#kodony stop UAA UAG UGA
#kodon start AUG

gb = 'sequence2.gb'
START = 'AUG'
STOP1 = 'UAA'
STOP2 = 'UAG'
STOP3 = 'UGA'
origin_flag=False
sequence = ''
seq=''
pozycja = ''
slownik = {"UUU":"F", "UUC":"F", "UUA":"L", "UUG":"L",
    "UCU":"S", "UCC":"s", "UCA":"S", "UCG":"S",
    "UAU":"Y", "UAC":"Y", "UAA":"STOP", "UAG":"STOP",
    "UGU":"C", "UGC":"C", "UGA":"STOP", "UGG":"W",
    "CUU":"L", "CUC":"L", "CUA":"L", "CUG":"L",
    "CCU":"P", "CCC":"P", "CCA":"P", "CCG":"P",
    "CAU":"H", "CAC":"H", "CAA":"Q", "CAG":"Q",
    "CGU":"R", "CGC":"R", "CGA":"R", "CGG":"R",
    "AUU":"I", "AUC":"I", "AUA":"I", "AUG":"M",
    "ACU":"T", "ACC":"T", "ACA":"T", "ACG":"T",
    "AAU":"N", "AAC":"N", "AAA":"K", "AAG":"K",
    "AGU":"S", "AGC":"S", "AGA":"R", "AGG":"R",
    "GUU":"V", "GUC":"V", "GUA":"V", "GUG":"V",
    "GCU":"A", "GCC":"A", "GCA":"A", "GCG":"A",
    "GAU":"D", "GAC":"D", "GAA":"E", "GAG":"E",
    "GGU":"G", "GGC":"G", "GGA":"G", "GGG":"G",}


with open(gb, 'r') as file:
    for line in file:
        line.strip('\n')
        if line.startswith('ORIGIN'):
            origin_flag = True
            continue
        else:
            pass
        if origin_flag:
            sequence_line = line.strip()
            sequence += ' '.join(line.replace('t', 'u').replace(' ', '').upper().split())
            sequence = ''.join([i for i in sequence if not i.isdigit() and i.isalnum()])



chain_index = 0;
starts = []
stops = []

#sequence = 'AUGAAAAAAAAAAUGUUUUUUUUUUAACCCCCCUAA'

for i in range(0,len(sequence),3):
    str = sequence[i:i+3]
    if(str == START):
        print('START {}'.format(i))
        starts.append(i)
    elif(str == STOP1 or str == STOP2 or str == STOP3):
        print('STOP')
        stops.append(i)

print("------")
print(starts)
print(stops)

seq = []


for i in range(0,len(stops)):
    for j in range(0,len(starts)):
        seq.append(sequence[starts[j]:stops[i]+3])


#print(seq)
seq.sort(key=len)
seq.reverse()
#print(seq)

translated = []
for str in seq:
    tmp = ''
    for x in range(0,len(str),3):
        tmp += slownik[str[x:x+3]]
    translated.append(tmp)


print(translated)