[ensembl-dev] Some Issues on Variation v64

Will McLaren wm2 at ebi.ac.uk
Wed Oct 12 18:41:16 BST 2011

Hi John,

Answers below:

On 12 October 2011 17:56, Ma, Man Chun John <manchunjohn-ma at uiowa.edu> wrote:
> Hi,
> I just tried to make a script to make extract Variation synonyms from v64, and encountered the following issues:
> 1.  Variation::get_VariationFeature_by_dbID didn't seem to work using the following segment:
> my $va=$registry->get_adaptor('rat','variation','variation');
> my $vfa=$registry->get_adaptor('rat','variation','variationfeature');
> print "Input: ENSRNOSNP971187\n";
> my $one_snp=$va->fetch_by_name("ENSRNOSNP971187");
> print "Ensembl Official name:", $one_snp->name, "\n";
> my @synonyms=@{$one_snp->get_all_synonyms};
> foreach (@synonyms){print "Synonym: ",$_, "\n";}
> my $one_vf=$one_snp->get_VariationFeature_by_dbID;
> which throwed:
> -------------------- EXCEPTION --------------------
> MSG: No dbID defined
> STACK Bio::EnsEMBL::Variation::Variation::get_VariationFeature_by_dbID C:\ensemb
> l-variation\modules\/Bio/EnsEMBL/Variation/Variation.pm:482
> STACK toplevel HGVS-fetch-test.pl:21
> Ensembl API version = 64
> ---------------------------------------------------

The use of this method implies you know our internal database
identifier for the variation feature entry, which most users won't
have access to.

Instead, you should retrieve variation feature objects using something like:

foreach my $vf(@{$one_snps->get_all_VariationFeatures}) {
   # do stuff with $vf

Generally in Ensembl a method that is named something like get_X_by_Y
implies that you need to pass Y as an argument.

> 2. The output from VariationFeature:: get_all_hgvs_notations leaves a lot to be desired. The genomic HGVS notation for the above SNP would be 17:g.39585392T>C-- however, merely using "17" as a reference name is clearly inadequate as one cannot deduce what species' 17 does this refer to. I would consider RGSC3.4:17: g.39585392T>C a better alternative. On the other hand, the parameter $reference_name didn't seem to work.

Thanks for this feedback - however we would consider it implicit which
species the HGVS notation applied to since you are retrieving it from
that particular species' database. It is not possible, for example, to
retrieve a human HGVS notation while using a rat database.

You can get transcript and protein specific HGVS notations using e.g.




which you may find these more useful.

You might also like to check our tutorial and API documentation further:


Hope this helps

Will McLaren
Ensembl Variation

> Cheers,
> John Ma
> Kwitek Lab
> Department of Pharmacology
> University of Iowa
> Iowa City, Iowa, USA
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