#!/usr/bin/env python3

name1 = input('Protein name 1: ')
name2 = input('Protein name 2: ')
extension = input('Alignment algorithm: ')
path = name1.lower() + '_' + name2.lower() + '.' + extension
file = open(path)
seq1 = ''
seq2 = ''

for line in file:
    if not line.startswith('#'):
        if line.startswith(name1.upper() + '_ECOLI'):
            seq1 += line.split()[2]
        elif line.startswith(name2.upper() + '_ECOLI'):
            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 in the alignment of {name1} and {name2}: {indel_count}')