skbio.alignment.AlignPath.from_aligned#

classmethod AlignPath.from_aligned(aln, gap_chars='-', starts=None)[source]#

Create an alignment path from aligned sequences.

Parameters:

alnTabularMSA or iterable of equal-length sequence-like: Aligned sequences. All sequences must have equal length.
gap_charsiterable of hashable, optional: Symbols that should be treated as gaps in aligned sequences. Default is “-“.
startsarray-like of int of shape (n_sequences,), optional: Start positions of sequences. If omitted, will be all zeros.

Returns:

AlignPath: The alignment path created from the aligned sequences.

See also

to_aligned
from_tabular

Notes

This method consumes aligned sequences, i.e., sequences with gaps inserted to make them equal in length. It is more general but less efficient than from_tabular.

Examples

>>> from skbio.alignment import AlignPath
>>> aln = [
...    'CGTCGTGC',
...    'CA--GT-C',
...    'CGTCGT-T'
... ]
>>> path = AlignPath.from_aligned(aln)
>>> path
<AlignPath, sequences: 3, positions: 8, segments: 5>