'''Align sequences from a FASTA file'''
# Reference: biopython 1.83+ | Verify API if version differs

from Bio import SeqIO
from Bio.Align import PairwiseAligner

if __name__ == '__main__':
    fasta_file = 'sequences.fasta'
    records = list(SeqIO.parse(fasta_file, 'fasta'))

    if len(records) < 2:
        print('Need at least 2 sequences to align')
    else:
        seq1, seq2 = records[0].seq, records[1].seq

        aligner = PairwiseAligner(mode='global', match_score=2, mismatch_score=-1, open_gap_score=-10, extend_gap_score=-0.5)
        alignments = aligner.align(seq1, seq2)

        print(f'Aligning {records[0].id} vs {records[1].id}')
        print(f'Score: {alignments[0].score}\n')
        print(alignments[0])