[ensembl-dev] Variation::OverlapConsequence::rank()

[Will McLaren]

Hello,

The ranks are given in this table:

http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences

Regards

Will


On 29 May 2014 17:26, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
>
> The method Bio::EnsEMBL::Variation::OverlapConsequence::rank() seems to
> return 'the relative rank of this OverlapConsequence when compared to other
> OverlapConsequence objects. This is used, for example, to determine the
> most severe consequence of a VariationFeature".
>
> As shown in this example each consequence term appears to have a unique
> rank independently of the collective consequence terms for the input
> variant. Is there a dictionary somewhere of ranks and corresponding terms?
>
> Location Allele Existing_variation SYMBOL SYMBOL_SOURCE Gene ENSP Feature
> Feature_type BIOTYPE STRAND CANONICAL EXON INTRON DISTANCE TSSDistance
> FeatureDistance Consequence Effect Rank
> 2:208228309 T rs17808606 AC007879.5 Clone_based_vega_gene ENSG00000223725
> - ENST00000412387 Transcript antisense -1 - - 3/4 - - 0
> intron_variant,nc_transcript_variant INTRONIC,WITHIN_NON_CODING_GENE 21,23
> 2:208231478 T rs17808718 AC007879.5 Clone_based_vega_gene ENSG00000223725
> - ENST00000412387 Transcript antisense -1 - - 3/4 - - 0
> intron_variant,nc_transcript_variant INTRONIC,WITHIN_NON_CODING_GENE 21,23
> 2:208440836 C rs17811997 CREB1 HGNC ENSG00000118260 ENSP00000412016
> ENST00000418081 Transcript nonsense_mediated_decay 1 - - 5/8 - - 0
> intron_variant,NMD_transcript_variant INTRONIC,NMD_TRANSCRIPT 21,22
>
> Thanks,
>
> --
> G.
>
> _______________________________________________
> 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/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140530/1d38a94d/attachment.html>