永不重复的循环？无法让python停止运行

Question

当我试着运行这段代码时，它永远不会结束，我想它被卡在了某个地方，但我不太确定，因为我是python新手

import re
codon = []
rcodon = []

dataset = "ggtcagaaaaagccctctccatgtctactcacgatacatccctgaaaaccactgaggaagtggcttttcagatcatcttgctttgccagtttggggttgggacttttgccaatgtatttctctttgtctataatttctctccaatctcgactggttctaaacagaggcccagacaagtgattttaagacacatggctgtggccaatgccttaactctcttcctcactatatttccaaacaacatgatga"
startcodon=0
n=0
print ("DNA sequence: ", dataset)

def find_codon(codon, string, start):
    i = start + 3
    while i < len(string):
        i = string.find(codon, i) # find the next substring
        if (i - start) % 3 == 0:  # check that it's a multiple of 3 after start
            return i
    return None

while(n < 1):
    startcodon=dataset.find("atg", startcodon)
    #locate stop codons
    taacodon=find_codon("taa", dataset, startcodon)
    tagcodon=find_codon("tag", dataset, startcodon)
    tgacodon=find_codon("tga", dataset, startcodon)

    stopcodon = min(taacodon, tagcodon, tgacodon)
    codon.append(dataset[startcodon:stopcodon+3])
    if(startcodon > len(dataset) or startcodon < 0):
        n = 2;
    startcodon=stopcodon
#reverse the string and swap the letters
n=0;
while(n < len(codon)):
        rcodon.append (codon[n][len(codon[n])::-1])
        #replace a with u
        rcodon[n] = re.sub('a', "u", rcodon[n])
        #replace t with a
        rcodon[n] = re.sub('t', "a", rcodon[n])
        #replace c with x
        rcodon[n] = re.sub('c', "x", rcodon[n])
        #replace g with c
        rcodon[n] = re.sub('g', "c", rcodon[n])
        #replace x with g
        rcodon[n] = re.sub('x', "g", rcodon[n])
        print("DNA sequence: ", codon[n] ,'\n', "RNA sequence:", rcodon[n])
        n=n+1
answer = 0
print("Total Sequences:  ", len(codon)-3)
while (int(answer) >=0):
        #str = "Please enter an integer from 0 to " + str(len(dataset)) + " or -1 to quit: "
        answer = int(input("Please enter a sequence you would like to see or -1 to quit:  "))
        if(int(answer) >= 0):
                print("DNA sequence: ", codon[int(answer)] ,'\n', "RNA sequence:", rcodon[int(answer)])

任何建议都会有帮助

这是一个关于转录DNA的项目没有生物细胞 目标是：创建一个程序，可以定位DNA序列中的“atg”，然后找到停止序列（tga、taa或tag），同时从初始atg开始以三个为单位计数

编辑： 我想让程序给我atg和终止密码子之间的序列，就像我的原始代码一样。但是，我的原始代码没有考虑从ATG移动3，以找到正确的停止序列。

我的原始代码：

import re
codon = []
rcodon = []


dataset = "ggtcagaaaaagccctctccatgtctactcacgatacatccctgaaaaccactgaggaagtggcttttcagatcatcttgctttgccagtttggggttgggacttttgccaatgtatttctctttgtctataatttctctccaatctcgactggttctaaacagaggcccagacaagtgattttaagacacatggctgtggccaatgccttaactctcttcctcactatatttccaaacaacatgatga"
startcodon=0
n=0
while(n < 1):
    startcodon=dataset.find("atg", startcodon, len(dataset)-startcodon)
    #locate stop codons
    taacodon=dataset.find("taa", startcodon+3, len(dataset)-startcodon)
    tagcodon=dataset.find("tag", startcodon+3, len(dataset)-startcodon)
    tgacodon=dataset.find("tga", startcodon+3, len(dataset)-startcodon)
    if(taacodon<tagcodon):
        if(taacodon<tgacodon):
            stopcodon=taacodon
            #print("taacodon", startcodon)
        else:
            stopcodon=tgacodon
            #print("tGacodon", startcodon)

    elif(tgacodon>tagcodon):
        stopcodon=tagcodon
        #print("taGcodon", startcodon)
    else:
        stopcodon=tgacodon
        #print("tGacodon", startcodon)
    #to add sequences to an array
    codon.append(dataset[startcodon:stopcodon+3])
    if(startcodon > len(dataset) or startcodon < 0):
        n = 2;
    startcodon=stopcodon

#reverse the string and swap the letters
n=0;
while(n < len(codon)):
        rcodon.append (codon[n][len(codon[n])::-1])
        #replace a with u
        rcodon[n] = re.sub('a', "u", rcodon[n])
        #replace t with a
        rcodon[n] = re.sub('t', "a", rcodon[n])
        #replace c with x
        rcodon[n] = re.sub('c', "x", rcodon[n])
        #replace g with c
        rcodon[n] = re.sub('g', "c", rcodon[n])
        #replace x with g
        rcodon[n] = re.sub('x', "g", rcodon[n])
        print("DNA sequence: ", codon[n] ,'\n', "RNA sequence:", rcodon[n])
        n=n+1
answer = 0
print("Total Sequences:  ", len(codon)-3)
while (int(answer) >= 0):
        #str = "Please enter an integer from 0 to " + str(len(dataset)) + " or -1 to quit: "
        answer = int(input("Please enter an sequence you would like to see or -1 to quit:  "))
        if(int(answer) >= 0):
                print("DNA sequence: ", codon[int(answer)] ,'\n', "RNA sequence:", rcodon[int(answer)])

