skbio.alignment.AlignPath.from_coordinates#

classmethod AlignPath.from_coordinates(coords)[source]#

Create an alignment path from an array of segment coordinates.

Parameters:
coordsarray_like of int of shape (n_sequences, 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.

See also

to_coordinates

Notes

The input is compatible with the underlying data structure of BioPython’s Alignment class [1].

References

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, sequences: 3, positions: 6, segments: 4>

One can convert a Biopython’s Alignment object into a scikit-bio alignment path using this method.

>>> from Bio import Align
>>> a = Align.PairwiseAligner()
>>> res = a.align("GATCGTC", "ATCGCTC")
>>> print(res[0])
target            0 GATCG-TC 7
                  0 -||||-|| 8
query             0 -ATCGCTC 7

>>> coords = res[0].coordinates
>>> coords
array([[0, 1, 5, 5, 7],
       [0, 0, 4, 5, 7]])

>>> from skbio.alignment import PairAlignPath
>>> path = PairAlignPath.from_coordinates(coords)
>>> path
<PairAlignPath, positions: 8, segments: 4, CIGAR: '1D4M1I2M'>