<div dir="ltr">Hello,<div><br></div><div>The ranks are given in this table:</div><div><br></div><div><a href="http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences">http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences</a><br>
</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 29 May 2014 17:26, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hi,</div><div><br></div><div>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".</div>
<div><br></div><div>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?</div>
<div><br></div><div><div>Location<span style="white-space:pre-wrap"> </span>Allele<span style="white-space:pre-wrap"> </span>Existing_variation<span style="white-space:pre-wrap"> </span>SYMBOL<span style="white-space:pre-wrap"> </span>SYMBOL_SOURCE<span style="white-space:pre-wrap"> </span>Gene<span style="white-space:pre-wrap"> </span>ENSP<span style="white-space:pre-wrap"> </span>Feature<span style="white-space:pre-wrap"> </span>Feature_type<span style="white-space:pre-wrap"> </span>BIOTYPE<span style="white-space:pre-wrap"> </span>STRAND<span style="white-space:pre-wrap"> </span>CANONICAL<span style="white-space:pre-wrap"> </span>EXON<span style="white-space:pre-wrap"> </span>INTRON<span style="white-space:pre-wrap"> </span>DISTANCE<span style="white-space:pre-wrap"> </span>TSSDistance<span style="white-space:pre-wrap"> </span>FeatureDistance<span style="white-space:pre-wrap"> </span>Consequence<span style="white-space:pre-wrap"> </span>Effect<span style="white-space:pre-wrap"> </span>Rank</div>
<div>2:208228309<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>rs17808606<span style="white-space:pre-wrap"> </span>AC007879.5<span style="white-space:pre-wrap"> </span>Clone_based_vega_gene<span style="white-space:pre-wrap"> </span>ENSG00000223725<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>ENST00000412387<span style="white-space:pre-wrap"> </span>Transcript<span style="white-space:pre-wrap"> </span>antisense<span style="white-space:pre-wrap"> </span>-1<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>3/4<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>intron_variant,nc_transcript_variant<span style="white-space:pre-wrap"> </span>INTRONIC,WITHIN_NON_CODING_GENE<span style="white-space:pre-wrap"> </span>21,23</div>
<div>2:208231478<span style="white-space:pre-wrap"> </span>T<span style="white-space:pre-wrap"> </span>rs17808718<span style="white-space:pre-wrap"> </span>AC007879.5<span style="white-space:pre-wrap"> </span>Clone_based_vega_gene<span style="white-space:pre-wrap"> </span>ENSG00000223725<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>ENST00000412387<span style="white-space:pre-wrap"> </span>Transcript<span style="white-space:pre-wrap"> </span>antisense<span style="white-space:pre-wrap"> </span>-1<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>3/4<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>intron_variant,nc_transcript_variant<span style="white-space:pre-wrap"> </span>INTRONIC,WITHIN_NON_CODING_GENE<span style="white-space:pre-wrap"> </span>21,23</div>
<div>2:208440836<span style="white-space:pre-wrap"> </span>C<span style="white-space:pre-wrap"> </span>rs17811997<span style="white-space:pre-wrap"> </span>CREB1<span style="white-space:pre-wrap"> </span>HGNC<span style="white-space:pre-wrap"> </span>ENSG00000118260<span style="white-space:pre-wrap"> </span>ENSP00000412016<span style="white-space:pre-wrap"> </span>ENST00000418081<span style="white-space:pre-wrap"> </span>Transcript<span style="white-space:pre-wrap"> </span>nonsense_mediated_decay<span style="white-space:pre-wrap"> </span>1<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>5/8<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>-<span style="white-space:pre-wrap"> </span>0<span style="white-space:pre-wrap"> </span>intron_variant,NMD_transcript_variant<span style="white-space:pre-wrap"> </span>INTRONIC,NMD_TRANSCRIPT<span style="white-space:pre-wrap"> </span>21,22</div>
</div><div><br></div>Thanks,<span class="HOEnZb"><font color="#888888"><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
</font></span></div>
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