生成排除特定序列的 DNA 序列

Question

我刚开始使用 python 学习编程。在 class 中，我们被要求生成一个随机 DNA 序列，该序列不包含特定的 6 字母序列 (AACGTT)。关键是要使函数始终 return 成为合法序列。目前，我的函数在大约 78% 的时间内生成正确的序列。我怎样才能使 return 成为 100% 的合法序列？感谢任何帮助。

这是我的代码现在的样子：

from random import choice
def generate_seq(length, enzyme):
    list_dna = []
    nucleotides = ["A", "C", "T", "G"]
    i = 0
    while i < 1000:
        nucleotide = choice(nucleotides)
        list_dna.append(nucleotide)
        i = i + 1

    dna = ''.join(str(nucleotide) for nucleotide in list_dna)
    return(dna) 


seq = generate_seq(1000, "AACGTT")
if len(seq) == 1000 and seq.count("AACGTT") == 0:
    print(seq)

Answer 1

一个选项是检查循环中的最后几个条目，并且仅在尚未创建 'bad' 序列时才继续追加。然而，这个可能导致具有 "AACGT" 序列的真实随机机会更高，只是使用不同的字母而不是最后一个 "T"

from random import choice
def generate_seq(length, enzyme):
    list_dna = []
    nucleotides = ["A", "C", "T", "G"]
    i = 0
    while i < 1000:
        nucleotide = choice(nucleotides)
        list_dna.append(nucleotide)
        #check for invalid sequence. If found, remove last element and redraw
        if ''.join(list_dna[-6:]) == "AACGTT":
            list_dna.pop()
        else:
            i = i + 1

    dna = ''.join(str(nucleotide) for nucleotide in list_dna)
    return(dna) 


seq = generate_seq(1000, "AACGTT")
if len(seq) == 1000 and seq.count("AACGTT") == 0:
    print(seq)

Answer 2

一个想法是检查前 5 个核苷酸是否等于 AACGT，在这种情况下只从 ["A", "C", "G"] 中选择。

from random import choice


def generate_seq(length, enzyme, bad_prefix="AACGT"):
    list_dna = []
    nucleotides = ["A", "C", "T", "G"]
    i = 0
    while i < 1000:
        if list_dna[-5:] != bad_prefix:
            nucleotide = choice(nucleotides)
        else:
            nucleotide = choice(["A", "C", "G"])
        list_dna.append(nucleotide)
        i = i + 1

    dna = ''.join(str(nucleotide) for nucleotide in list_dna)
    return dna


seq = generate_seq(1000, "AACGTT")
if len(seq) == 1000 and seq.count("AACGTT") == 0:
    print(seq)

生成排除特定序列的 DNA 序列

Generating DNA sequence excluding specific sequence

python

dna-sequence