[ensembl-dev] variation api - only get variation features that are snps

Andrea Edwards edwardsa at cs.man.ac.uk
Mon Nov 29 12:23:21 GMT 2010


Hello

I have some code below which gets all of the variation features for cow 
that are mapped to know chromosomes. However this code gets all 
variation features and I would like to get just snps. Could you suggest 
how i do this? Also i'm new to the api so if you spot i'm doing 
something in an inefficient manner and feel like pointing it out then 
that's fine by me

thanks a lot

======================================

my $slice_adaptor = $registry->get_adaptor('bos_taurus', 'core', 
'slice'); #get the database adaptor for Slice objects
my $vf_adaptor = $registry->get_adaptor('bos_taurus', 'variation', 
'variationfeature'); #get adaptor to VariationFeature object



@slices = @{ $slice_adaptor->fetch_all('chromosome', undef, 0, 1) };
foreach $slice (@slices) {

     unless ($slice->seq_region_name() =~ /Un/) {

         #return ALL variations defined in $slice
         $vfs = $vf_adaptor->fetch_all_by_Slice($slice);



         foreach my $vf (@{$vfs}) {
             # Variation feature representing a single nucleotide 
polymorphism
             #insert into my database

         }#end for each variation feature
     }#end unless slice is a chromosome
}#end for each slice





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