Question

我要计算DNA序列中的碱基数，返回序列中每种碱基的计数，还打印出两列表，其中第一列是碱基，第二列是关联的基本数量。我可以获得返回基数的函数，但是我不确定如何打印表格。我想使用基本的python函数进行此分析，尽管我认为使用某些python模块会更容易。

代码：

 def base_counter(DNA):
    A = 0
    T = 0
    G = 0
    C = 0
    for base in DNA:
        if base == "A":
            A = A + 1
        elif base == "T":
            T = T + 1
        elif base == "G":
            G = G + 1
        elif base == "C":
            C = C + 1
        else:
            pass
    return A,T,G,C

参数输入：

dna="AAGCTACGTGGGTGACTTT"

函数调用：

counts=base_counter(dna)
print(counts)

输出：

(4, 6, 6, 3)

所需的输出：

print(counts)
  A   4
  T   6
  G   6
  C   3

和

counts
(4, 6, 6, 3)

Answer 1

您可以使用curl -X GET -u "apikey:{apikey}" "https://gateway.watsonplatform.net/tone-analyzer/api/v3/tone?version=2017-09-21&text=Team,%20I%20know%20that%20times%20are%20tough!%20Product%20sales%20have%20been%20disappointing%20for%20the%20past%20three%20quarters.%20We%20have%20a%20competitive%20product,%20but%20we%20need%20to%20do%20a%20better%20job%20of%20selling%20it!"来计算基数，并使用collections.Counter以列方式设置数据。这是一个例子

pandas

Answer 2

1）您有一个错误-您的return向右缩进了一个额外的标签

2）使用dict：

def base_counter(DNA):
    dna_dict = {
        "A": 0,
        "T": 0,
        "G": 0,
        "C": 0,
    }
    for base in DNA:
        if base == "A":
            dna_dict["A"] += 1
        elif base == "T":
            dna_dict["T"] += 1
        elif base == "G":
            dna_dict["G"] += 1
        elif base == "C":
            dna_dict["C"] += 1
    return dna_dict


dna = "AAGCTACGTGGGTGACTTT"

counts = base_counter(dna)
for base, count in counts.items():
    print(base, count)

但是如果您必须按原样保留该功能：

def base_counter(DNA):
    A = 0
    T = 0
    G = 0
    C = 0
    for base in DNA:
        if base == "A":
            A = A + 1
        elif base == "T":
            T = T + 1
        elif base == "G":
            G = G + 1
        elif base == "C":
            C = C + 1
    return A,T,G,C


dna = "AAGCTACGTGGGTGACTTT"

counts = base_counter(dna)
for base, count in zip("ATGC", counts):
    print(base, count)

Answer 3

从功能内：

out_str="A    "+str(A)+"\n"+\
      "T    "+str(T)+"\n"+\
      "G    "+str(G)+"\n"+\
      "C    "+str(C)
return out_str

现在您可以调用并打印它，它将以您想要的格式打印：

result=base_counter(DNA)
print(result)

用于OP的请求完整代码：

def base_counter(DNA):
    A = 0
    T = 0
    G = 0
    C = 0
    for base in DNA:
        if base == "A":
            A = A + 1
        elif base == "T":
            T = T + 1
        elif base == "G":
            G = G + 1
        elif base == "C":
            C = C + 1
    out_str = "A    " + str(A) + "\n"+\
    "T    " + str(T) + "\n"+\
    "G    " + str(G) + "\n"+\
    "C    " + str(C)
    return out_str

base=base_counter("AAGCTACGTGGGTGACTTT")
print(base)

输出：

Answer 4

您可以使用另一个功能来打印结果：

def print_bases(bases):
print("A    "+str(bases[0])+"\n"
  "T    "+str(bases[1])+"\n"
  "G    "+str(bases[2])+"\n"
  "C    "+str(bases[3]))
print_bases(counts)

从计数DNA序列到元组到表

4 个答案: