[ensembl-dev] Variation::OverlapConsequence::rank()
Will McLaren
wm2 at ebi.ac.uk
Mon Jun 2 13:19:16 BST 2014
The VEP can still report these Ensembl consequence terms, using "--terms
ensembl"
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_terms
You can also retrieve the terms from the OverlapConsequence objects in
%Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES using the
display_term() method; you could use this in a plugin if you wished to
display both SO (in the main Consequence column) and Ensembl (in the
plugin's own field) terms.
Will
On 2 June 2014 13:03, Genomeo Dev <genomeodev at gmail.com> wrote:
> Thanks. Actually the terms in ConsequenceType.pm are quite a useful
> grouping for a broad classification. I would love to see them at least in
> the API in future releases as it would make a good common ground for those
> reporting broad variant consequences.
>
> G.
>
>
> On 30 May 2014 11:52, Laurent Gil <lgil at ebi.ac.uk> wrote:
>
>> Hi Genomeo,
>>
>> Actually it's because the terms are grouped by the Old Ensembl term,
>> using the highest rank of the terms which belong to this "group",
>> e.g:
>> The Old Ensembl term " Within non coding gene" should be ranked 23 but
>> the term " non_coding_exon_variant" is ranked 20, so we displayed it in the
>> table at the rank 20.
>>
>> Thanks for spotting that. We built the table a long time ago and it
>> definitively need to be updated.
>> We will change the table in the next release to match the ranking of each
>> individual consequence term.
>>
>> Best regards,
>>
>> Laurent
>>
>> On 30/05/2014 11:41, Will McLaren wrote:
>>
>> Seems nc_transcript_variant is out of order in that table, thanks for
>> spotting that.
>>
>> ConsequenceType.pm is not used by the current API code and will be
>> deprecated. The Ensembl terms are no longer the preferred terms to use; the
>> SO equivalents are what we recommend for use now.
>>
>> You can get the consequence types and their various attributes from the
>> hash:
>>
>> %Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES
>>
>> e.g. to get a hash with the ranks in:
>>
>> my %ranks = map {$_->SO_term => $_->rank} values
>> %Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES;
>>
>> print "$_\t$ranks{$_}\n" for sort {$ranks{$a} <=> $ranks{$b}} keys
>> %ranks;
>>
>> Regards
>>
>> Will
>>
>>
>> On 30 May 2014 10:21, Genomeo Dev <genomeodev at gmail.com> wrote:
>>
>>> Hi Will,
>>>
>>> I wonder if that is the latest table as seems not consistent with
>>> these ranks obtained from OverlapConsequence::rank()
>>>
>>> 21 INTRONIC
>>> 22 NMD_TRANSCRIPT
>>> 23 WITHIN_NON_CODING_GENE
>>> 24 UPSTREAM
>>> 25 DOWNSTREAM
>>> 36 REGULATORY_REGION
>>> 38 INTERGENIC
>>>
>>> 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:
>>>
>>> our %CONSEQUENCE_DESCRIPTIONS = (
>>> 'ESSENTIAL_SPLICE_SITE' => 'In the first 2 or the last 2 basepairs of
>>> an intron',
>>> 'STOP_GAINED' => 'In coding sequence, resulting in the gain
>>> of a stop codon',
>>> 'STOP_LOST' => 'In coding sequence, resulting in the loss
>>> of a stop codon',
>>> 'COMPLEX_INDEL' => 'Insertion or deletion that spans an
>>> exon/intron or coding sequence/UTR border',
>>> 'FRAMESHIFT_CODING' => 'In coding sequence, resulting in a
>>> frameshift',
>>> 'NON_SYNONYMOUS_CODING' => 'In coding sequence and results in an
>>> amino acid change in the encoded peptide sequence',
>>> 'SPLICE_SITE' => '1-3 bps into an exon or 3-8 bps into an
>>> intron',
>>> 'PARTIAL_CODON' => 'Located within the final, incomplete
>>> codon of a transcript whose end coordinate is unknown',
>>> 'SYNONYMOUS_CODING' => 'In coding sequence, not resulting in an
>>> amino acid change (silent mutation)',
>>> 'REGULATORY_REGION' => 'In regulatory region annotated by
>>> Ensembl',
>>> 'WITHIN_MATURE_miRNA' => 'Located within a microRNA',
>>> '5PRIME_UTR' => 'In 5 prime untranslated region',
>>> '3PRIME_UTR' => 'In 3 prime untranslated region',
>>> 'INTRONIC' => 'In intron',
>>> 'NMD_TRANSCRIPT' => 'Located within a transcript predicted to
>>> undergo nonsense-mediated decay',
>>> 'WITHIN_NON_CODING_GENE' => 'Located within a gene that does not code
>>> for a protein',
>>> 'UPSTREAM' => 'Within 5 kb upstream of the 5 prime end
>>> of a transcript',
>>> 'DOWNSTREAM' => 'Within 5 kb downstream of the 3 prime end
>>> of a transcript',
>>> 'HGMD_MUTATION' => 'Mutation from the HGMD database -
>>> consequence unknown',
>>> 'INTERGENIC' => 'More than 5 kb either upstream or
>>> downstream of a transcript',
>>> );
>>>
>>> Regards,
>>>
>>> G.
>>>
>>>
>>> On 30 May 2014 09:50, Will McLaren <wm2 at ebi.ac.uk> wrote:
>>>
>>>> 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
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>>>>>
>>>>
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>>>
>>>
>>> --
>>> G.
>>>
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>>>
>>
>>
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>
>
> --
> 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/
>
>
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