RNA 到蛋白質模擬程序的 TypeErorr？

Question

這是我在做什么：

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)

如上圖所示。 （多虧了一個叫 Random Davis 的用戶告訴我糾正我在描述上的錯誤，現在我展示了我現在擁有的一切，可能會好一點）

當我嘗試運行它時，類型錯誤告訴我 str object 不可調用，有人可以幫我解決這個問題嗎？

更多信息：很抱歉沒有早點說這個，我試圖獲得像 UUU <-> Phe、UUA <-> Leu 和 AUU <-> Ile 這樣的轉換。 並在檢測到 UAA、UAG、UGA 后阻止蛋白質生成。

Answer 1

我會先重寫你的

range(0, len(rna), 3)

你想從你的輸入中得到 3 x 3 嗎？ 例如，如果您輸入“ABCDE”，則首先要輸入“ABC”，然后輸入“BCD”，等等，這樣正確嗎？

如果是這樣，我會這樣做：

p = rna[i:i+3]

其中 rna 是您的輸入字符串。

還有，如果你找到了UUU、UUC或UUA，你想做什么？ 如果你找到所有這些怎么辦？

我希望你覺得這有幫助。

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) 

請注意，我正在迭代輸入並忽略最后兩個字符，這就是我們迭代直到 range(len(rna)-2) 的原因。

Answer 2

所以如果你把整個 RNA 串變成一個密碼子串：

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

---

解釋： for i in range(len(rna)-2):將為我們提供一個索引號，指向我們想要讀取的 RNA 字符串部分：

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

rna[i:i+3]給出了從第i個字母開始的三個字母

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]

對於每個三字母序列，如果它是密碼子，它會將密碼子的名稱添加到氨基酸中

amino_acid += CODON_TABLE[three_letter]

然后它將i向前跳過 2，以避免尋找另一個以我們已經使用過的字母開頭的密碼子：

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

如果它發現不是密碼子的東西，它會忽略它並移動到接下來的三個字母。 （我不是生物學家，不知道是不是每個三字母序列都是密碼子？）

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