python - 创建随机 DNA 序列并将其保存为 csv 文件

Question

这里是python新手！我想生成 20 个不同的 DNA 序列，每个序列的长度为 150。我还希望将序列保存为 csv 文件，但这部分似乎不起作用。我会感谢任何提示！

from random import choice
import csv

output = open("random_sequences.csv", "w")
        
def make_random_sequence():
    random_sequence = ""
    bases = ["A", "T", "G", "C"]
    for i in range(0, 150):
        random_sequence = random_sequence + choice(bases)
    print(random_sequence)


def random_sequences():
    for i in range(0, 20):
        altogether = make_random_sequence()
    return altogether
            
    for row in altogether:
        csv.writer(outfile).writerow(row)

output.close()

标签： pythondna-sequence

Answer 1

几个问题之一：

def random_sequences():
    for i in range(0, 20):
        altogether = make_random_sequence()
    return altogether
            
    for row in altogether:                     # will never be executed
        csv.writer(outfile).writerow(row)      # as the function returned earlier

另一个问题：

csv 模块newline=""在打开文件时需要参数。

---

您可以简化 DNS 数据的随机生成 - 将字符串添加到字符串非常慢：

import random

def make_random_sequence():
    return random.choices("ATGC", k=150)  # just create 150 of them as list

with open("output.csv","w",newline="") as f:
    writer = csv.writer(f)
    for _ in range(20):
        writer.writerow(make_random_sequence())

输出.csv：

A,A,A,A,A,C,C,T,G,T,G,T,G,T,T,A,A,A,A,C,C,C,A,T,C,A,A,T,G,T,T,A,C,C,G,G,G,G,G,A,G,T,C,A,G,A,G,T,T,T,A,C,T,G,T,A,C,T,A,A,G,A,C,C,T,G,C,G,A,T,A,C,A,T,C,T,T,T,A,C,G,G,A,T,A,A,C,T,A,G,A,G,A,T,G,T,C,C,G,C,T,G,G,A,C,A,T,C,G,T,A,A,C,G,T,C,G,G,G,A,A,G,T,C,A,G,T,A,A,A,C,T,G,T,T,G,A,C,A,A,C,G,T,C,C,C,G,G,A,T
C,T,C,C,A,C,T,A,C,T,T,C,A,C,T,C,T,G,T,C,C,G,G,T,G,G,T,T,C,A,C,C,C,G,C,A,A,G,C,T,A,A,A,C,C,A,A,C,C,G,A,C,G,G,T,G,A,C,A,C,A,G,G,G,A,T,C,T,T,T,C,G,T,T,A,T,A,A,G,T,A,C,T,C,A,T,T,C,A,A,G,T,G,A,T,A,A,C,T,G,T,G,G,A,T,G,A,G,A,A,G,A,T,C,T,A,T,C,T,G,C,G,G,C,C,G,T,C,C,G,A,C,G,C,T,G,T,A,A,T,T,A,T,T,G,C,G,T,A,T
[....]
C,C,T,T,G,T,T,T,C,G,A,C,A,C,A,T,G,A,T,C,G,C,T,C,C,G,T,G,T,T,A,G,T,A,A,G,A,T,T,T,A,C,T,A,A,G,C,G,G,C,A,A,G,A,A,G,G,C,C,C,T,T,A,G,A,G,A,G,T,T,C,T,G,A,A,T,T,G,C,C,G,A,T,A,G,C,G,T,G,T,T,T,T,A,A,C,C,T,T,G,T,A,A,T,C,C,A,G,G,T,A,C,C,C,C,G,G,G,C,A,A,G,A,T,G,T,T,A,G,C,T,G,G,C,G,C,T,C,A,T,G,T,T,C,T,A,A,G,A,T