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<div class="moz-cite-prefix">Hello,<br>
<br>
Thank you for information.<br>
I was already running VEP with --check_existing flag but i had no
idea on how to retrieve the rsID (I was looking the Variation API
so i thought that <br>
<pre wrap="">$tva->variation_feature->variation_name;
</pre>
would be enough.<br>
<br>
As you said I just wanted reference sequence on either side of the
variant so not even rsID needed.. but it's good to know how I can
obtain it for a near future :)<br>
<br>
Just to prevent from asking these kind of question, how can i
print all the content from the $va object for example?<br>
<br>
I mean how can I know this <i>"you will then find a simplified
hash representing each overlapping variant in the array
@{$vf->{existing}} (where $vf = $tva->variation_feature)."</i>
I can't see a "existing" method in the API, I suppose that is
comming from the own VEP script.<i><br>
<br>
</i><br>
I also changed the (I don't know if I should undo this change)<br>
<pre>sub feature_types {
return ['Transcript', 'Feature'];
}</pre>
I was playing around this but the information on VEP script web
doesn't clarify this too much. It has to do with handlers and
overwriting but I don't understand very well.<br>
<br>
Updated script in repo if anyone wants to use it.<br>
<br>
Thank you very much Will.<br>
<br>
Best regards,<br>
Guillermo.<i><br>
<br>
</i>I don't want to spam list for questions like that, but I can't
find that <br>
On 04/24/13 10:50, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX3zAp_YROy2FeqG7MXyJ==suE44H6K9Jp6v=nNg4L3Jsw@mail.gmail.com"
type="cite">
<pre wrap="">Hello,
A variation feature object is created by the VEP to represent each
line of your input. If you don't give it a name in your input, then
the VEP constructs a name from the coordinates, which is what you are
seeing. Names can be added for variants in the third column (VCF) or
sixth column (tab-delimited input).
If you want the rsID of any existing variants that overlap yours, you
must run the VEP with the --check_existing flag; you will then find a
simplified hash representing each overlapping variant in the array
@{$vf->{existing}} (where $vf = $tva->variation_feature).
If you are looking for the original flanking sequence submitted with
the existing variant to dbSNP, then we don't store this in the
database. However, if you just want to retrieve the reference sequence
either side of your variant, that is easily done by getting and
expanding the feature slice attached to the variant (here I'm getting
100bp either side):
my $five_prime_seq = $vf->feature_Slice->expand(100, -1)->seq;
my $three_prime_seq = $vf->feature_Slice->expand(-1, 100)->seq;
Regards
Will
On 24 April 2013 09:13, Guillermo Marco Puche
<a class="moz-txt-link-rfc2396E" href="mailto:guillermo.marco@sistemasgenomicos.com"><guillermo.marco@sistemasgenomicos.com></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hello,
I updated the code in my git repo, and I still can't make it
work:<a class="moz-txt-link-freetext" href="https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm">https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm</a>
I still don't get why this is returning a string of type 1_41304886_C/T and
not the rsID.
$tva->variation_feature->variation_name;
Thank you.
Best regards,
Guillermo.
On 04/23/13 16:45, Guillermo Marco Puche wrote:
Hello,
I'm developing a plugin for VEP that calculates 5' & 3' flanking sequence
for each rs.
I've the plugin 95% completed. I'm just missing how are rs IDs called on
VEP.
Looking into Enseml Variation API I've found this:
<a class="moz-txt-link-freetext" 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>
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.
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.
Plugin code can be found in Github:
<a class="moz-txt-link-freetext" href="https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm">https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm</a>
Thank you !
Best regards,
Guillermo.
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</pre>
</blockquote>
</blockquote>
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