RNA to PROTEIN 程序问题

Question

我的代码有一些问题，希望得到帮助。

程序的第一部分是为了验证用户的输入；所以他们只能输入 A U G C T（或小写）。但是，如果我确实输入了其他任何内容，我会收到一条很长的错误消息，但我想要的只是程序重新启动功能验证 check()。

此外，如果用户确实输入了有效序列，出于某种原因我的代码没有将有效的 RNA 序列翻译成蛋白质序列。我认为这可能与将 input_rna 中的 str 分成 3 个字母的块的 chunks 函数有关。

import re

input_rna = input("Type RNA sequence: ")

def chunks(l, n):
    for i in range(0, len(l), n):
        yield l[i:i+n]

def translate():
    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",}

    translated = "".join(amino_acids[i] for i in chunks("".join(input_rna), 3))

def validation_check():
    global input_rna
    if re.match(r"[A, U, G, C, T, a, u, g, c, t]", input_rna):
        print("Correct! That is a valid sequence.")
        translate()
    else:
        print("That is not a valid RNA sequence, please try again.")
        validation_check()
validation_check()

Answer 1

正则表达式错误，试试：

if re.match(r"^[AUGCT]+$", input_rna, re.IGNORECASE):

以下更好，因为在 RNA 中尿嘧啶而不是胸腺嘧啶...

if re.match(r"^[AUGC]+$", input_rna, re.IGNORECASE):

注意：算法翻译有问题，还有

list(chunks("".join(input_rna), 3))

你得到：

['ACG', 'AUG', 'AGU', 'CAU', 'GCU', 'U']

最后 "ACGAUGAGUCAUGCUU" 的问题，如果长度不是 3 的倍数

解决方案：

"".join(amino_acids[i] for i in chunks("".join(input_rna), 3) if len(i)==3)

Answer 2

除了指出的其他问题外，您的 validation_check 函数不允许用户再次输入字符串。这意味着您将不断尝试一遍又一遍地验证它，而不会更改它。

您可能想要做的更像是：

def validation_check():
    input_rna = raw_input("Type RNA sequence: ").upper()
    if re.match(r"^[AUGCT]+$", input_rna):
        print("Correct! That is a valid sequence.")
        print translate(input_rna)
    else:
        print("That is not a valid RNA sequence, please try again.")
        validation_check()

这避免了使用全局变量，允许用户重新输入，并且不会自动导致无限循环。

（即便如此，在这里使用递归可能不好，因此您应该考虑将其实现为 while 循环。）

您会注意到其他一些事情：

raw_input 而不是 input，因为后者有一个隐含的 eval。除非你绝对需要，否则你想避开它。
.upper() 所以你有标准化的字符串来验证和关闭。由于您的基础字典仅使用大写字符串，因此这比使用其他地方推荐的 re.I 更有意义。
我有 translate return 翻译的蛋白质，然后打印出来。你可能想做点别的。

我还为您的字典查找添加了一个默认值：

translated = "".join(amino_acids.get(i, '!') for i in chunks("".join(rna), 3))

这样，如果您遇到奇怪的事情，您可以尝试继续处理，而不必处理 KeyError（如果用户输入您没有密钥的序列，则会引发此问题因为，比如 'CUT')

我还注意到您允许但不翻译基数 'T'。你可能想看看那个。

无论如何，我得到的完整代码是：

import re

def chunks(l, n): 
    for i in range(0, len(l), n): 
        # print i
        chunk = l[i:i+n]
        # print chunk
        yield l[i:i+n]

def translate(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",}
    translated = "".join(amino_acids.get(i, '!') for i in chunks("".join(rna), 3)) 
    return translated

def validation_check():
    input_rna = raw_input("Type RNA sequence: ").upper()
    if re.match(r"^[AUGCT]+$", input_rna):
        print("Correct! That is a valid sequence.")
        print translate(input_rna)
    else:
        print("That is not a valid RNA sequence, please try again.")
        validation_check()

# in case you ever need to import this, don't always call validation_check
if __name__ == "__main__":
     validation_check()

RNA to PROTEIN 程序问题

RNA to PROTEIN program questions

python

bioinformatics