使用 python 搜索特定的重复

Question

输入文件示例：

1  AAcgGGGGGGtacctgt    yes
2  TTcccccctgtAAcgta   no
3  tcgAAAAaatacgacc     no
4  AAcgtataatacctgt   no
...

我想编写一个程序来扫描每个序列并检查单体核苷酸重复 (mnr)

示例输出：

1,AAcgGGGGGGtacctgt,yes
2,TTcccccctgtAAcgta,no

定义：单体核苷酸是：A、T、C、G的重复（不区分大小写）

我正在寻找的一排会是这样的： AAAAaaAAgtc 或者 gtAAAAAAAAAAc 或者 aaaaaaAAA 或者 aaaaaaaaaa 或者 ccccccccccc 或者 CCCCCcccCCC 或者...

我试过这个正则表达式但不起作用：

import csv
import re
list=[]
with open('sequences.txt', 'r') as f:
    reader = csv.reader(f,delimiter="\t")
    seq=re.findall(r'[Aa]{6, }','sequences.txt')
    for line in reader:
        if line.__contains__(seq):
            print(list.append(line))

任何帮助表示赞赏。

Answer 1

这里是您想要的紧凑型解决方案：

import csv
with open('sequences.txt', 'r') as f:
    reader = csv.reader(f, delimiter=",")
    for line in reader:
        seq_lower = line[1].lower()
        if 'aaaaaa' in seq_lower or 'cccccc' in seq_lower or 'tttttt' in seq_lower or 'gggggg' in seq_lower:
            print(line)

在这里，我假设您在处理 DNA 序列时只考虑了 a,c,g,t 的 mnrs。

Answer 2

更新：已经提出了使用正则表达式的部分解决方案。请注意，以下解决方案不适用于正则表达式，而是查找长度为 6 或更长的任何字符的任何序列。

测试数据：

number,sequence,status
1,kjhfklashfkldflkhasdfl,0
2,aaaaaljgkldfkjgldkfjgfldj,0
3,bbbbbbjigdfsjgjg,0
4,ccCccCCcjjfijsdfjsdf,0
5,klsjdflsjdfhdddddjnjlkhngjk,0
6,kjkljfhnlasjkdfheeeeeeejjjeeeeeeeeeekjdkljfleeef,0
7,jhfshffFffFFFFffkljjjj908u89,0

查找长度为 6 或更大的 MNR 的代码：

import csv

def contains_mnr(sequence):
    start_char = "$" # choose a character that is sure not to be in the sequence
    count = 0
    seq_lower = sequence.lower()

    for pos in range(0, len(seq_lower)):
        if seq_lower[pos] == start_char:
            count += 1
        else:
            start_char = seq_lower[pos]
            count = 1
        if count >= 6:
            return True

    return False

with open("input.csv", "r") as input_file:
    with open("output.csv", "w") as output_file:
        reader = csv.DictReader(input_file, dialect=csv.unix_dialect())
        writer = csv.writer(output_file, dialect=csv.unix_dialect())
        writer.writerow(reader.fieldnames)

        for row in reader:
            if contains_mnr(row["sequence"]):
                writer.writerow([
                    row["number"],
                    row["sequence"],
                    row["status"]
                ])

请注意，CSV 方言可能需要根据运行代码和生成数据文件的系统进行调整。

输出上面给出的测试数据：

"number","sequence","status"
"3","bbbbbbjigdfsjgjg","0"
"4","ccCccCCcjjfijsdfjsdf","0"
"6","kjkljfhnlasjkdfheeeeeeejjjeeeeeeeeeekjdkljfleeef","0"
"7","jhfshffFffFFFFffkljjjj908u89","0"