[ensembl-dev] hardcoded value in Slice::get_all_Structural_VariationFeatures

Laurent Gil lgil at ebi.ac.uk
Mon Apr 23 13:52:31 BST 2012

Hi Jay,

Actually the CNV_PROBE are probe sequences from Illumina and Affymetrix 
They have been stored historically as structural variations in the 
Ensembl Variation database, although they are different from the usual 
structural variation data (i.e. DGVa data).
We separate the CNV probes from the structural variation with the API, 
using the methods like get_all_CopyNumberVariantProbeFeatures for example.
We try to use the sequence ontology terms or the sequence ontology 
identifiers instead of the ensembl terms because they are much more 
stable. That's why we used the identifier SO:0000051 (probe).



On 23/04/2012 13:30, Jay Humphrey wrote:
> I'm just curious about why this function has a table value 
> "SO:0000051" hardcoded into it?  Source comments refer to it as 
> CNV_PROBE, so why not just use "CNV_PROBE", since that's also in the 
> table?
> In Bio::EnsEMBL::Slice
> sub get_all_CopyNumberVariantProbeFeatures {
>   my $self   = shift;
>   my $source = shift;
>   return 
> $self->get_all_StructuralVariationFeatures($source,0,'SO:0000051');
> }

More information about the Dev mailing list