[ensembl-dev] 1000 Genomes SNPS

[Andrea Edwards]

HI Pontus

I did in fact run out of memory every time! I wasn't aware of any sort 
of iterator on the api. Are they new as i don't remember them when i 
read teh tutorials late last year?

Do you have any comments about which of my 2 approaches is best? I 
presume you can use an iterator on the second approach as that is 
basically the code you supplied (minus an iterator). Could you use an 
iterator on the first approach?

thanks

On 02/03/2011 15:22, Pontus Larsson wrote:
> Hi Chris,
>
> Andrea is right, we have grouped these variations together into 
> various variation sets. For example, you can get all variations 
> belonging to the different pilots from the sets '1000 genomes - Low 
> coverage', '1000 genomes - High coverage - Trios' and '1000 genomes - 
> High coverage exons' for pilot 1,2 and 3, respectively. You'll need to 
> use the VariationSet and VariationSetAdaptor modules for this. It is 
> not possible to retrieve the variations conditional on submission date.
>
> As Andrea points out, if you call the 'get_all_Variations' method on a 
> VariationSet object, the API will create all variation objects and 
> return them. For large sets like these, this can easily cause you to 
> run out of memory but you can use the 'get_Variation_Iterator' method 
> to get an Iterator object and iterate over the variations instead.
>
> /Pontus
>
>
> 2011/3/2 <cj5 at sanger.ac.uk <mailto:cj5 at sanger.ac.uk>>
>
>     Hi,
>     Is it possible using the variations API to get a list of SNPS
>     which have
>     been submitted from the 1000 Genomes project?
>
>     I have a vague idea that it should be possible to retrieve such a list
>     using the SS (submission) ID and/or the validation status, however
>     I am
>     unsure of the details and what version of the API should be used.
>
>     The latest 100 genomes pilot release (2010_07) would be great, but any
>     earlier release would also be useful.
>
>     Thanks
>     Chris
>
>
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