Subsetting a feature table for some samples is not uncommon and would come in very handy in the API.
We figured with Yoshiki through the creation of an intermediate pandas dataframe (eg. below), which could be relatively easily avoided thanks to some additional argument in the method " filter_samples ": for example " include_ids " (subset positive) to do the inverse of " exclude_ids " (i.e. subset negative). Thanks!
from qiime2.plugins.feature_table.methods import filter_samples
x = pd.DataFrame(index=pd.Series(name=’#SampleID’, data=<list_of_sample_names>))