[Help Request] Migrating from pairwise2 -> PairwiseAligner

[jday1]

Setup

I am reporting a problem with Biopython version, Python version, and operating
system as follows:

import sys; print(sys.version)
import platform; print(platform.python_implementation()); print(platform.platform())
import Bio; print(Bio.__version__)

1.82

I am trying to migrate from align.localds to PairwiseAligner and require assistance as I am not sure how to replicate the behaviour I need. I have attached a code snippet with a test illustrating the localds's output. Could someone please show me how to replicate this with the PairwiseAligner.

In particular, how do I get an output which includes the - character and what is the equivalent of penalize_end_gaps.

from Bio import pairwise2
from Bio.Align import substitution_matrices, PairwiseAligner


SUBSTITUTION_MATRIX = substitution_matrices.load("BLOSUM62")


def using_pairwise_aligner(seq1, seq2, matrix, gap_open, gap_extend, penalize_end_gaps) -> tuple[str, str]:
    aligner = PairwiseAligner()
    
    # How do I replicate the result?
    pass


def test_align_format_sequences():
    
    input_seq1, input_seq2 = "GCVLDGNYQIW", "GCLIQGRFDILF"

    expected_seq1, expected_seq2 = "GCVLDGNYQIW-", "GCLIQGRFDILF"
    
    # Old method
    alignment = pairwise2.align.localds(input_seq1, input_seq2, SUBSTITUTION_MATRIX, -10.0, -0.5, penalize_end_gaps=(False, False))[0]
    actual_seq1, actual_seq2 = alignment.seqA, alignment.seqB

    assert (actual_seq1, actual_seq2) == (expected_seq1, expected_seq2)


    # New method
    actual_seq1, actual_seq2 = using_pairwise_aligner(input_seq1, input_seq2, SUBSTITUTION_MATRIX, -10.0, -0.5, penalize_end_gaps=(False, False)) 
    assert (actual_seq1, actual_seq2) == (expected_seq1, expected_seq2)