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pnnl-predictive-phenomics / emll

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Adding new class for wrapping typical ADVI workflow #6

Open mcnaughtonadm opened 8 months ago

mcnaughtonadm commented 8 months ago

This PR will address #15 .

To be able to utilize a template JSON file with the emll code. It is necessary to break the components needed to run the ADVI into their own methods. Here we break the scripts present in the run_hackett_inference.py into a separate class called BMCA (can be renamed to whatever, this is just a placeholder) that loads the cobra model, along with the paths to the various data sources.

mcnaughtonadm commented 8 months ago

The line: https://github.com/PNNL-CompBio/emll/blob/cfe80dc70c58d5a639df9c6311d41c47c1d7b1fe/src/emll/bmca.py#L72

should be rewritten to accept any type of cobra model input.