巨蟒歪斜基因组

Question

我正在尝试编写扭曲的基因组功能，但不断得到错误:

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

这个问题比你想象的要简单。最大的问题似乎是:你的return语句在循环中，而不是在循环之后;当你想要一个数组时，你使用了一个字典;你的范围的末端偏离了1;你有一个不必要的递归调用Skew()。

下面是代码的简化:

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))

你能让我知道我能以字典的形式使用它吗?

如果你想让skew容器是一个字典，就像你原来的那样，你可以这样做:

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())]

但是，我不推荐这样做。字典通常用于表示稀疏数组，但这里的情况并非如此。实现这一点的另一种方法是使用OrderedDict——它将允许您避免列表推导并简单地返回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