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<p>Hi Fong,</p>
<p>Haplosaurus can export sequences if you switch the output to JSON
using --json. The output contains by default sequences for the CDS
haplotypes (cds_haplotypes seq) and for the protein haplotypes
(protein_haplotypes seq).<br>
</p>
Each transcript analysed will be summarised in a JSON object written
on one line of the output file.<br class="Apple-interchange-newline">
<p>The JSON format has the same structure as the REST API json:
<a class="moz-txt-link-freetext" href="https://rest.ensembl.org/documentation/info/transcript_haplotypes_get">https://rest.ensembl.org/documentation/info/transcript_haplotypes_get</a>.<br>
</p>
<p>I have added an update to our documentation as it was not very
clear and it should be out with the next release. <br>
</p>
<p>Best wishes,</p>
<p>Irina<br>
</p>
<br>
<div class="moz-cite-prefix">On 15/08/2018 10:17, Fong Chan wrote:<br>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">I
was wondering if there a way to get the VEP plugin
ProteinSeq.pm (<a
href="https://github.com/Ensembl/VEP_plugins/blob/release/93/ProteinSeqs.pm"
moz-do-not-send="true">https://github.com/Ensembl/VEP_plugins/blob/release/93/ProteinSeqs.pm</a>)
to work with Haplosaurus output (<a
href="https://www.ensembl.org/info/docs/tools/vep/haplo/index.html"
moz-do-not-send="true">https://www.ensembl.org/info/docs/tools/vep/haplo/index.html</a>).
I am interested in producing mutated peptide sequences that
incorporates the haplotypes.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Fong<o:p></o:p></span></p>
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