Ejemplo n.º 1
0
def add_pseudocount(table: biom.Table, pseudocount: int = 1) -> biom.Table:
    # This is ugly, and it requires a sparse and dense representation to
    # be in memory at the same time, but biom.Table.transform only operates
    # on non-zero values, so it isn't useful here (as we need to operate on
    # all values).
    result = biom.Table([
        v + pseudocount
        for v in table.iter_data(dense=True, axis='observation')
    ], table.ids(axis='observation'), table.ids())
    return result