[ensembl-dev] vep script json output

Will McLaren wm2 at ebi.ac.uk
Fri Aug 21 10:17:03 BST 2015


Hi Rodrigo,

Can you please provide an example of some input that causes this problem to
appear in the output?

Thanks

Will McLaren
Ensembl Variation

On 20 August 2015 at 23:14, Rodrigo Garcia <rgarcia at inmegen.gob.mx> wrote:

> Hello!
>
> Creating json files is a great feature but I think I may have found a bug
> on the variant_effect_predictor.pl script.
>
> Using the --json flag some -not all- of the objects exported have the
> string ARRAY and some hash instead of an array on pubmed and clin_sig
> fields.
>
> Like so: "pubmed":["ARRAY(0xf2b8178)"]
>
> or sometimes: "clin_sig":["ARRAY(0x14211470)"]
>
> Some entries are fine, with several pubmed IDs or different clinical
> significances, all properly formatted in JSON.
> But not all.
>
> Cheers!
>
> Rodrigo
>
>
>
> P.S. Hi list! My name is Rodrigo, I do some bioinformatics work for a
> mexican genomics institute. I'm a happy user of VEP and other ensembl
> tools. Thanks, great software!
>
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