stevenweaver
commented
1 year ago Dear Chris,
Sure. Please see @sjspielman's excellent documentation of the JSON results files. There is an entire section on BUSTED.
https://hyphy.org/resources/json-fields.pdf
If you have any additional, specific questions on how to obtain what you are looking for from the json file, I'd be able to help. Command line tools like jq might prove useful when working with json. Otherwise, JSON support is usually available in the programming language of your choice.
Best, Steven
github-actions[bot]
I'm looking for the best way to interpret the results of BUSTED. I am running BUSTED on Hyphy 2.5.36 via conda. The main result seems to be a table of Selection, dN/dS, Proportion, and Notes. If I upload the .json file to Hyphy Vision, I can easily see the number of sites with ER>=10 for positive selection, the p-value, and other information like the number of sequences or the total codon sites in the alignment. Is there a way to access this type of information directly from the BUSTED outfiles? I am working with a couple of hundred gene families, and uploading each to Hyphy Vision is not feasible. Is there a way to get this information from the .json file? I'm likely missing something, but any help would be greatly appreciated :)
Best, Chris