[ensembl-dev] VEP Flanking sequence plugin

[Guillermo Marco Puche]

Hello,

Thank you for information.
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

$tva->variation_feature->variation_name;

would be enough.

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 :)

Just to prevent from asking these kind of question, how can i print all 
the content from the $va object for example?

I mean how can I know this /"you will then find a simplified hash 
representing each overlapping variant in the array @{$vf->{existing}} 
(where $vf = $tva->variation_feature)."/ I can't see a "existing" method 
in the API, I suppose that is comming from the own VEP script./

/
I also changed the (I don't know if I should undo this change)

sub feature_types {
     return ['Transcript', 'Feature'];
}

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.

Updated script in repo if anyone wants to use it.

Thank you very much Will.

Best regards,
Guillermo./

/I don't want to spam list for questions like that, but I can't find that
On 04/24/13 10:50, Will McLaren wrote:
> 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
> <guillermo.marco at sistemasgenomicos.com>  wrote:
>> Hello,
>>
>> I updated the code in my git repo, and I still can't make it
>> work:https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm
>>
>> 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:
>> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html
>>
>> 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:
>> https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm
>>
>>
>>
>>
>> Thank you !
>>
>> Best regards,
>> Guillermo.
>>
>>
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