RNA到蛋白质模拟程序的TypeErorr？

Question

我正在做的事情是：

def dna_complement(dna):
  coup = ""
  for letter in dna:
    if letter == "C":
      coup += "G"
    if letter == "G":
      coup += "C"
    if letter == "A":
      coup += "T"
    if letter == "T":
      coup += "A"
  return coup
  

def convert_to_rna(dna):
  coup2 = ""
  for letter in dna:
    if letter == "C":
      coup2 += "G"
    if letter == "G":
      coup2 += "C"
    if letter == "A":
      coup2 += "U"
    if letter == "T":
      coup2 += "A"
  return coup2

def translate(rna):
  amino_acid = ""
  for len in rna:
    if range(0, len(rna), 3) == "UUU" :
      amino_acid = CODON_TABLE.get("UUU")
    if range(0, len(rna), 3) == "UUC" :
      amino_acid = CODON_TABLE.get("UUC")
    if range(0, len(rna), 3) == "UUA" :
      amino_acid = CODON_TABLE.get("UUA")
  


CODON_TABLE = {'UUU':'Phe','UUC':'Phe','UUA':'Leu','UUG':'Leu','CUU':'Leu','CUC':'Leu','CUA':'Leu','CUG':'Leu','AUU':'Ile','AUC':'Ile','AUA':'Ile','AUG':'Met','GUU':'Val','GUC':'Val','GUA':'Val','GUG':'Val','UCU':'Ser','UCC':'Ser','UCA':'Ser','UCG':'Ser','CCU':'Pro','CCC':'Pro','CCA':'Pro','CCG':'Pro','ACU':'Thr','ACC':'Thr','ACA':'Thr','ACG':'Thr','GCU':'Ala','GCC':'Ala','GCA':'Ala','GCG':'Ala','UAU':'Tyr','UAC':'Tyr','UAA':'STOP','UAG':'STOP','CAU':'His','CAC':'His','CAA':'Gln','CAG':'Gln','AAU':'Asn','AAC':'Asn','AAA':'Lys','AAG':'Lys','GAU':'Asp','GAC':'Asp','GAA':'Glu','GAG':'Glu','UGU':'Cys','UGC':'Cys','UGA':'STOP','UGG':'Trp','CGU':'Arg','CGC':'Arg','CGA':'Arg','CGG':'Arg','AGU':'Ser','AGC':'Ser','AGA':'Arg','AGG':'Arg','GGU':'Gly','GGC':'Gly','GGA':'Gly','GGG':'Gly'}

""" the rna is "UUCUCUACGGUAACAGGGGGCCGGAGGACGACGACGAGAAUCGCCCCGGUGUAGCCGGUGGCGACGGGACGGGGACCUCCCACCGGGGUGGCCGGCAAUGUCGCUCGUAUG" # This is already converted from DNA to RNA so there's no worry about the original RNA
"""

dna="AAGAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTCTTAGCGGGGCCACATCGGCCACCGCTGCCCTGCCCCTGGAGGGTGGCCCCACCGGCCGTTACAGCGAGCATAC" 

def main():
  print("\nWelcome to the DNA program: The Code of Life.")
  print("\nSample DNA strand:\n")
  print("Regular DNA:")
  print_bases(dna)
  print("DNA after complement: ")
  dna2 = dna_complement(dna)
  print_bases(dna2)
  print("DNA after RNA convertion: ")
  rna = convert_to_rna(dna)
  print_bases(rna)
  print("The result of translation: ")
  amino_acid = translate(rna)
  print(amino_acid)

如上图所示。(多亏一个名叫兰登戴维斯的用户告诉我要在描述中纠正我的错误，现在我已经把我现在拥有的一切都展示出来了，这可能会更好一些)

当我试图运行这个类型错误时，告诉我str对象是不可调用的，有人能帮我吗？

更多信息:很抱歉之前没有这么说，我试图得到UUU <-> Phe、UUA <-> Leu和AUU <-> Ile这样的转换。一旦检测到UAA，UAG，UGA，蛋白质就停止生成。

Answer 1

因此，如果你把整个RNA字符串转换成密码子字符串：

CODON_TABLE = {'UUU':'Phe','UUC':'Phe','UUA':'Leu','UUG':'Leu','CUU':'Leu','CUC':'Leu'} # etc

def translate(rna):
    amino_acid = ""
    for i in range(len(rna)-2):
        three_letter = rna[i:i+3]
        if three_letter in CODON_TABLE:
            amino_acid += CODON_TABLE[three_letter]
            # if a match is found, don't look for a new codon starting with
            # the second or third letter of this codon
            i += 2 
        return amino_acid

