biom.table.Table.iter_pairwise

Table.iter_pairwise(dense=True, axis='sample', tri=True, diag=False)

Pairwise iteration over self

Parameters:

densebool, optional

Defaults to True. If False, yield compressed sparse row or compressed sparse columns if axis is ‘observation’ or ‘sample’, respectively.

axis{‘sample’, ‘observation’}, optional

The axis to iterate over.

tribool, optional

If True, just yield [i, j] and not [j, i]

diagbool, optional

If True, yield [i, i]

Returns:

GeneratorType

Yields [(val_i, id_i, metadata_i), (val_j, id_j, metadata_j)]

Raises:

UnknownAxisError

Examples

>>> from biom import example_table

By default, only the upper triangle without the diagonal of the resulting pairwise combinations is yielded.

>>> iter_ = example_table.iter_pairwise()
>>> for (val_i, id_i, md_i), (val_j, id_j, md_j) in iter_:
...     print(id_i, id_j)
S1 S2
S1 S3
S2 S3

The full pairwise combinations can also be yielded though.

>>> iter_ = example_table.iter_pairwise(tri=False, diag=True)
>>> for (val_i, id_i, md_i), (val_j, id_j, md_j) in iter_:
...     print(id_i, id_j)
S1 S1
S1 S2
S1 S3
S2 S1
S2 S2
S2 S3
S3 S1
S3 S2
S3 S3