[ensembl-dev] odd results from getting variation features

[Andrea Edwards]

Sorry - please ignore last email. I had copied and paste and used 
vf->start instead of vf->seq_region_start!

My apologies.

On 28/12/2010 15:41, Andrea Edwards wrote:
> Hi
>
> Please see some code below to get watson snps. I am getting subslices 
> of each chromosome and then getting the watson snps (variation 
> features) for each slice. The variation features are sorted into order
>
> The first subslice is bases 1 - 10,000 and contains  no variation 
> features
>
> The second subslice is bases 10,001 - 20,000 and contains variants at 
> these positions
>
> 904
> 1081
> 4626
>
> How can this be? I have pasted more output below to show further 
> subslices contain variation features not within the subslice range
>
> thanks a lot
>
>
> ===========================================================
>
> 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;
>
>
> my @sub_slices = @{split_Slices( \@sorted_slices, $max_size, $overlap 
> )  };
>
> my $snp_id = 0;
>
> foreach my $slice (@sub_slices) {
>     print "subslice start: ", $slice->start, " end: ", $slice->end, "\n";
>     unless ($slice->seq_region_name() =~ /Un/) {
>         my @vfs 
> =@{$watson_set->get_all_VariationFeatures_by_Slice($slice)};
>         my @sorted_vfs = sort { $a->start() <=> $b->start() } @vfs;
>
>             foreach my $vf (@sorted_vfs){
>                 print vf->start();
>             }
>   }
>
>
> =======================================================
> subslice start: 1 end: 10000
>
> subslice start: 10001 end: 20000
>
> 904
> 1081
> 4626
>
>
>
> subslice start: 20001 end: 30000
>
> 547
> 600
> 620
>
>
> subslice start: 30001 end: 40000
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev