Python 偏斜基因组

Question

我正在尝试编写倾斜基因组函数，但不断出现错误：

Failed test #2.
Test Dataset: AGCGTGCCGAAATATGCCGCCAGACCTGCTGCGGTGGCCTCGCCGACTTCACGGATGCCAAGTGCATAGAGGAAGCGAGCAAAGGTGGTTTCTTTCGCTTTATCCAGCGCGTTAACCACGTTCTGTGCCGACTTT
Your output: ['0', '0']
Correct output: ['0', '0', '1', '0', '1', '1', '2', '1', '0', '1', '1', '1', '1', '1', '1', '1', '2', '1', '0', '1', '0', '-1', '-1', '0', '0', '-1', '-2', '-2', '-1', '-2', '-2', '-1', '-2', '-1', '0', '0', '1', '2', '1', '0', '0', '-1', '0', '-1', '-2', '-1', '-1', '-2', '-2', '-2', '-3', '-3', '-4', '-3', '-2', '-2', '-2', '-1', '-2', '-3', '-3', '-3', '-2', '-2', '-1', '-2', '-2', '-2', '-2', '-1', '-1', '0', '1', '1', '1', '2', '1', '2', '2', '3', '2', '2', '2', '2', '3', '4', '4', '5', '6', '6', '6', '6', '5', '5', '5', '5', '4', '5', '4', '4', '4', '4', '4', '4', '3', '2', '2', '3', '2', '3', '2', '3', '3', '3', '3', '3', '2', '1', '1', '0', '1', '1', '1', '0', '0', '1', '1', '2', '1', '0', '1', '1', '0', '0', '0', '0']

我的代码：

Genome = "CATGGGCATCGGCCATACGCC"
def SymbolArray(Genome, symbol):
    array = {}
    n = len(Genome)
    ExtendedGenome = Genome + Genome[0:n//2]
    for i in range(n):
        array[i] = PatternCount(symbol, ExtendedGenome[i:i+(n//2)])
    return array
def Skew(Genome):
    skew = {}
    skew[0]=0
    n = len(Genome)
    for i in range(1, n+1):       
        skew[i] = skew[i-1]
        if Genome[i-1] == "G": 
            skew[i] = skew[i-1]+1
        elif Genome[i-1] == "C":
            skew[i] = skew[i-1]-1 
        else:
            skew[i] = skew[i-1]
        return skew
    for i in skew.items():
        Skew(Genome)

Answer 1

问题比你做的要简单。最大的问题似乎是：您的 return 语句在循环中而不是在循环之后；您在需要数组的地方使用字典；你的范围的末端是 1；您对 Skew().

进行了不必要的递归调用

这是您的代码的工作简化：

Genome = "AGCGTGCCGAAATATGCCGCCAGACCTGCTGCGGTGGCCTCGCCGACTTCACGGATGCCAAGTGCATAGAGGAAGCGAGCAAAGGTGGTTTCTTTCGCTTTATCCAGCGCGTTAACCACGTTCTGTGCCGACTTT"

def Skew(genome):
    skew = [0]

    for i in range(1, len(genome)):       
        skew.append(skew[-1])

        if genome[i - 1] == "G": 
            skew[i] = skew[i - 1] + 1
        elif genome[i - 1] == "C":
            skew[i] = skew[i - 1] - 1

    return skew

print(Skew(Genome))

Can you also let me know can I use it in dictionary form?

如果您希望 skew 容器成为字典，就像您原来的那样，您可以执行以下操作：

def Skew(genome):
    skew = {0:0}

    for i in range(1, len(genome)):

        if genome[i - 1] == "G":
            skew[i] = skew[i - 1] + 1
        elif genome[i - 1] == "C":
            skew[i] = skew[i - 1] - 1
        else:
            skew[i] = skew[i - 1]

    return [value for (key, value) in sorted(skew.items())]

不过，我不推荐它。字典通常用于表示稀疏数组，但这里不是这种情况。实现这一点的另一种方法是使用 OrderedDict——它可以让您避免列表理解，只需 return skew.values().

Answer 2

def Skew(Genome):
    skew = {}

    for base in range(1, len(Genome)+1): # since we start at 1 and not 0 as we should we are adding one to the length

        if Genome[base - 1] == "G":  # subtracting one since we start at one so base at the 0 position  has to be included 
            skew[base] = skew[base - 1] + 1
        elif Genome[base - 1] == "C":
            skew[base] = skew[base - 1] - 1
        else:
            skew[base] = skew[base - 1]  


    return skew

Python 偏斜基因组

Python Skew Genome

python

dictionary

skew