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Hi Wojtek,<br>
<br>
I went to speak with Kevin to better understand what you're trying
to accomplish. Based on our conversation, you'll want to look at the
pep2genomic() method in the Transcript object.<br>
<br>
For these transcripts you're trying to evaluate if the data you've
used to load an Ensembl db is correct, use the translateable_seq()
function to retrieve the sequence as would be translated based on
the input data. Then cycle through the sequence looking for the stop
codon characters. You can then take those positions in the protein
and feed them in to pep2genomic( x, x ) to find the genomic
coordinates.<br>
<br>
The Ensembl API documentation [1] details the return type for this
call, a series of Coordinate and Gap objects containing the genomic
coordinates.<br>
<br>
If you have any further questions, or if we didn't properly
understand what you were trying to accomplish, let us know. Thanks.<br>
<br>
[1]
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1TranscriptMapper.html#afb66982442190f4eaa711fdee89b0418">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1TranscriptMapper.html#afb66982442190f4eaa711fdee89b0418</a><br>
<br>
<div class="moz-cite-prefix">On 03/05/18 11:39, Wojtek Bażant wrote:<br>
</div>
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cite="mid:47c708f49a43fd94f5246e43f55e6a32@sanger.ac.uk">
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<p>Hi ensembl-dev,</p>
<p>Sometimes the annotation I try to load up has transcripts that
don't translate to valid proteins. I then go to look at them in
a genome viewer to get an idea what's wrong, and it's helpful to
know where to look.</p>
<p>I've tried to work with the values reported to me by the
ProteinTranslation healthcheck log, until I realised they're
nonsense - I think this code is wrong:</p>
<p><a
href="https://github.com/Ensembl/ensj-healthcheck/blob/release/92/perl/Bio/EnsEMBL/Healthcheck/Translation.pm#L306"
moz-do-not-send="true">https://github.com/Ensembl/ensj-healthcheck/blob/release/92/perl/Bio/EnsEMBL/Healthcheck/Translation.pm#L306</a></p>
<p>It takes the protein sequence (in the peptide alphabet), looks
for indexes of '*', adds these to the beginning of transcript
start ( in the dna alphabet), and claims these to be locations
of stop codons.</p>
<p>I currently have no good way of doing this. I have been
translating the exons in all three phases, saving them to a
file, and then text searching for bits of the sequence around
the *. Does Ensembl offer a better way that I couldn't find, or,
can you think of one?Thanks,Wojtek</p>
<br>
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