如何计算Fasta文件中dna序列的熵 [英] how to calculate the entropy of a dna sequence in a fasta file

问题描述

我需要计算Fasta文件中从10000到11000的dna序列的熵 这就是我所知道的，但是我需要计算第10,000至11,000个碱基之间的序列的熵.

I need to calculate the entropy of a dna sequence in a fasta file, from the base 10000 to the base 11000 here is what I know, but I need to calculate the entropy of the sequence between the 10,000th to 11,000th base

from math import log  

def logent(x):  
    if x<=0:     
        return 0  
    else:  
        return -x*log(x)  

def entropy(lis):   
    return sum([logent(elem) for elem in lis])

for i in SeqIO.parse("hsvs.fasta", "fasta"):
    lisfreq1=[i.seq.count(base)*1.0/len(i.seq) for base in ["A", "C","G","T"]]

entropy(lisfreq1)

推荐答案

您的序列只是一个字符串，因此您可以简单地

Your sequence is just a string, you can therefore simply slice it, e.g.

seq_start = 10000
seq_end = 11000 + 1
for i in SeqIO.parse("hsvs.fasta", "fasta"):
    sub_seq = i.seq[seq_start:seq_end]
    lisfreq1=[sub_seq.count(base)*1.0/len(sub_seq) for base in ["A", "C","G","T"]]

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