[ensembl-dev] VEP Flanking sequence plugin
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue Jun 4 10:38:13 BST 2013
Hello Will,
I'm gonna try out your code. And report back.
I'm using local ensembl71 database installation and also homo_sapiens
cache downloaded from ensembl to display 1kg population frequencies.
So both --database & --cache.
Regards,
Guillermo.
On 06/04/2013 10:05 AM, Will McLaren wrote:
> Hi Guillermo,
>
> Are you using --offline, --cache or --database?
>
> You may need to manually add a slice to the $vf object in some cases;
> you should be able to do that with something like:
>
> if(!defined($vf->{slice})) {
> my $sa = $self->{config}->{sa} ||
> Bio::EnsEMBL::Registry->get_adaptor($self->{config}->{species},
> 'core', 'slice');
> $vf->{slice} = $sa->fetch_by_region('chromosome', $vf->{chr});
> }
>
> before the lines where you are asking for the flanking sequence.
>
> Will
>
> On 3 June 2013 11:27, Guillermo Marco Puche
> <guillermo.marco at sistemasgenomicos.com
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
> Hello,
>
> My plugin start giving errors.
>
> ERROR: Forked process failed
> Plugin 'flanking_sequence' went wrong: *Can't call method "expand"
> on an undefined value at
> /share/apps/scripts/genomics/global/annotation/ensembl_71_genetonic/vep_config/Plugins/flanking_sequence.pm
> <http://flanking_sequence.pm> line 72.*
>
> I've tried to fix the code adding if(defined ...) but seems to
> have no effect. I didn't see this bug until today.
>
> How can I check if the value of any of the two expand
> feature_slice really exists?
> I thought this would exist for all features. So I suppose I'm
> wrong and what is causing the plugin to fail obtaining the
> flanking sequence is the expand method call but I've no idea on
> how to fix it.
>
> Here's plugin code updated:
> https://github.com/guillermomarco/vep_plugins_71/blob/master/flanking_sequence.pm
>
> Regards,
> Guillermo.
>
>
>
> On 04/24/2013 12:11 PM, Guillermo Marco Puche wrote:
>> 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> <mailto: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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>>
>>
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