[ensembl-dev] variation api

[Andrea Edwards]

Hi

Given a novel variation feature i was wondering how to find out if a 
dbSNP record existed for it. In other words, i was wondering if any 
known snps were colocated with it. I saw this code in wll mclaren's snp 
predictor program

     # find any co-located existing VFs
         my $existing_vf = "-";

         if(defined($new_vf->adaptor->db) && $check_existing == 1) {
             my $fs = $new_vf->feature_Slice;
             if($fs->start > $fs->end) {
                 ($fs->{'start'}, $fs->{'end'}) = ($fs->{'end'}, 
$fs->{'start'});
             }
             foreach my 
$existing_vf_obj(@{$new_vf->adaptor->fetch_all_by_Slice($fs)}) {
                 $existing_vf = $existing_vf_obj->variation_name
                     if $existing_vf_obj->seq_region_start == 
$new_vf->seq_region_start
                     and $existing_vf_obj->seq_region_end == 
$new_vf->seq_region_end;
             }
         }


questions:

1. I believe the feature slice for a feature is  defined as the region 
exactly spanned by the feature. Does that mean its one bp for a snp?

2. Is it possible that the 'matching' dbsnp record could describe the 
snp as being on the opposite strand to my snp, or does ensembl do any 
internal procesing to make sure all snps are on the forward strand?

3. why might the feature slice start be greater than the feature slice 
end? I know this script is used for other variations than snps so it 
might have something to do with that perhaps?

4. Can i just confirm the variation_name will give the dbsnp id if it is 
a known snp. Could it give anything else? I presume the same snp can be 
held in multiple databases used as external references by ensembl.

5. I must be reading this code wrong because it doesnt look to me as if 
it concatenates a list of dbsnp ids in the variable $existing_vf, it 
looks as though it is overwriting this variable with each snp found


thanks a lot
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