skbio.alignment.AlignPath.from_aligned#

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

Create an alignment path from aligned sequences.

Parameters:

alniterable of Sequence, str or sequence: Aligned sequences. Can be skbio sequences, strings or sequences of any scalars.
gap_charsstr or container, optional: Characters that should be treated as gaps in aligned sequences. Default is “-“.
startsarray_like of int of shape (2,), 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 is more general but less efficient than from_tabular. It works with various sequence formats.

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>