skbio.alignment.TabularMSA.from_path_seqs#

classmethod TabularMSA.from_path_seqs(path, seqs)[source]#

Create a tabular MSA from an alignment path and the original sequences.

Parameters:

pathAlignPath: Alignment path.
seqsiterable of GrammaredSequence: Original sequences.

Returns:

TabularMSA: The created tabular MSA object.

See also

skbio.alignment.AlignPath.from_tabular

Examples

>>> from skbio import DNA, TabularMSA
>>> from skbio.alignment import AlignPath
>>> seqs = [
...    DNA('CGTCGTGC'),
...    DNA('CAGTC'),
...    DNA('CGTCGTT'),
... ]
>>> path = AlignPath(
...    lengths=[2, 2, 2, 1, 1],
...    states=[0, 2, 0, 6, 0],
...    starts=[0, 0, 0],
... )
>>> msa = TabularMSA.from_path_seqs(path, seqs)
>>> msa
TabularMSA[DNA]
---------------------
Stats:
    sequence count: 3
    position count: 8
---------------------
CGTCGTGC
CA--GT-C
CGTCGT-T