Is it possible to use the data without a biom as input

[SilasK]

For the python input it would be great if a simple pandas table or numpy array could be used as input.

[cameronmartino]

Hi @SilasK,

The issue is loading in large sparse tables. We chose biom as a requirement because these tools were developed for microbiome data and loading mostly zeros into memory is a pain. However, I can see the ease of use in the next version or the one after we will consider allow both types as input. At least for the Python API, since the data is already loaded.

[harper357]

In case you didn't know, Pandas does have a sparse format.