[ensembl-dev] VEP 93 some string fields look like numbers in the json output

[Laurent Gil]

Dear Michael,

Which version of VEP 93 have you installed ?
We put a fix about this NANS gene issue in the version 93.4 
(https://github.com/Ensembl/ensembl-vep/releases/tag/release%2F93.4).

For the transcript IDs which are an ID, we will have a look at try to 
force it as a string.

Best regards,

Laurent

On 18/12/2018 23:46, Michael Yourshaw wrote:
> I'm using VEP version 93, locally installed with the cache.
>
> This VCF input in the NANS gene:
>         chr9 98056788 rs3199064 T G ...
>
> yields the VEP json output:
>         ...,"gene_symbol":NaN,...
>
> and fails a python script, which expects a string, because an unquoted 
> NaN is treated as a float and casts to the string "nan".
>
> A similar problem can happen when the transcript_id looks like a number:
>         chr9 98056788 rs3199064 T G
> yields
>         ...,"transcript_id":3494,...
> In this latter case, casting transcript_id as a string works, but the 
> need to cast is a trap for the unwary.
>
> The json writer seems to be too clever for its own good, as values 
> that don't look like numbers, such as "ENST00000495319" and "IGHA2" 
> have the expected double-quoting in the json.
>
> Indeed it seems odd that NANS becomes float NaN, whereas NANP and 
> other NAN* genes remain proper json strings.
>
> ॐ
> Michael Yourshaw
> myourshaw at gmail.com <mailto:myourshaw at ucla.edu>
>
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