[ensembl-dev] Problem with retrieving VariationAnnotations

Tjaart de Beer tjaart at ebi.ac.uk
Tue Jul 3 10:41:12 BST 2012


Thanks Will,

That solved my problem.

Tjaart


> Hi Tjaart,
>
> You want to fetch variation sets, not variation annotations (these are
> generally phenotype annotations).
>
> my $vsa = $reg->get_adaptor("human", "variation", "variationset");
>
> foreach my $vs(@{$vsa->fetch_all_by_Variation}) {
>    # etc
> }
>
> Will
>
> On 3 July 2012 10:30, Tjaart de Beer <tjaart at ebi.ac.uk> wrote:
>> Hi all,
>>
>> I currently have a list of RSID's from the 1000 Genomes project for
>> which
>> I would like to determine the population in the 1000 Genomes which they
>> belong too. My thoughts were to take every rsid, query Ensembl and find
>> out either the frequency of the allele in each population or at least
>> the
>> population set it belongs too. I tried the following example from the
>> Ensembl Variation tutorial but it doesn't seem to work:
>>
>> use strict;
>> use warnings;
>> use Bio::EnsEMBL::Registry;
>>
>> my $registry = 'Bio::EnsEMBL::Registry';
>>
>> $registry->load_registry_from_db(
>>     -host => 'ensembldb.ensembl.org',
>>     -user => 'anonymous',
>> );
>>
>> # Fetch a variation object
>> my $var_adaptor = $registry->get_adaptor('human', 'variation',
>> 'variation');
>> my $var = $var_adaptor->fetch_by_name('rs149944086');
>>
>> # Fetch all the variation annotations associated with the variation
>> my $va_adaptor = $registry->get_adaptor('homo_sapiens', 'variation',
>> 'variationannotation');
>> foreach my $va (@{$va_adaptor->fetch_all_by_Variation($var)})
>> {
>>     print $va->variation_names."\n";
>>     print $va->source_name."\n";
>>     print $va->study_name."\n";
>> }
>>
>>
>> According to the webinterface
>> (http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=1:870729-871729;v=rs149944086;vdb=variation;vf=30949909)
>> of Ensembl this rsid is annotated and I can see that it was imported
>> from
>> dbSNP. I can also see the 1000 Genomes allele frequencies on the
>> webpage.
>> But when I run my script I get no output whatsoever. I also updated the
>> API this morning.
>>
>> I have two questions which I hope someone can help me with:
>>
>> 1. What is wrong with my script? Or am I missing something?
>> 2. Is there a better approach for me to find out which rsid occurs in
>> which 1000 Genome population (along with its frequency)?
>>
>> Thanks!
>>
>> --
>> Dr. Tjaart de Beer
>> Thornton group
>> EMBL-EBI
>> Cambridge
>> United Kingdom
>>
>>
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>


--
Dr. Tjaart de Beer
Thornton group
EMBL-EBI
Cambridge
United Kingdom





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