<div dir="ltr">Hi Will,<div><br></div><div>I wonder if that is the latest table as seems not consistent with these ranks obtained from OverlapConsequence::rank()<div><br></div><div><div>21<span class="" style="white-space:pre"> </span>INTRONIC</div>
<div>22<span class="" style="white-space:pre"> </span>NMD_TRANSCRIPT</div><div>23<span class="" style="white-space:pre"> </span>WITHIN_NON_CODING_GENE</div><div>24<span class="" style="white-space:pre"> </span>UPSTREAM</div>
<div>25<span class="" style="white-space:pre"> </span>DOWNSTREAM</div><div>36<span class="" style="white-space:pre"> </span>REGULATORY_REGION</div><div>38<span class="" style="white-space:pre"> </span>INTERGENIC</div></div>
<div><br></div><div>In particular ranks 36 and 38 go beyond the number of entries in that table. Also note that in ConsequenceType.pm, there are fewer ensembl display terms compared to those shown under 'old Ensembl terms' in the table, in case those are meant to be the same:</div>
<div><br></div><div><div>our %CONSEQUENCE_DESCRIPTIONS = (</div><div> 'ESSENTIAL_SPLICE_SITE' => 'In the first 2 or the last 2 basepairs of an intron',</div><div> 'STOP_GAINED' => 'In coding sequence, resulting in the gain of a stop codon',</div>
<div> 'STOP_LOST' => 'In coding sequence, resulting in the loss of a stop codon',</div><div> 'COMPLEX_INDEL' => 'Insertion or deletion that spans an exon/intron or coding sequence/UTR border',</div>
<div> 'FRAMESHIFT_CODING' => 'In coding sequence, resulting in a frameshift',</div><div> 'NON_SYNONYMOUS_CODING' => 'In coding sequence and results in an amino acid change in the encoded peptide sequence',</div>
<div> 'SPLICE_SITE' => '1-3 bps into an exon or 3-8 bps into an intron',</div><div> 'PARTIAL_CODON' => 'Located within the final, incomplete codon of a transcript whose end coordinate is unknown',</div>
<div> 'SYNONYMOUS_CODING' => 'In coding sequence, not resulting in an amino acid change (silent mutation)',</div><div> 'REGULATORY_REGION' => 'In regulatory region annotated by Ensembl',</div>
<div> 'WITHIN_MATURE_miRNA' => 'Located within a microRNA',</div><div> '5PRIME_UTR' => 'In 5 prime untranslated region',</div><div> '3PRIME_UTR' => 'In 3 prime untranslated region',</div>
<div> 'INTRONIC' => 'In intron',</div><div> 'NMD_TRANSCRIPT' => 'Located within a transcript predicted to undergo nonsense-mediated decay',</div><div> 'WITHIN_NON_CODING_GENE' => 'Located within a gene that does not code for a protein',</div>
<div> 'UPSTREAM' => 'Within 5 kb upstream of the 5 prime end of a transcript',</div><div> 'DOWNSTREAM' => 'Within 5 kb downstream of the 3 prime end of a transcript',</div>
<div> 'HGMD_MUTATION' => 'Mutation from the HGMD database - consequence unknown',</div><div> 'INTERGENIC' => 'More than 5 kb either upstream or downstream of a transcript',</div>
<div>);</div></div><div class="gmail_extra"><br></div><div class="gmail_extra">Regards,</div><div class="gmail_extra"><br></div><div class="gmail_extra">G.<br><br><div class="gmail_quote">On 30 May 2014 09:50, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><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" target="_blank">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"><div><div class="h5">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>
</div></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div><div class="h5"><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><font color="#888888"><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
</font></span></div>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
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