indels.py

def count_indels(alignment):
    total = 0
    sequences = [''.join(sequence.split('\n')[1:]) for sequence in alignment.split('>')][1:]
    names = [sequence.split('\n')[0] for sequence in alignment.split('>')][1:]
    for seq_id, sequence in enumerate(sequences):
        indels = 0
        closed = True
        for index, symbol in enumerate(sequence[:-1]):
            if symbol == '-' and closed:
                closed = False
            elif symbol != '-' and not closed:
                indels += 1
                closed = True
        if not closed:
            indels += 1
        print(names[seq_id], indels)
        total += indels
    print(f'Total {total}')
    return


PATH = input()
with open(PATH) as file:
    alignment = file.read()
count_indels(alignment)