[ensembl-dev] Why do I get duplicated Variation Features

[Benoît Ballester]

It looks like the usual HAP/PAR headache _again_  :(

Any idea on how not to get VariationFeature twice when giving a slice falling in those region. 

Ps: my slice comes from a $feature->slice. Do I have to transform/project my slice to top-level ? I thought it was done by default. 

Ben


On 4 Jul 2012, at 15:46, Benoît Ballester wrote:

> Hi, 
> 
> I am trying to fetch some variants for some slices but get duplicated variation features. I don't understand why, as I would expect one variant per slice.
> 
> eg: 
> 7:Y:347772:347784:1  rs71900610      GA/-    Y       347778  347779  deletion        dbSNP   INTERGENIC
> 7:Y:347772:347784:1  rs71900610      GA/-    Y       347778  347779  deletion        dbSNP   INTERGENIC
> 
> or 
> 
> 48:Y:386863:386872:1     rs10600708      ACAC/-  Y       386864  386867  deletion        dbSNP   INTERGENIC
> 48:Y:386863:386872:1     rs10600708      ACAC/-  Y       386864  386867  deletion        dbSNP   INTERGENIC
> 
> or 
> 
> 22:Y:116772:116785:-1   rs36189917      G/A     Y       116775  116775  SNP     dbSNP   UPSTREAM
> 22:Y:116772:116785:-1   rs36189917      G/A     Y       116775  116775  SNP     dbSNP   INTERGENIC
> (here UPSTREAM/INTERGENIC difference)
> 
> 
> I am sure I am missing something obvious somewhere, but so far I couldn't put my finger on it.  
> 
> 
> My code is pretty straightforward :
> 
> my $vfs = $vfa->fetch_all_by_Slice($slice);
> 	foreach my $vf (@$vfs) {
> 	    my $v = $vf->variation();
> 	#print into on slice/variant/variantion-feature
>        }
>  }
> 
> 
> Any feedback appreciated,
> 
> Ben
> 
> --
> Benoit Ballester, PhD
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--
Benoit Ballester, PhD
Vertebrate Genomics - Ensembl
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, United Kingdom