Answer 1

上述代码存在多个问题。我将使用原稿，因为那是后期编辑（所以我假设它是最新的）

dataset = "ggtcagaaaaagccctctccatgtctactcacgatacatccctgaaaaccactgaggaagtggcttttcagatcatcttgctttgccagtttggggttgggacttttgccaatgtatttctctttgtctataatttctctccaatctcgactggttctaaacagaggcccagacaagtgattttaagacacatggctgtggccaatgccttaactctcttcctcactatatttccaaacaacatgatga"
startcodon=0
n=0
while(n < 1):
    startcodon=dataset.find("atg", startcodon, len(dataset)-startcodon)
    #locate stop codons
    taacodon=dataset.find("taa", startcodon+3, len(dataset)-startcodon)
    tagcodon=dataset.find("tag", startcodon+3, len(dataset)-startcodon)
    tgacodon=dataset.find("tga", startcodon+3, len(dataset)-startcodon)

这不是三人一组跳。这是通过字符串并确定其位置。这就是为什么无论发生什么，你都会得到相同的值

if(taacodon<tagcodon):
        if(taacodon<tgacodon):
            stopcodon=taacodon
            #print("taacodon", startcodon)
        else:
            stopcodon=tgacodon
            #print("tGacodon", startcodon)

    elif(tgacodon>tagcodon):
        stopcodon=tagcodon
        #print("taGcodon", startcodon)
    else:
        stopcodon=tgacodon
        #print("tGacodon", startcodon)

我想这是为了找到第一个终止密码子。但是，如果find找不到字符串，它将返回一个值-1（因为您没有标记，所以即使它不存在，它也将始终是停止密码子）

n=0;
while(n < len(codon)):
        rcodon.append (codon[n][len(codon[n])::-1])
        #replace a with u
        rcodon[n] = re.sub('a', "u", rcodon[n])
        #replace t with a
        rcodon[n] = re.sub('t', "a", rcodon[n])
        #replace c with x
        rcodon[n] = re.sub('c', "x", rcodon[n])
        #replace g with c
        rcodon[n] = re.sub('g', "c", rcodon[n])
        #replace x with g
        rcodon[n] = re.sub('x', "g", rcodon[n])
        print("DNA sequence: ", codon[n] ,'\n', "RNA sequence:", rcodon[n])
        n=n+1

使用dicts和fstrings，可以更有效地清洁物品。我也不太明白为什么c到x，然后x到g

最后，您的数据集不包含来自第一个atg的终止密码子。所以它不能按你想要的方式转录

我在数据集末尾添加了一个终止密码，以获得您希望的输出，您可以这样做：

dataset = "ggtcagaaaaagccctctccatgtctactcacgatacatccctgaaaaccactgaggaagtggcttttcagatcatcttgctttgccagtttggggttgggacttttgccaatgtatttctctttgtctataatttctctccaatctcgactggttctaaacagaggcccagacaagtgattttaagacacatggctgtggccaatgccttaactctcttcctcactatatttccaaacaacatgtaaa"

rdict={'a':'u','t':'a','c':'g','g':'c'}
start_codon=dataset.find("atg")
for nucleotides in range(start_codon+3,len(dataset),3):
    if dataset[nucleotides:nucleotides+3] in {'taa','tag','tga'}:
        stop_codon=nucleotides
DNA=[]
RNA=[]
for bases in range(start_codon,stop_codon,1):
    DNA.append(dataset[bases])
    RNA.append(rdict[dataset[bases]])

print(f"DNA Sequence: {''.join(DNA)}\nRNA Sequence: {''.join(RNA)}")

while True:
    answer=input('\nplease input sequence you would like to see or exit to quit:  ')
    if answer == 'exit':
        break
    try:
        print(f'DNA Sequence: {DNA[int(answer)]}\nRNA Sequence: {RNA[int(answer)]}')
    except:
        print('Entry invalid, please input number')

（实际上，您可以简化这个过程，并使用列表理解使其更加简短，但我已经写出了循环，并制作了其中的两个循环，这样您就可以得到大致的想法）

Answer 2

关于无止境循环，您面临的问题是由于您的函数注意到，一旦您找到一个可能的i并且它不是3的倍数，您应该向它添加3，否则i = string.find(codon, i)将返回相同的i值，更正应该是：

def find_codon(codon, string, start):
    i = start + 3
    while i < len(string):
        i = string.find(codon, i) # find the next substring
        if (i - start) % 3 == 0:  # check that it's a multiple of 3 after start
            return i
        else:
            i += 3
    return None

然后，在使用min和None值时会出现问题，并出现以下错误：

stopcodon = min(taacodon, tagcodon, tgacodon) TypeError: '<' not supported between instances of 'NoneType' and 'int'

您应该将返回值设置为一些大的数字，这将指示未找到任何内容，而不是None