'''Local alignment to find best matching regions'''
# Reference: biopython 1.83+ | Verify API if version differs

from Bio.Align import PairwiseAligner
from Bio.Seq import Seq

if __name__ == '__main__':
    long_seq = Seq('NNNNNACCGGTAACGTAGNNNNNNNN')
    short_seq = Seq('ACCGGTAACGTAG')

    aligner = PairwiseAligner(mode='local', match_score=2, mismatch_score=-1, open_gap_score=-10, extend_gap_score=-0.5)

    alignments = aligner.align(long_seq, short_seq)
    print(f'Found {len(alignments)} optimal alignment(s)')
    print(f'Score: {alignments[0].score}\n')
    print(alignments[0])

    # Show aligned coordinates
    alignment = alignments[0]
    print(f'\nAligned regions:')
    print(f'Target: positions {alignment.aligned[0]}')
    print(f'Query: positions {alignment.aligned[1]}')