python中序列中基的频率

我想找出序列中每个碱基的相对数量。结果应显示在列表中。这是我的尝试：

def get_freqs(Sequ):
    rel_Anz=[]
    laenge = len(Sequ)
    A_freq = (Sequ.count('A')/ laenge)
    T_freq = (Sequ.count('T')/ laenge)
    C_freq = (Sequ.count('C')/ laenge)
    G_freq = (Sequ.count('G')/ laenge)

    rel_Anz= [A_freq, T_freq, C_freq, G_freq]
    return rel_Anz

    print("The frequence of each base (A,T,C,G) is ", rel_Anz)

get_freqs (ATTAAACC)

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我不知道我应该如何包括我想计数的序列。我应该在之前定义它吗？

首先，假设您想要将一个核苷酸序列传递给函数，您可能想要将其作为字符串传递，因此它看起来像这样：

get_freqs ('ATTAAACC')

还是像这样

get_freqs ("ATTAAACC")

其次，在打印结果之前返回：

return rel_Anz
print("The frequence of each base (A,T,C,G) is ", rel_Anz)

返回后函数中的每个语句都不会执行，因此应该是：

print("The frequence of each base (A,T,C,G) is ", rel_Anz)
return rel_Anz

最后，类似的方法应该会奏效：

def get_freqs(Sequ):
    rel_Anz=[]
    laenge = len(Sequ)
    A_freq = (Sequ.count('A')/ laenge)
    T_freq = (Sequ.count('T')/ laenge)
    C_freq = (Sequ.count('C')/ laenge)
    G_freq = (Sequ.count('G')/ laenge)

    rel_Anz= [A_freq, T_freq, C_freq, G_freq]
    print("The frequence of each base (A,T,C,G) is ", rel_Anz)
    return rel_Anz

get_freqs ('ATTAAACC')

---

如果您希望它更清晰、更通俗：

def get_freqs(seq):
    length = len(seq)

    a_freq = seq.count('A')/ length 
    t_freq = seq.count('T')/ length 
    c_freq = seq.count('C')/ length 
    g_freq = seq.count('G')/ length 

    return [a_freq, t_freq, c_freq, g_freq]

relative_frequencies = get_freqs ('ATTAAACC')
print("The frequence of each base (A,T,C,G) is ", relative_frequencies)

或者更密集：

def get_freqs(seq):
    return [seq.count(nucl)/len(seq) for nucl in 'ATCG']

relative_frequencies = get_freqs('ATTAAACC')
print("The frequence of each base (A,T,C,G) is ", relative_frequencies)

---

首先，假设您想要将一个核苷酸序列传递给函数，您可能想要将其作为字符串传递，因此它看起来如下所示：

get_freqs ('ATTAAACC')

还是像这样

get_freqs ("ATTAAACC")

其次，在打印结果之前返回：

return rel_Anz
print("The frequence of each base (A,T,C,G) is ", rel_Anz)

返回后函数中的每个语句都不会执行，因此应该是：

print("The frequence of each base (A,T,C,G) is ", rel_Anz)
return rel_Anz

最后，类似的方法应该会奏效：

def get_freqs(Sequ):
    rel_Anz=[]
    laenge = len(Sequ)
    A_freq = (Sequ.count('A')/ laenge)
    T_freq = (Sequ.count('T')/ laenge)
    C_freq = (Sequ.count('C')/ laenge)
    G_freq = (Sequ.count('G')/ laenge)

    rel_Anz= [A_freq, T_freq, C_freq, G_freq]
    print("The frequence of each base (A,T,C,G) is ", rel_Anz)
    return rel_Anz

get_freqs ('ATTAAACC')

---

如果您希望它更清晰、更通俗：

def get_freqs(seq):
    length = len(seq)

    a_freq = seq.count('A')/ length 
    t_freq = seq.count('T')/ length 
    c_freq = seq.count('C')/ length 
    g_freq = seq.count('G')/ length 

    return [a_freq, t_freq, c_freq, g_freq]

relative_frequencies = get_freqs ('ATTAAACC')
print("The frequence of each base (A,T,C,G) is ", relative_frequencies)

或者更密集：

def get_freqs(seq):
    return [seq.count(nucl)/len(seq) for nucl in 'ATCG']

relative_frequencies = get_freqs('ATTAAACC')
print("The frequence of each base (A,T,C,G) is ", relative_frequencies)

我强烈建议使用

输出：

Counter({'A': 9, 'C': 9, 'T': 6, 'G': 3})
A frequency is: 0.3333333333333333
T frequency is: 0.2222222222222222
C frequency is: 0.3333333333333333
G frequency is: 0.1111111111111111

将其包装到函数中：

def get_freq(sequence):
    c = Counter(sequence.upper())
    l = len(sequence)
    result = {}
    for k,v in c.items():
        result.update({k: round(v/l, 2)})
    return result

get_freq('ATTAAACC')

{'A': 0.5, 'T': 0.25, 'C': 0.25}

我强烈建议使用

输出：

Counter({'A': 9, 'C': 9, 'T': 6, 'G': 3})
A frequency is: 0.3333333333333333
T frequency is: 0.2222222222222222
C frequency is: 0.3333333333333333
G frequency is: 0.1111111111111111

将其包装到函数中：

def get_freq(sequence):
    c = Counter(sequence.upper())
    l = len(sequence)
    result = {}
    for k,v in c.items():
        result.update({k: round(v/l, 2)})
    return result

get_freq('ATTAAACC')

{'A': 0.5, 'T': 0.25, 'C': 0.25}

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