'''Find conserved positions in an alignment'''
# Reference: biopython 1.83+ | Verify API if version differs

from Bio import AlignIO
from collections import Counter

def find_conserved_positions(alignment, threshold=0.8):
    conserved = []
    for col_idx in range(alignment.get_alignment_length()):
        column = alignment[:, col_idx]
        counts = Counter(column)
        if '-' in counts:
            del counts['-']
        if not counts:
            continue
        most_common_char, most_common_count = counts.most_common(1)[0]
        conservation = most_common_count / len(alignment)
        if conservation >= threshold:
            conserved.append((col_idx, most_common_char, conservation))
    return conserved

if __name__ == '__main__':
    alignment = AlignIO.read('alignment.fasta', 'fasta')

    print('Fully conserved positions (100%):')
    for pos, char, cons in find_conserved_positions(alignment, threshold=1.0):
        print(f'  Position {pos}: {char}')

    print('\nHighly conserved positions (80%+):')
    for pos, char, cons in find_conserved_positions(alignment, threshold=0.8):
        print(f'  Position {pos}: {char} ({cons*100:.0f}%)')