DICT功能在RNA翻译程序中不起作用

Question

我想知道下面的代码可能出什么毛病，为什么我得到一个错误KeyError：'['？

该程序旨在将输入的DNA序列翻译为RNA序列，然后从存储在RNA中的RNA序列[]从dict生成AMINO ACID序列。

谢谢

DNA = "ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGC"
RNA = []

AMINO_ACIDS = {"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",}

RNA_2 = str(RNA)
for char in DNA:
    if char == "G":
        RNA.append("C")
    elif char == "C":
        RNA.append("G")
    elif char == "A":
        RNA.append("U")
    elif char == "T":
        RNA.append("A")

translated = ''.join(AMINO_ACIDS[i] for i in RNA_2)

print("DNA sequence: " + DNA)
print()
print("Length of DNA sequence in base pairs: " + str(len(DNA)))
print()
print("RNA sequence of DNA sequence: " +("".join(RNA)))
print()
print("AMINO ACID sequence: " + str(translated))

Answer 1

您不需要RNA_2 ，但确实需要一种将RNA字符串分成三个字符串的块的方法。 从这篇文章中借用一个块函数：

def chunks(l, n):
    """ Yield successive n-sized chunks from l.
    """
    for i in xrange(0, len(l), n):
        yield l[i:i+n]

DNA = "ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGC"
RNA = []

AMINO_ACIDS = {"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",}

for char in DNA:
    if char == "G":
        RNA.append("C")
    elif char == "C":
        RNA.append("G")
    elif char == "A":
        RNA.append("U")
    elif char == "T":
        RNA.append("A")


translated = ''.join(AMINO_ACIDS[i] for i in chunks("".join(RNA), 3))

print("DNA sequence: " + DNA)
print()
print("Length of DNA sequence in base pairs: " + str(len(DNA)))
print()
print("RNA sequence of DNA sequence: " +("".join(RNA)))
print()
print("AMINO ACID sequence: " + str(translated))

结果：

DNA sequence: ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGC
()
Length of DNA sequence in base pairs: 69
()
RNA sequence of DNA sequence: UGUUCUACGGUAACAGGGGGCCGGAGGACGACGACGACGAGAGGCCCCGGUGCCGGUGGCGACGGGACG
()
AMINO ACID sequence: CSTVTGGRRTTTTRGPGAGGDGT

有关原始错误的更多信息。 我认为您可能会误解RNA_2 = str(RNA)作用。 这并不意味着“现在和永远，RNA_2将成为RNA的字符串版本，并在RNA发生变化时保持最新”。 它的意思是“立即获取RNA的内容，将其变成字符串，这就是RNA_2的含义，即使RNA稍后发生变化也是如此”。 因此，即使您将值附加到RNA后， RNA_2也将是“ []”。 这是您的KeyError的来源。 “ [”是RNA_2的第一个字符，“ [”在AMINO_ACIDS不存在。

但是，即使在完成附加循环之后执行了RNA_2 = str(RNA) ，我也不认为它会给您想要的结果。 它应该是['U', 'G', 'U', 'U', 'C', ...而不是"UGUUC" 。 如果需要后者， "".join(RNA)使用"".join(RNA)而不是str(RNA) 。

但是，即使您使用"".join(RNA) ，也无法对其进行迭代并尝试访问AMINO_ACIDS ，因为AMINO_ACID的键都是三个字符长，并且在字符串上进行迭代可以一次给您一个字符。 那就是chunk来历，让您一次迭代三个字符。