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

[Genomeo Dev]

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.
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