使用python计算字典中的基因突变 [英] Counting genetic mutations in dictionary using python

问题描述

我有这种格式的数据:

> abc12
ATCGACAG

> def34
ACCGACG

>abc12
ATCGACAG

>def34
ACCGACG

等

我已经将每个基因存储在字典中，并以>开头的行作为值.因此字典就像{'abc12':'ATCGACAG'等}

I have stored each gene into a dictionary with the lines beginning with > as values. So the dictionary is something like {'abc12':'ATCGACAG', etc.}

现在，我希望能够比较每个基因，以便它计算每个位点上A，T，C或G的数目.

Now I want to be able to compare each gene, so that it counts the number of A's, T's, C's, or G's at each site.

我唯一能想到的就是将字典分解成每个核苷酸位点的列表，并使用带有计数器的zip().这是最好的方法吗?如果是这样，如何将字典分为每个站点的列表?

The only thing I can come up with is to break the dictionary into lists for each nucleotide site and using zip() with a counter. Is this the best way, and if so, how do I break the dictionary into a list for each site?

推荐答案

使用 collections.Counter :

>>> from collections import Counter
>>> Counter('ATCGACAG')
Counter({'A': 3, 'C': 2, 'G': 2, 'T': 1})
>>> Counter('ACCGACG')
Counter({'C': 3, 'A': 2, 'G': 2})

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