[ensembl-dev] Variation set: fetch_all_by_Variation() outputting hash values

Anja Thormann anja at ebi.ac.uk
Wed Jul 23 13:59:46 BST 2014

Hi Henry,

maybe you could have a look at our code conventions: http://www.ensembl.org/info/docs/api/core/core_tutorial.html#conventions

They explain in detail how we name methods in our API and what can be derived from the naming about how results look like.


On 22 Jul 2014, at 23:42, Gong, Henry wrote:

> Hi Anja,
> It looks like I had assumed that simply calling VariationSet would produce a name, similar to 
> my @vstates = @{$tva->variation_feature->get_all_validation_states()};
> print
>         "\t",join(",", @vstates); #evidence
> Though I see now that an evidence value is qualitatively different from a variation set.
> I don't intend on calling all the variations per set; my application is only looking at potentially hundreds (per transcript or per gene), but I'll consider using iterators to save a little memory.
> I added your suggestion as
>     foreach my $tva(@{$tvas}) {
>         my @vsets = @{$vs_adaptor->fetch_all_by_Variation($tva->variation_feature->variation)};
>         print $tva->variation_feature->display_id, "\t";
>         foreach my $vs(@vsets) {
>             my $set_name = $vs->name();
>             print $set_name,",";
>         }
>         print "\n";
>     }
> and it does indeed work!
> Thanks,
> Henry Gong
> Junior Specialist
> UCSF Dept of Neuro Surgery
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