added additional code to output intermediate modeling results in main.py #128
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yeastdnnexplorer/__main__.py
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| os.makedirs(bootstrap_results_dir, exist_ok=True) | ||
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| # Save "all" results | ||
| ci_dict_all = lasso_res["all"]["ci_dict"] |
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Do not bother outputing the alphas.
There is repeated code here. The only thing that is different here is 'all' or 'top10'. DRY
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make sure the names of the output tables are the same. since it is going into args.output_dirpath/<response_tf>/, you do not need to append the response_tf to the filename
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
Co-authored-by: Chase Mateusiak <chasem@wustl.edu>
…trap models, and updated the interactor_workflow function in main.py to accurately return a single directory with all intermediate and final results
| "sig_coefs": sig_coef_dict, | ||
| "predictors": X, | ||
| "response": y, | ||
| "classes": stratification_classes, | ||
| } | ||
| # this adds the bootstrap lasso outputs so that we can create our own CIs | ||
| if method == "bootstrap_lassocv": |
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I'm not sure why the output typing needed to change -- it doesn't look like it did.
We'll make this an issue for later -- I think it is probably better to return this key no matter what, and fill it with None when the method isn't bootstrap_lasso.
If you change output in the future, do adjust the docstring :return: documentation, too
| # Save the results from bootstrapping for further analysis | ||
| if args.method == "bootstrap_lassocv": | ||
| # Iterate through "all" and "top" | ||
| for suffix, lasso_results in lasso_res.items(): |
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