Question

我正在尝试使用python脚本为多种文件类型的DNA序列生成反向互补。这是我到目前为止所写的内容

import gzip
import re

############## Reverse Complement Function #################################
def rev_comp(dna):
    dna_upper = dna.upper() #Ensures all input is capitalized
    dna_rev = dna_upper[::-1] #Reverses the string

    conversion = {'A':'T','C':'G','G':'C','T':'A','Y':'R','R':'Y',\
       'S':'S','W':'W','K':'M','M':'K','B':'V','V':'B',\
       'D':'H','H':'D','N':'N','-':'-'}

    rev_comp = ''
    rc = open("Rev_Comp.fasta", 'w')
    for i in dna_rev:
        rev_comp += conversion[i]
        rc.write(str(rev_comp))
    print("Reverse complement file Rev_Comp.fasta written to directory")    

x = input("Enter filename (with extension) of the DNA sequence: ")

if x.endswith(".gz"):    #Condition for gzip files
    with gzip.open(x, 'rb') as f:
        file_content = f.read()
        new_file = open("unzipped.fasta", 'w')
        new_file.write(str(file_content))
        print("unzipped.fasta written to directory")

xread = x.readlines()
fast = ''

if x.endswith(".fasta"):   #condition for fasta files
    for i in xread:
        if not i.startswith('>'):
            fast = fast + i.strip('\n')

if x.endswith(".fastq"):        #condition for fastq files
    for i in range(1,len(xread),4):
        fast = fast + xread[i].strip('\n')

rev_comp(x)

最后我想到的是

AttributeError: 'str' object has no attribute 'readlines'

当我尝试使用.fastq文件运行脚本时。这到底是怎么了？我希望脚本编写Rev_comp.fasta，但事实并非如此。

Answer 1

x不是文件句柄，而只是文件名。你需要做

with open(x) as xhandle:
    xread = xhandle.readlines()

如果不将所有行读入内存，总体逻辑可能会更好。同样，.gz案件最终出现在不确定的范围内；您是否需要在x处理结束时将gz设置为解压缩数据的名称，还是将其后的代码放入else:分支中？

Answer 2

x是来自用户的输入，它是一个字符串。您需要open的文件才能在其上调用readlines。

根据您现有的代码：

x = input("Enter filename (with extension) of the DNA sequence: ") # x stores a string

file_x = open(x, 'r')  # You must open a file ...

xread = file_x.readlines()  # and call readlines on the file instance.

# Although it is not explicitly necessary, remember to close the file when you'done, is good practice.
file_x.close()

或使用file as a context manager

with open(x) as file_x:
    xread = file_x.readlines()

AttributeError：“ str”对象没有属性“ readlines”。我的代码在哪里出错？

2 个答案: