Question

I have the following function. The program looks at each file and prints the lines occuring in all 4 files to a new file. I’ve tried file1.close() but I get an error about closing a set? I think I could use a with statement but not sure how to do this, I’m very new to programming.

def secretome():
    file1 = set(line.strip() for line in open(path + "goodlistSigP.txt"))
    file2 = set(line.strip() for line in open(path + "tmhmmGoodlist.txt"))
    file3 = set(line.strip() for line in open(path + "targetpGoodlist.txt"))
    file4 = set(line.strip() for line in open(path + "wolfPsortGoodlist.txt"))
    newfile = open(path + "secretome_pass.txt", "w")
    for line in file1 & file2 & file3 & file4:
        if line:
            newfile.write(line + '\n')
    newfile.close()

Answer 1

I would suggest removing the repetition by extracting your set generation into a function:

def set_from_file(path):
    with open(path) as file:
        return set(lines.strip() for line in file)

def secretome():
    files = ["goodlistSigP.txt", "tmhmmGoodlist.txt", "targetpGoodlist.txt", "wolfPsortGoodlist.txt"]
    data = [set_from_file(os.path.join(path, file)) for file in files]
    with open(path + "secretome_pass.text", "w") as newfile:
        newfile.writelines(line + "/n" for line in set.union(*data) if line)

Note that you are doing intersection in your code, but you talk about wanting a union, so I used union() here. There are also a couple of list comprehensions/generator expressions.