from Bio.SubsMat import MatrixInfo
from Bio import SeqIO

def global_alignment_score(input):
    return tmp(input)[1]

def tmp(input):
    blosum = MatrixInfo.blosum62
    fasta_sequences = SeqIO.parse(open(input), 'fasta')
    first = str(next(fasta_sequences).seq)
    second = str(next(fasta_sequences).seq)
    sigma = 5

    matr = [[]]
    start = 0
    startstr = ""

    #1 = rechts 0 = schuin 2 = onder
    # init randen
    for i in range(0, len(first) + 1):
        matr[0].append((startstr, start))
        start -= sigma
        startstr += "1"
    start = -5
    startstr = "2"
    for i in range(1, len(second) + 1):
        matr.append([(startstr, start)])
        start -= sigma
        startstr += "2"

    for lengt in range(1, len(second) + 1):
        for width in range(1, len(first) + 1):
            count = matr[lengt - 1][width - 1][1]
            tmp = matr[lengt - 1][width - 1][0]
            if (first[width - 1], second[lengt - 1]) in blosum:
                count += blosum[(first[width - 1], second[lengt - 1])]
            else:
                count += blosum[(second[lengt - 1], first[width - 1])]



            if matr[lengt - 1][width][1] - sigma > count:
                count = (matr[lengt - 1][width][1])
                tmp+='2'
            elif matr[lengt][width - 1][1] - sigma > count:
                count = (matr[lengt][width - 1][1])
                tmp+='1'
            else :
                tmp += "0"
            matr[lengt].append((tmp,count))


    code = matr[-1][-1][0]
    fi = []
    se = []
    index1 = 0
    index2 = 0
    for i in range(0, len(code)):
        if code[i] == '0':
            fi.append(first[index1])
            se.append(second[index2])
            index1 += 1
            index2 += 1
        elif code[i] == '1':
            fi.append(first[index1])
            se.append('-')
            index1 += 1
        else:
            fi.append('-')
            se.append(second[index2])
            index2 += 1

    return [(''.join(fi),''.join(se)), matr[-1][-1][1]]

def global_alignment(input):
    return tmp(input)[0]



print(global_alignment('data01.faa'))