[ensembl-dev] RegulatoryFeature (and MotifFeature?) not fully qualifying correctly in BaseVepPlugin

[Graham Ritchie]

Hi Michael,

I have now committed a fix to both the release 65 branch and the HEAD code, so if you update your checkout this bug should be resolved.

Cheers,

Graham


On 12 Jan 2012, at 23:31, Michael Yourshaw wrote:

> In BaseVepPlugin sub _check_types, it appears that if a user specifies ‘RegulatoryFeature’ in feature_types, the fully qualified feature that gets built and added to $wanted is Bio::EnsEMBL::RegulatoryFeature whereas the $type of the feature is Bio::EnsEMBL::Funcgen::RegulatoryFeature. This causes unexpected failure to run. While there is an obvious work-around, it would be nice to take the shortcut.
> 
> I haven’t stepped through the code, but it looks like something similar happens with MotifFeature.
> 
> ॐ
> 
> 
> Michael Yourshaw
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
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