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Import data from Geneshot HDF5
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| # Read in data from the HDF store | |
| assert os.path.exists(hdf_fp) | |
| cag_annot = pd.read_hdf(hdf_fp, "/annot/cag/all").set_index("CAG") | |
| cag_abund = pd.read_hdf(hdf_fp, "/abund/cag/wide").set_index("CAG") | |
| corncob_df = pd.read_hdf(hdf_fp, "/stats/cag/corncob") | |
| betta_df = pd.read_hdf(hdf_fp, "/stats/enrichment/betta") | |
| manifest = pd.read_hdf(hdf_fp, "/manifest").set_index("specimen") | |
| specimen_summary = pd.read_hdf(hdf_fp, "/summary/all").set_index("specimen") |
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