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SBIMB / StellarPGx

Calling star alleles in highly polymorphic pharmacogenes (e.g. CYP450 genes) by leveraging genome graph-based variant detection.
MIT License
30 stars 7 forks source link

json output #11

Closed wenjiany closed 2 years ago

wenjiany commented 2 years ago

Is that possible to provide a JSON output in addition to the text report?

A JSON format would help avoid writing additional scripts to parse the result. Thanks.

twesigomwedavid commented 2 years ago

@wenjiany,

Thanks for raising this issue. We provide a script for parsing all the text reports for your samples (see https://github.com/SBIMB/StellarPGx/tree/master/scripts/general).

This script is written in bash and requires two arguments i.e. a list of your sample_IDs (without extensions), and the output file.

Hope this helps

We will look into automatically outputting a combined summary in future versions.

Thanks, David

wenjiany commented 2 years ago

Thanks for quick response! I was going to write a parsing script... The script worked. You can close the issue.