[ensembl-dev] VEP ProteinSeq with Haplosaurus output

[Irina Armean]

Hi Fong,

Haplosaurus can export sequences if you switch the output to JSON using 
--json. The output contains by default sequences for the CDS haplotypes 
(cds_haplotypes seq) and for the protein haplotypes (protein_haplotypes  
seq).

Each transcript analysed will be summarised in a JSON object written on 
one line of the output file.

The JSON format has the same structure as the REST API json: 
https://rest.ensembl.org/documentation/info/transcript_haplotypes_get.

I have added an update to our documentation as it was not very clear and 
it should be out with the next release.

Best wishes,

Irina


On 15/08/2018 10:17, Fong Chan wrote:
>
> Hi,
>
> I was wondering if there a way to get the VEP plugin ProteinSeq.pm 
> (https://github.com/Ensembl/VEP_plugins/blob/release/93/ProteinSeqs.pm) 
> to work with Haplosaurus output 
> (https://www.ensembl.org/info/docs/tools/vep/haplo/index.html). I am 
> interested in producing mutated peptide sequences that incorporates 
> the haplotypes.
>
> Thanks,
>
> Fong
>
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