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

[Sung Gong]

Cheers Graham! It works fine now after updating local API.
cvs -q update -d -P -r branch-ensembl-64
Thanks,
Sung

On 19 October 2011 13:12, Graham Ritchie <grsr at ebi.ac.uk> wrote:
> 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
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>