[ensembl-dev] VEP.pm error in svf_to_consequences

Will McLaren wm2 at ebi.ac.uk
Fri Apr 20 09:29:51 BST 2012


Hi Michael,

I think this is cropping up due to an outdated API module.

I put in a post-release fix for this sometime last month:

http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm?root=ensembl&r1=1.34.2.5&r2=1.34.2.6

Can you update your ensembl-variation API checkout and try again?

Cheers

Will

On 19 April 2012 21:27, Michael Yourshaw <myourshaw at ucla.edu> wrote:
> VEP 2.4 fails with this error:
> Can't locate object method "stable_id" via package
> "Bio::EnsEMBL::Funcgen::MotifFeature" at
> /share/apps/myourshaw/ensembl/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm
> line 1123, <GEN1> line 5028.
>
> There is no $feature->stable_id
>
> $feature_type = MotifFeature (this variant also throws Gene, Transcript,
> and RegulatoryFeature feature_types that have stable ids).
> $feature is a Bio::EnsEMBL::Funcgen::MotifFeature
> $feature contains (inter alia):
> dbID = 618345
> display_label = PU1:MA0080.1
> end = 39460062
> interdb_stable_id = undef
> score = 1
> slice (looks like all of chr 22?)
> start = 39460057
> strand = 1
>
> This looks like it might be a data error. It is the only such error on chr
> 22 of the 1000 genomes data, but there may be more in the other chromosomes.
>
> My temporary fix in VEP.pm:
>         my $base_line = {
>             Feature_type     => $feature_type,
>             Feature          => $feature->can('stable_id') ?
> $feature->stable_id : undef,
>             #cDNA_position    => format_coords($svo->cdna_start,
> $svo->cdna_end),
>             #CDS_position     => format_coords($svo->cds_start,
> $svo->cds_end),
>             #Protein_position => format_coords($svo->translation_start,
> $svo->translation_end),
>         };
>
>
> The input VCF line (exerpted from 1000 Genomes) start with:
> 22 39432459 MERGED_DEL_2_106019 TGGAAGC …
>
> See attached file for the whole line
>
>
>
>>
> Michael Yourshaw
>
> UCLA Geffen School of Medicine
> Department of Human Genetics, Nelson Lab
> 695 Charles E Young Drive S
> Gonda 5554
>
> Los Angeles CA 90095-8348 USA
>
> myourshaw at ucla.edu
>
> 970.691.8299
>
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