[ensembl-dev] VEP - TranscriptVariationAllele.pm errors

[Stuart Meacham]

Hi

Thanks for the reply, it seems that my source alternate allele(s) had 
slashes ('/') instead of commas (',') which were ok for the VEP but not 
for the TranscriptVariationAllele.pm when doing it's HGVS jiggerypokkery!

eg:

X       2726228 2726230 G/-,A   +       rs55927445

is fine

X       2726228 2726230 G/-/A   +       rs55927445

is not

even though this is how it is displayed in ensembl @ 
http://www.ensembl.org/Homo_sapiens/Variation/Summary?r=X:2725728-2726728;source=dbSNP;v=rs55927445;vdb=variation;vf=12794020

Thanks

Stuart

On 08/05/13 13:09, Sarah Hunt wrote:
> Hi Stuart,
> Hope all goes well with you! Do you have any input you can share to 
> help debug this one?
> Sarah
>
> On Wed, May 8, 2013 at 12:02 PM, Stuart Meacham <sm766 at cam.ac.uk 
> <mailto:sm766 at cam.ac.uk>> wrote:
>
>     Hi,
>
>     When using the VEP (Ensembl 71) with apparently well formed data I
>     am getting some errors generated by the above mentioned module. It
>     appears $hgvs_notation->{type} is queried when not defined at
>     several locations in the module. I am using the 'ensembl' data
>     format as input and outputting a vcf with the --everything flag.
>     The VEP is producing output for all 715 records provided. The
>     errors are for locations on ch1 and chrX.
>
>     For reference:
>
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 934.
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 938.
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 976.
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 984.
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 753.
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 769.
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 775.
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 775.
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 806.
>     Use of uninitialized value in string eq at
>     /home/sm766/src/vep/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm
>     line 825.
>
>     Thanks
>
>     Stuart
>
>
>     _______________________________________________
>     Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>     Posting guidelines and subscribe/unsubscribe info:
>     http://lists.ensembl.org/mailman/listinfo/dev
>     Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/