Question

I want to know how to save an array to a file. You already helped me a lot, but I have more naive questions (I’m new to Python):

@<TRIPOS>MOLECULE 
NAME123 
line3 
line4 
line5 
line6 
@<TRIPOS>MOLECULE 
NAME434543 
line3 
line4 
line5 
@<TRIPOS>MOLECULE 
NAME343566 
line3 
line4 

I am currently have this code, but it’s save only the last item from the array no the all listed in the items_grep. How to fix this?

items = []
with open("test.txt", mode="r") as itemfile: 
    for line in itemfile: 
        if line.startswith("@<TRIPOS>MOLECULE"): 
            items.append([]) 
            items[-1].append(line) 
        else: 
            items[-1].append(line)      
#
# list to grep
items_grep = open("list.txt", mode="r").readlines()
# writing files
for i in items:
    if i[1] in items_grep:
        open("grep.txt", mode="w").write("".join(i))

Thank you in advance!

Answer 1

The reason your file is only showing the last value is because every time you open the file with the w flag, it erases the existing file. If you open it once and then use the file object, you’ll be fine, so you’d do (note, this is not a very clean/pythonic way of doing it, just being clear about how the open command works)

myfile = open("grep.txt", "w")
for i in ...
    if i[1] ...:
         myfile.write(i + '\n')

Easy way to handle this would be to do a list comprehension first and then join, e.g.:

newstr = '\n'.join([''.join(i) for i in items if i[1] in items_grep])

Then just write the entire string to the file at once. Note that without adding the \n between items, you won’t end up with each item on a new line, instead they will all be added one after the other without spaces.

You should also consider using the with keyword to auto close the file.

with open("grep.txt","w") as f:
    f.write(newstr)