永無止境的循環？ 無法讓 python 停止運行

Question

當我嘗試運行此代碼時，它永遠不會完成，我認為它卡在某個地方但我不太確定，因為我是 python 的新手。

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)])

任何意見將是有益的。

這是一個關於在沒有biopython 的情況下轉錄 DNA 的項目目標：創建一個程序，該程序可以定位 DNA 序列中的“atg”，然后在從初始 atg 開始計數時找到終止序列（tga、taa 或標簽）。

編輯：我希望程序給我 atg 和終止密碼子之間的序列，就像我的原始代碼一樣。 但是，我的原始代碼沒有考慮從 atg 移動 3 來找到正確的停止序列。

我的原始代碼：

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

您面臨的關於無限循環的問題是由於您的 function 注意到，一旦您找到可能的i並且它不是 3 的倍數，您應該向其添加 3，否則i = string.find(codon, i)將返回相同i的價值，更正應該是：

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，您將在使用具有None值的min時遇到問題，並出現以下錯誤：

stopcodon = min(taacodon, tagcodon, tgacodon) TypeError: '<' 在 'NoneType' 和 'int' 的實例之間不支持

您應該將返回值設置為某個較大的數字，這將表明沒有找到任何東西，而不是None

Answer 2

上述代碼存在多個問題。 我將使用原版，因為那是后期編輯（所以我假設它是最新的）。

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)

這不是按 3 組跳躍。這是通過字符串並定位其 position。 這就是為什么無論如何你總是會得到相同的價值。

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)

我認為這是為了找到第一個終止密碼子。 但是，如果 find 找不到字符串，則 find 返回值 -1（並且由於您沒有標記，因此它始終是終止密碼子，即使它不存在）。

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，大大地清理東西。 我也不太明白為什么你有 c 到 x，然后 x 到 g。

最后，您的數據集不包含來自第一個 atg 的終止密碼子。 所以它不能以你想要的方式轉錄。

我在您的數據集末尾添加了一個終止密碼子，以獲取您希望執行此操作的 output：

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')

（您實際上可以簡化這一點並使用列表推導來使其更短，但我已經寫出了循環並制作了其中的 2 個，以便您了解總體思路）。