[ensembl-dev] variation set method get all features by slice returns unordered features?

[Pontus Larsson]

Hi Andrea,

The API doesn't return variation features in any guaranteed order. If 
you need to have the features sorted, I would suggest that you sort them 
via a customized sort command after fetching them. Something like this 
should work:

my @sorted_vfs = sort { $a->start() <=> $b->start() } @vfs;

HTH
/Pontus


On 27/12/2010 20:50, Andrea Edwards wrote:
> Hi
>
> I have this code to get watson snps:
>
> ================================================================
>
> my @unsorted_slices = @{ $slice_adaptor->fetch_all('chromosome', 
> undef, 0, 1) };
>
> my @sorted_slices = sort by_num_then_letter @unsorted_slices;
>
> # Base pair overlap between returned slices
> my $overlap = 0;
>
> # Maximum size of returned slices
> my $max_size = 10000;
> # Maximum size of returned slices
> my $max_size = 10000;
>
> # Break chromosomal slices into smaller 100k component slices
> my @slices = @{split_Slices( \@sorted_slices, $max_size, $overlap )  };
> my $snp_id = 0;
> foreach my $slice (@slices) {
>
>     unless ($slice->seq_region_name() =~ /Un/) {
>         my @vfs 
> =@{$watson_set->get_all_VariationFeatures_by_Slice($slice)};
>         foreach my $vf (@vfs) {
>             next if ($vf->var_class ne 'snp');
>             $snp_id++;
>
>             #insert snp to my database
>
> ============================================================================= 
>
>
> @sorted_slices contains chromosome slices sorted into numerical then 
> alphabetical order, though this doesn't really matter
> as my code didn't get past chromosome 1 before it lost connection to 
> the server.
>
> I then tried to start the code from the chromosome segment where it 
> had left off and i found that the snps weren't in 'base pair' order in 
> the database. For example, on chromosome 1 the first snp was at locus 
> 4626 and the next snp was at base 1081. (this position was obtained 
> from     $locus = $vf->start();)
>
> So it appears to me that the method 
> get_all_VariationFeatures_by_Slice($slice) on the variation set object 
> does not return snps in base order. Is this correct? How do i retrieve 
> them in order?
>
> Thanks
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Pontus Larsson, Ph.D.
Ensembl Variation

EMBL-EBI
Wellcome Trust Genome Campus
Hinxton, Cambridge, CB10 1SD
UK
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~