[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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>>
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