[ensembl-dev] identifying known variants that map to multiple genome locations

[Andrea Edwards]

Hi

My email was very confusing - I'm sorry about that. I'll try again

I am retrieving a set of variation feature objects like so


# get all VariationFeatures in a region
$slice = $sa->fetch_by_region('chromosome', '7');
  foreach $vf (@{$vfa->fetch_all_by_Slice($slice)}) {


how would i check the variation feature object that i have returned maps 
to a single genome location?

I don't have a variation object, but now i have a vf object (which is 
what i was getting at in my last email but explained badly) so I could 
create a variation object from it and do this

$v = $va->fetch_by_name(vf->variation_name);
$count =  @{$vfa->fetch_all_by_Variation($v)}
if $count>  1 then it maps to more than one place

But this seemed circuitous and I was wondering if there was a better way.





On 09/12/2010 09:43, Will McLaren wrote:
> Hi Andrea,
>
> I'm not quite sure why you're creating a variation feature object for
> a known variant in that way; you should be retrieving it via the
> variation object using either
>
> $v->get_all_VariationFeatures
>
> or
>
> $variation_feature_adaptor->fetch_all_by_Variation($v)
>
> There is no way to get the other variation features from the variation
> feature itself; the quickest way (or the least amount of code) would
> be:
>
> $vf->variation->get_all_VariationFeatures
>
> Will
>
> On 8 December 2010 23:38, Andrea Edwards<edwardsa at cs.man.ac.uk>  wrote:
>> Esteemed api developers,
>>
>> Is there any easy way with the perl api to tell if a known variant (by this
>> i mean one that has a an rsID and that i have created like this:
>>
>> # Variation feature representing a single nucleotide polymorphism
>> $vf = Bio::EnsEMBL::Variation::VariationFeature->new
>> (-start =>  100,
>> -end =>  100,
>> -strand =>  1,
>> -slice =>  $slice,
>> -allele_string =>  'A/T',
>> -variation_name =>  'rs635421',
>> -map_weight =>  1,
>> -variation =>  $v);
>>
>> is known to map to another region of the genome other than the region have
>> specified with the slice/start/end properties?
>>
>> dbSNP variants can be assigned to multiple genome locations when it hasn't
>> been possible to unambiguously assign them to a single location.
>>
>> If i can't tell from the variation feature directly i believe i can do this:
>>
>> $vfa = $reg->get_adaptor("human","variation","variationfeature");
>> $va = $reg->get_adaptor("human","variation","variation");
>>
>> # fetch all genome hits for a particular variation
>> $v = $va->fetch_by_name('rs56');
>> $count =  @{$vfa->fetch_all_by_Variation($v)}
>> if $count>  1 then it maps to more than one place?
>>
>> I was hoping to be able to do it directly from teh variation feature
>>
>> thanks
>>
>>
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>>