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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
318 stars 120 forks source link

Expose the get_json() to the gemini scripts #898

Open kounkou opened 6 years ago

kounkou commented 6 years ago

Hello @brentp ,

First of all, thanks a lot for the quality of Gemini, it rocks ! :+1:

I was playing with the following scripts :

autosomal_recessive
comp_hets
de_novo
x_linked_dominant
x_linked_de_novo
x_linked_recessive
autosomal_dominant

ex : $ gemini de_novo --columns "chrom,start,end" test.db

and as I got the result of the commands, I was wondering if I could just output the results to a json file. But the 

--format json

command isn't supported as for gemini query. Is there any reason why the json output format isn't currently supported ? Could we expose the get_json for these scripts please ? Indeed I saw that you did solve a similar problem for #73 #748 ....

Best !

brentp commented 6 years ago

There is no particular reason, I'd accept a pull request to address this.