'''Analyze gap distribution in alignment'''
# Reference: biopython 1.83+ | Verify API if version differs

from Bio import AlignIO

if __name__ == '__main__':
    alignment = AlignIO.read('alignment.fasta', 'fasta')
    print(f'Alignment: {len(alignment)} sequences, {alignment.get_alignment_length()} columns\n')

    print('Gaps per sequence:')
    for record in alignment:
        gaps = str(record.seq).count('-')
        gap_pct = gaps / len(record.seq) * 100
        print(f'  {record.id}: {gaps} gaps ({gap_pct:.1f}%)')

    print('\nGaps per column (showing columns with gaps):')
    for col_idx in range(alignment.get_alignment_length()):
        column = alignment[:, col_idx]
        gaps = column.count('-')
        if gaps > 0:
            gap_pct = gaps / len(alignment) * 100
            print(f'  Column {col_idx}: {gaps} gaps ({gap_pct:.1f}%)')