[ensembl-dev] getting watson snps with ensembl

[Will McLaren]

Hi Andrea,

We have a variation set named "ENSEMBL:Watson" - you can retrieve SNPs this way:

my $watson_set = $variation_set_adaptor->fetch_by_name("ENSEMBL:Watson");

# you could use $watson_set->get_all_Variations but this would take a
long time, so instead process by slice
foreach my $slice(@{$slice_adaptor->fetch_all('chromosome')}) {
   foreach my $vf(@{$watson_set->get_all_VariationFeatures_by_Slice($slice)}) {
      ...
   }
}

Note this will still take a long time as the underlying SQL is doing a
very large table join - to reduce times further just make the slices
shorter.

Will

On 30 November 2010 22:22, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:
> Hi
>
> Is there any way to get all of the watson snps using the perl api. The
> var_class property of a variation feature only applies to the dnsnp
> classification of a variation (e.g. snp, indel etc)
>
> To get watson snps from dbsnp you have to use the limits
>
> Using the option:
>
> Individual SNP: Watson
>
> SNP Class: SNP
>
> Is there an equivalent to this in the perl api?
>
> thanks
>
>
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