BiopythonDeprecationWarning in Bio.pairwise2

[shi-scala]

Hi,

I've been trying to resolve this deprecation by using the Bio.Align.PairwiseAligner module but have not been able to do so.
We use a python function to determine the alignment score in order to align tuples of sequence and secondary structure:
As an example:
SeqA = [('F', 'E'), ('T', 'E'), ...]
SeqB = [('F', 'E'), ('T', 'E'), ...]

How can I use a custom python function to determine the score between such tuples using Bio.Align.PairwiseAligner?

Thank you

[mdehoon]

How can I use a custom python function to determine the score between such tuples using Bio.Align.PairwiseAligner?

If you can write the sequences as

SeqA = ["FE", "TE", ...]
SeqB = ["FE", "TE", ...]

then define your alphabet as

>>> alphabet = ("EE", "FE", "TE", ...)

Create a substitution matrix and fill it

>>> from Bio.Align import substitution_matrices
>>> a = substitution_matrices.Array(alphabet, dims=2)
>>> for key1 in alphabet:
...     for key2 in alphabet:
...        a[key1+key2] = yourfunction(key1, key2)

Create the aligner and set its substitution matrix to the substitution matrix you just created:

>>> from Bio.Align import PairwiseAligner
>>> aligner = PairwiseAligner()
>>> aligner.substitution_matrix = a

and align:

>>> alignments = aligner.align(["EE", "EF", "FF"], ["EE", "FF"])
>>> alignment = next(alignments)
>>> print(alignment)
EE EF FF
|| -- ||
EE -- FF

[shi-scala]

That's a really cool implementation.
Thank you, I'll give it a try.