_region=1" target="_blank" class="">https://rest.ensembl.org/map/cdna/ENSG00000115263/1..1000?content-type=application/json;include_original_region=1</a>.</div>
</div>
</blockquote>
<blockquote type="cite" class="">
<div dir="ltr" class="">
<div class=""><br class="">
</div>
<div class="">Q4: What is the meaning of the variable "gap" in the json
response? Is it gap=0 means exon, and gap=1 un-mappable
region? When I exceed the end position of the transcript in
the "range" parameter I always get the excess as a region
flagged as gap=1.</div>
</div>
</blockquote>
<blockquote type="cite" class="">
<div dir="ltr" class="">
<div class=""><br class="">
</div>
<div class="">Q5: When I get an excess region as a result of asking a
cDNA sequence that goes beyond the length of transcript, why
are the genomic coordinates "start" and "end" reported as if
they were in cdna coordinate system? E.g., the request: <a href="https://rest.ensembl.org/map/cdna/ENST00000375497/1..1000?content-type=application/json;include_original_region=1" target="_blank" class="">https://rest.ensembl.org/map/cdna/ENST00000375497/1..1000?content-type=application/json;include_original_region=1</a> yields
a last block whose coordinates are start=800, end=1000 for
both coordinate systems: "cdna" and "chromosome". Would it not
make more sense to just report NA or Null instead?</div>
</div>
</blockquote>
<blockquote type="cite" class="">
<div dir="ltr" class="">
<div class=""><br class="">
</div>
<div class="">Q6: What is the meaning of the "rank" variable in the json
output?</div>
</div>
</blockquote>
<blockquote type="cite" class="">
<div dir="ltr" class="">
<div class=""><br class="">
</div>
<div class="">Many thanks in advance!</div>
<div class=""><br class="">
</div>
<div class="">Cheers, Ramiro</div>
</div>
<br class="">
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