[ensembl-dev] Can't locate object method "variation_feature" via package "Bio::EnsEMBL::Variation::VariationFeature"

[Graham Ritchie]

Hi Sung,

Sorry about this, this is a bug I introduced when fixing the previous issue! I have now fixed it and if you update your CVS checkout this should be resolved. Please let us know if not.

Cheers,

Graham


On 19 Oct 2011, at 11:07, Sung Gong wrote:

> Hi,
> 
> Many thanks to Ensembl developers for making the data accessible easily via API.
> 
> I found an error message while running my script which is basically to
> interrogate the variation effect for the variant shown below:
> chr5    70807017        70807017        T/-     +
> 
> The error message looks like:
> Can't locate object method "variation_feature" via package
> "Bio::EnsEMBL::Variation::VariationFeature" at
> /data/Install/Perl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm
> line 62.
> 
> I tried the local version of 'variant_effect_predictor.pl' which is
> found at 'ensembl-variation/scripts/examples/variant_effect_predictor.pl'
> It shows:
> 2011-10-19 10:47:54 - Starting...
> 2011-10-19 10:47:54 - Detected format of input file as ensembl
> 2011-10-19 10:47:54 - Read 1 variants into buffer
> 2011-10-19 10:47:54 - Analyzing chromosome 5
> 2011-10-19 10:47:54 - Reading transcript data from cache and/or database
> [================================================================================================================================================================================================================================]
> [ 100% ]
> 2011-10-19 10:47:55 - Retrieved 11 transcripts (0 mem, 0 cached, 11
> DB, 0 duplicates)
> 2011-10-19 10:47:55 - Analyzing variants
> [================================================================================================================================================================================================================================]
> [ 100% ]
> 2011-10-19 10:47:55 - Calculating and writing output
> Can't locate object method "variation_feature" via package
> "Bio::EnsEMBL::Variation::VariationFeature" at
> /data/Install/Perl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VariationEffect.pm
> line 62, <GEN0> line 1.
> 
> Lastly, tired the web version of VEP with the same variant above, but
> nothing returned at all.
> 
> Can developers have a look at the source code?
> 
> I am using Ensembl 64 API and I applied a patch where Graham recently
> debugged on regarding 'null type consequence'.
> 
> Cheers,
> Sung
> 
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