skbio.alignment.PairAlignPath.from_coordinates

classmethod PairAlignPath.from_coordinates(coords)

Generate an alignment path from an array of segment coordinates.

Parameters:

coordsarray_like of int of shape (n_seqs, n_segments)

Array where each value defines the start positions (index) of each segment for each sequence.

Returns:

AlignPath

The alignment path created from the given coordinates.

Examples

>>> import numpy as np
>>> from skbio.alignment import AlignPath
>>> coordinates = np.array([[0, 1, 1, 3, 4],
...                         [0, 1, 3, 3, 3],
...                         [0, 1, 1, 3, 3]])
>>> path = AlignPath.from_coordinates(coordinates)
>>> path
AlignPath
Shape(sequence=3, position=6)
lengths: [1 2 2 1]
states: [0 5 2 6]