Python生物資訊學①将RNA序列翻譯成蛋白質序列。

環境

OS version      : Win10 x64
python_version  : Python 3.6.5       

執行個體代碼

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

# 讀取RNA序列字元串
rna = ''
for line in open('A06662-RNA.fasta'):
    if not line.startswith('>'): 
        rna = rna + line.strip()      

# translate one frame at a time
for frame in range(3):
    prot = '' 
    print ('Reading frame ' + str(frame + 1))
    for i in range(frame, len(rna), 3):
        codon = rna[i:i + 3]
        if codon in codon_table:
            if codon_table[codon] == 'STOP':
                prot = prot + '*'
            else: 
                prot = prot + codon_table[codon]
        else:
            # handle too short codons
            prot = prot + '-'   
 
    # format to blocks of 48 columns
    i = 0
    while i < len(prot):
        print (prot[i:i + 48])
        i = i + 48