Projet2 | Python Fiddle

alphabet = ['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y','-']
M = 5643
L = 48
q = 21

function getSequenceFamily(filename):
    
    from Bio import SeqIO

fasta_sequences = SeqIO.parse(open(filename),'fasta')
	
    family =[]
    
    with open(output_file) as out_file:
    for fasta in fasta_sequences:
        family.append(fasta.seq.tostring())
    
    return family

function getOccurenceMatrix(filename):
    
    family = getSequenceFamily(filename)
    
    '''matrice 48X21'''
    occMatrix = [[0]*L for i in range(q)]
    
    
    for col in range(L):
        for seq_number in range(M):
            
            AA=alphabet.index(family[seq_number][col])
            occurenceMatrix[col][AA]++
            #occurenceMatrix[i -> (0,48)][AA Concernee]++
            
    return occurenceMatrix

function scoreMatrix(filename):
    
    scoreMatrix = list(getOccurenceMatrix(filename))
    
    for i in range(len(scoreMatrix[0])):
        for j in range(len(scoreMatrix)):
            
            scoreMatrix[i][j] += 1
            scoreMatrix[i][j] /= M+q
            
	return scoreMatrix

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