说明：for i in range(len(rna)-2):将给出我们想要阅读的RNA字符串部分的索引号：

UUCUCUAC   len = 8
012345      i = 0-5 = range(6)

rna[i:i+3]给出了从i第一开始的三个字母

UUCUCUAC  = rna
UUC       i = 0, three_letter = rna[0:3]
 UCU      i = 1, tl = rna[1:4]
  CUC     i = 2, tl = rna[2:5]
   UCU    i = 3, tl = rna[3:6]
    CUA   i = 4, tl = rna[4:7]
     UAC  i = 5, tl = rna[5:8]

对于每一个三个字母的序列，如果是密码子，它会将密码子的名称添加到氨基酸中。

amino_acid += CODON_TABLE[three_letter]

然后跳过i 2，以避免查找以我们已经使用过的字母开头的另一个密码：

UUCUCUAC
UUC       Phe
 UCU      (skip)
  CUC     (skip)
   UCU    Ser
    CUA   (skip)
     UAC  (skip)

如果它发现了一些不是密码子的东西，它就会忽略它，移到接下来的三个字母上。(我不是生物学家，我不知道每个三个字母的序列是否都是密码子？)

UUCZUCUAC
UUC        Phe
 UCU       (skip)
  CUC      (skip)
   ZUC     (not found)
    UCU    Sre

Answer 2

我会先重写你的

range(0, len(rna), 3)

你想从你的输入中得到3乘3吗？例如，如果您的输入是"ABCDE"，首先要"ABC"，然后要"BCD“等等，对吗？

如果是这样的话，我会这样做：

p = rna[i:i+3]

其中rna是你的输入字符串。

另外，如果你发现了UUU，UUC或UUA，你想做什么？如果你们都找到了呢？

我希望你觉得这有帮助。

def translate(rna):
  amino_acid = []
  for i in range(len(rna) - 2):
    p = rna[i:i+3]
    if p == "UUU" :
      amino_acid.append(CODON_TABLE["UUU"])
    if p == "UUC" :
      amino_acid.append(CODON_TABLE["UUC"])
    if p == "UUA" :
      amino_acid.append(CODON_TABLE["UUA"])
  
  return amino_acid

CODON_TABLE = {'UUU':'Phe','UUC':'Phe','UUA':'Leu','UUG':'Leu','CUU':'Leu','CUC':'Leu','CUA':'Leu','CUG':'Leu','AUU':'Ile','AUC':'Ile','AUA':'Ile','AUG':'Met','GUU':'Val','GUC':'Val','GUA':'Val','GUG':'Val','UCU':'Ser','UCC':'Ser','UCA':'Ser','UCG':'Ser','CCU':'Pro','CCC':'Pro','CCA':'Pro','CCG':'Pro','ACU':'Thr','ACC':'Thr','ACA':'Thr','ACG':'Thr','GCU':'Ala','GCC':'Ala','GCA':'Ala','GCG':'Ala','UAU':'Tyr','UAC':'Tyr','UAA':'STOP','UAG':'STOP','CAU':'His','CAC':'His','CAA':'Gln','CAG':'Gln','AAU':'Asn','AAC':'Asn','AAA':'Lys','AAG':'Lys','GAU':'Asp','GAC':'Asp','GAA':'Glu','GAG':'Glu','UGU':'Cys','UGC':'Cys','UGA':'STOP','UGG':'Trp','CGU':'Arg','CGC':'Arg','CGA':'Arg','CGG':'Arg','AGU':'Ser','AGC':'Ser','AGA':'Arg','AGG':'Arg','GGU':'Gly','GGC':'Gly','GGA':'Gly','GGG':'Gly'}

rna = "UUCUCUACGGUAACAGGGGGCCGGAGGACGACGACGAGAAUCGCCCCGGUGUAGCCGGUGGCGACGGGACGGGGACCUCCCACCGGGGUGGCCGGCAAUGUCGCUCGUAUG" # This is already converted from DNA to RNA so there's no worry about the original RNA

translate(rna) 

注意，我正在迭代输入，忽略了最后两个字符，这就是为什么我们迭代到range(len(rna)-2)的原因。