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<div class="moz-cite-prefix">Hello,<br>
<br>
I updated the code in my git repo, and I still can't make it work:<a
moz-do-not-send="true"
href="https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm">https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm</a><br>
<br>
I still don't get why this is returning a string of type
1_41304886_C/T and not the rsID.<br>
<br>
<pre>$tva->variation_feature->variation_name;</pre>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 04/23/13 16:45, Guillermo Marco Puche wrote:<br>
</div>
<blockquote cite="mid:51769E81.70601@sistemasgenomicos.com"
type="cite">
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charset=ISO-8859-1">
Hello,<br>
<br>
I'm developing a plugin for VEP that calculates 5' & 3'
flanking sequence for each rs.<br>
<br>
I've the plugin 95% completed. I'm just missing how are rs IDs
called on VEP.<br>
Looking into Enseml Variation API I've found this:
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<a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html</a><br>
<br>
It seems that I need VariationFeature adaptor set so I can call
"variation_name" method get the rs and then call
"five_prime_flanking_seq" & "three_prime_flanking_seq" methods
to get the flanking sequence.<br>
<br>
I don't know why even after changing adaptor I'm still getting
"2_26739423_T/C" if I'm not using TranscriptVariation adaptor but
VariantFeature I should be getting rsxxxxxx ID.<br>
<br>
Plugin code can be found in Github:
<meta http-equiv="content-type" content="text/html;
charset=ISO-8859-1">
<a moz-do-not-send="true"
href="https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm">https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm</a><br>
<br>
<br>
<br>
<br>
Thank you !<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
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<br>
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</pre>
</blockquote>
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