#!usrbinenv python3

name = input('Protein name: ')
extension = input('Alignment algorithm: ')
path = name.lower() + '.' + extension
file = open(path)
seq1 = ''
seq2 = ''

for line in file
    if not line.startswith('#')
        if line.startswith(name.upper() + '_ECOLI')
            seq1 += line.split()[2]
        elif line.startswith(name.upper() + '_BACSU')
            seq2 += line.split()[2]

flag = False        #True, if indel is opened
indel_count = 0

for c in seq1
    if c == '-' and not flag   #indel opens
        flag = True
        indel_count += 1
    elif c != '-' and flag     #indel closes
        flag = False

flag = False

for c in seq2
    if c == '-' and not flag   #indel opens
        flag = True
        indel_count += 1
    elif c != '-' and flag     #indel closes
        flag = False

print(f'Amount of indels for {name}: {indel_count}')