从计算 DNA 序列到 table 的元组

Question

我想计算 DNA 序列中的碱基数，return 序列中每种类型碱基的计数，并打印出两列 table 其中第一列是碱基，第二列是相关的碱基计数。我可以获得 return 基本计数的函数，但我不确定如何打印 table。我想用基本 python 函数来做这个分析，尽管我认为用一些 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)

期望的输出：

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

和

counts
(4, 6, 6, 3)

Answer 1

1) 你有一个错误 - 你的 return 向右多缩进了一个制表位

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)

但如果您必须保持功能不变：

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 2

从函数内部：

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)

OP 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 3

您可以使用collections.Counter 来计算碱基，并使用pandas 以列方式设置数据。这是一个例子

from collections import Counter
import pandas as pd

# Count the bases
dna="AAGCTACGTGGGTGACTTT"
count = Counter(dna)
tup = ()
for _, value in sorted(count.items()):
  tup += (value,)
print(tup  # Outputs (4, 3, 6, 6)

# Set it in a pandas dataframe
df = pd.DataFrame(list(dict(count).items()), columns=['Base', 'Count'])
print(df.to_string(index=False))
# Output
# Base  Count
#   A      4
#   G      6
#   C      3
#   T      6

Answer 4

您可以创建另一个函数来打印结果：

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)

从计算 DNA 序列到 table 的元组

Tuple to table from counting DNA sequences

python

dna-sequence