skbio.alignment.TabularMSA.reassign_index

TabularMSA.reassign_index(mapping=None, minter=None)[source]

Reassign index labels to sequences in this MSA.

State: Experimental as of 0.4.1.

Parameters
  • mapping (dict or callable, optional) – Dictionary or callable that maps existing labels to new labels. Any label without a mapping will remain the same.

  • minter (callable or metadata key, optional) – If provided, defines an index label for each sequence. Can either be a callable accepting a single argument (each sequence) or a key into each sequence’s metadata attribute.

Raises

ValueError – If mapping and minter are both provided.

See also

index()

Notes

If neither mapping nor minter are provided, index labels will be reset to the TabularMSA constructor’s default.

Examples

Create a TabularMSA object with default index labels:

>>> from skbio import DNA, TabularMSA
>>> seqs = [DNA('ACG', metadata={'id': 'a'}),
...         DNA('AC-', metadata={'id': 'b'}),
...         DNA('CCG', metadata={'id': 'c'})]
>>> msa = TabularMSA(seqs)
>>> msa.index
RangeIndex(start=0, stop=3, step=1)

Assign new index to the MSA using each sequence’s ID as a label:

>>> msa.reassign_index(minter='id')
>>> msa.index
Index(['a', 'b', 'c'], dtype='object')

Assign default index:

>>> msa.reassign_index()
>>> msa.index
RangeIndex(start=0, stop=3, step=1)

Alternatively, a mapping of existing labels to new labels may be passed via mapping:

>>> msa.reassign_index(mapping={0: 'seq1', 1: 'seq2'})
>>> msa.index
Index(['seq1', 'seq2', 2], dtype='object')