计算用于对齐的共同信息时出现错误[关闭]

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[<6天前关闭。

我有一个列表，表示序列（B）和所有可能的字母的对齐方式，如下所示：

B = [
['A','U','-','C','-','G','-','-','C','U','G','C'],
['A','A','A','U','C','A','-','A','G','A','-','A'],
['C','U','G','-','-','G','A','A','-','A','A','U'],
]

set1 = ['A','G','C','U','-']

我正在尝试使用以下函数为集合中的每个元素计算序列比对中所有位置之间的互信息（https://en.wikipedia.org/wiki/Mutual_information）
def MI(sequences,i,j):
    Pi = Counter(sequence[i] for sequence in sequences)
    Pj = Counter(sequence[j] for sequence in sequences)
    Pij = Counter((sequence[i],sequence[j]) for sequence in sequences)
   return sum(Pij[(x,y)]*log(Pij[(x,y)]/(Pi[x]*Pj[y])) for x,y in Pij) 

for r in range(len(set)):
    for s in range(0, len(B[0])):
        for t in range(0,len(B[0])):
            print(MI(str(set[r]),s,t))

我得到以下输出：
0.0

Traceback (most recent call last):
  File "test.py", line 51, in <module>
    print(MI(str(set[r]),s,t))
  File "test.py", line 27, in MI
    Pj = Counter(sequence[j] for sequence in sequences)
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/collections/__init__.py", line 568, in __init__
    self.update(*args, **kwds)
  File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/collections/__init__.py", line 655, in update
    _count_elements(self, iterable)
  File "test.py", line 27, in <genexpr>
    Pj = Counter(sequence[j] for sequence in sequences)
IndexError: string index out of range

Answer 1

请执行以下代码更改

for s in range(0, len(B[0])):

您尝试使用s，t实现什么？

Answer 2

这解决了问题：

for r in range(len(set)):
    for s in range(0, len(B[0])):
        for t in range(0,len(B[0])):
            print(MI(B,s,t))