[ensembl-dev] VEP annotation V2.2 and --most_severe

Salih Tuna st5 at sanger.ac.uk
Mon May 28 13:52:44 BST 2012


Thanks Will,
I will try this very soon.
Best,
salih


On 28/05/2012 09:35, "Will McLaren" <wm2 at ebi.ac.uk> wrote:

> Hi Salih,
> 
> You'd have a to write a small perl script to do this, as the
> consequence rankings are stored internally in our API.
> 
> You will need to import the consequence type hash into your script as follows:
> 
> my %cons = %Bio::EnsEMBL::Variation::Utils::Constants::OVERLAP_CONSEQUENCES;
> 
> # assuming you are using the Ensembl (default) consequence terms
> # create a hash with the consequence name and rank
> my %ranks = map {$_->{display_term} => $_->{rank}} %cons;
> 
> # now we can sort a list of consequences by their rank
> my @cons_list = qw(NON_SYNONYMOUS_CODING FRAMESHIFT_CODING NMD_TRANSCRIPT);
> 
> # lowest rank number is most severe
> my @sorted = sort {$ranks{$a} <=> $ranks{$b}} @cons_list;
> 
> Hope this helps,
> 
> Cheers
> 
> Will
> 
> On 23 May 2012 18:32, Fiona Cunningham <fiona at ebi.ac.uk> wrote:
>>  Dear Salih,
>> 
>> Apologies, I'm not sure if I followed exactly what you want to do
>> here. Would this be equivalent to doing something like a 'diff' on the
>> 2 different output files? Maybe this would solve your problem.
>> 
>> Best wishes,
>> 
>> Fiona
>> 
>> -----------------------------------------------------------------------------
>> ------
>> Fiona Cunningham
>> Ensembl Coordinator, Ensembl Variation Project Leader.
>> EMBL-EBI, Genome Campus, Hinxton, UK
>> www.ensembl.org || www.lrg-sequence.org
>> fiona at ebi.ac.uk   || t: +44 1223 494612
>> 
>> 
>> On 20 May 2012 09:58, Salih Tuna <st5 at sanger.ac.uk> wrote:
>>> Apologies,
>>> I meant the option --per_gene for the most severe consequences...
>>> 
>>> 
>>> 
>>> On 20/05/2012 09:27, "Salih Tuna" <st5 at sanger.ac.uk> wrote:
>>> 
>>> Hi,
>>> I am using VEP annotation V2.2
>>> I did some annotation without using the option ‹most_severe. Now I would
>>> like to eliminate the most severe ones for each gene. Is it possible to run
>>> just this single module rather than running whole code again?
>>> 
>>> Thanks,
>>> Salih
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