This notebook describes how to apply the mock community evaluations presented in (Bokulich, et al. (in preparation)) to reproduce the analyses in that paper, or to extend them to other data sets.
To prepare results from another classifier for analysis, you'll need to have BIOM files with taxonomy assignments as an observation metadata category called
taxonomy. An example of how to generate these is presented in the data generation notebook in this directory, which was used to generated the precomputed data in the tax-credit repository.
Your BIOM tables should be called
table.biom, and nested in the following directory structure:
results_dir/ mock-community/ dataset-id/ reference-db-id/ method-id/ parameter-combination-id/ table.biom
results_dir is the name of the top level directory, and you will set this value in the first code cell of the analysis notebooks. You can name this directory whatever you want to.
mock-community describes the specific analysis that is being run, and must be named
mock-community for the framework to find your results.
This directory structure is identical to that for the precomputed results. You can review that directory structure for an example of how this should look.
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