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

Sung Gong sung at bio.cc
Wed Oct 19 11:07:38 BST 2011


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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