How to save an array to a file

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!

Jeff Tratner · Accepted Answer · 2012-06-12 22:48:22Z

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)

edited Jun 12, 2012 at 22:48

answered Jun 12, 2012 at 22:37

Jeff Tratner

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8 Comments

John Amraph Over a year ago

Thank's a lot! The problem was with the join, can you please describe more details. Why the last only?

Jeff Tratner Over a year ago

updated to add the answer to the question. you reopen the file in every iteration of your for loop (so it erases every time)

Jeff Tratner Over a year ago

@JohnAmraph So, the reason that the '\n'.join() fixed the problem for you is because it combined all your file writes into one statement (so none of them overwrote each other :P)

John Amraph Over a year ago

So, it's kind of join-ing the writing?

jpaugh Over a year ago

If you wanted to open a file multiple times without erasing ("truncating") the content, you'd have to first close the file, then reopen it in append mode open(fname, 'a'), rather than write mode open(fname, 'w'). Write mode always assumes you want to discard the previous content, and this is also how most programs (text editors, e.g.) save files.

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