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univieCUBE / deepnog

Protein orthologous group assignment with deep learning
BSD 3-Clause "New" or "Revised" License
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CLI set confidence threshold #7

Closed VarIr closed 4 years ago

VarIr commented 4 years ago

There should be an option to set the confidence threshold from the CLI, so that users can easily choose on their own.

LokiLuciferase commented 4 years ago

You mean like, allowing to mask predictions with a confidence below XY%? Sure, that's trivial to implement.

VarIr commented 4 years ago

Yes exactly. The logic is already there, but there is no option to change it from the client. Users could easily achieve the same by filtering the output data frame, but I think it would be more convenient to let the program do it.

Would you like to work on this?

LokiLuciferase commented 4 years ago

So for the stdout output of predict I have added this to one of yesterdays PRs since it was just two or three lines of code. Do you think for API usage it's required as well? If so I can refactor it to be a part of TrexClassifier

VarIr commented 4 years ago

I am slightly confused, as this is basically independent from phenotrex, but related to deepnog stand-alone output?

I don't think API is necessary. Users already meddling with the code directly should be able to filter a pandas dataframe on your own.

LokiLuciferase commented 4 years ago

oh, damn. sorry, my bad, wrong repo. 😁 I didn't change anything about deepnog, I just added a flag to mask the output of phenotrex predict (unrelated to deepnog prediction output). But yeah, I can tackle this in deepnog.