[ensembl-dev] vep script json output

Rodrigo Garcia rgarcia at inmegen.gob.mx
Thu Aug 20 23:14:33 BST 2015


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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