calour.amplicon_experiment.AmpliconExperiment.save_biom

AmpliconExperiment.save_biom(f, fmt='hdf5', add_metadata='taxonomy')[source]

Save experiment to biom format

Parameters:
  • f (str) – the file to save to
  • fmt (str, optional) – the output biom table format. options are: ‘hdf5’ (default) save to hdf5 biom table. ‘json’ same to json biom table. ‘txt’ save to text (tsv) biom table.
  • add_metadata (str or None, optional) – add metadata column from Experiment.feature_metadata to biom table. Don’t add if it is None.