I wrote some code to pull certain lines from a large text file and noticed some strange things missing, so I ran the following code to make sure the for loop was actually hitting every line in the file:
xf=open("bigFile.txt", r)
xxf=open("newFile.txt",w)
for line in xf:
xxf.write(line)
This ends up not copying all the lines for some reason. Could anyone tell me what I'm not understanding or doing wrong? It ends up only making a file about 60-70% as big as it should be? Any insight would be greatly appreciated.
EDIT: Thanks for the input skrrgwasme & Shreevardhan. To clarify, my ultimate goal is not just to copy the file, in my working code I put some comparison operators before writing the line, for example:
for line in xf:
firstChar=line[:1]
if firstChar==1:
xxf.write(line)
That is why I am using the "for line in file". Should I do this some other way?
To copy a file, it's better to use functions from shutil module like copyfile(), copy(), or copy2().
For example
from shutil import copyfile, copy2
copyfile('bigFile.txt', 'newFile.txt')
or
copy2('bigFile.txt', 'newFile.txt')
You need to close your file. There's no guarantee that buffers you're writing into are being flushed to disk before your script exits. You can do this very easily by using a context manager:
with open("bigFile.txt") as xf, open("newFile.txt", "w") as xxf:
for line in xf:
xxf.write(line)
In your current code, you would write xf.close() and xxf.close(), but using a context manager like this will handle it for you, and even close the files if an exception occurs.
Also, if you really are simply copying the file, you can also use shutil.copyfile().
Related
This is the first time I'm working with PARI/GP under Windows. I have to create a file and save it to write my code.
I tried the \r and \w and didn't work. I couldn't also find much documentation. How could I do it?
You can read with read, readstr, readvec, fileread, and filereadstr. Try typing ?read, for example, to see the quick help entry for that command.
Likewise, you can write with write, write1, writebin, writetex, filewrite, and filewrite1.
I have a python program and it seems that whenever I open it with this line of code active:
content = open('Word_list.txt').read().splitlines() it just closes itself (by open I mean double clicking it from file explorer, works fine every other way). I tried with a small list variable and my program works file when it's like that so I need to convert a 4MB file (4,250,000 lines) into a python list variable. Is there any way to do that and will there be any slowdowns because of what i'm doing here?
Oh, and I should mention that I tried other ways of importing the text file (for loops and whatnot) and that seemed to crash instantly too. Thanks!
Because you are running it through Explorer the window is closing before you can see an error message, so add some error handling code:
try:
content = open('Word_list.txt').read().splitlines()
except Exception as exc:
import traceback
print(traceback.format_exc())
input()
I managed to use Notepad++ and their macro system to put the required " ",'s over all of the words, completing my objecting using another program instead of python.
My input file is a gzipped file containing genomic information. I'm trying to parse the content on a line-by-line basis and have run into a strange problem.
Any given line looks something like this:
AC=26;AF=0.00519169;AN=5008;NS=2504;DP=17308;EAS_AF=0;AMR_AF=0.0072;AFR_AF=0.0015;EUR_AF=0.0109;SAS_AF=0.0082;AA=A|||;VT=SNP
However, when I print out what is being read in...
import gzip
with gzip.open(myfile.gz, 'rt') as f:
for line in f:
print(line)
The line looks like this:
AC=26;AF=0.00519169;AN=5008;NS=2504;DP=17308;EAS_AF=0;AMR_AF=0.0072;AFR_AF=0.0015;EUR_AF=0.0109;SAS_AF=0.0082;AA=A|||
Whatever information comes after the "|||" has been truncated.
Moreover, I can't even search the lines for strings that follow the "|||" (e.g. "VT=SNP" in line always returns False) I also can't line.strip("|||")
Any advice on what is causing this or what I need to look at?
Thank you for any help
EDIT: ok, it looks like there was something wrong with the gzip file. I uncompressed it and the script ran fine. Then I recompressed it and the script again ran fine (using gzip.open). Is there any straightforward way to compare the two compressed files (ie, the one that doesn't get read properly vs the one that works) so that I might get a hint at the root cause?
I'm starting to learn about the io. functions, and am trying to implement them in my code. I've searched for the answer to this and nothing seems to give a clear cut yes or no, or at least I don't see one. I'm hoping someone here will know the answer and be able to help with this.
I'm wanting to create a text file that I can write to as time progresses. It'll basically be a log to which I'll be appending lines of output. Apparently io.open("textfile.txt") does not create the file, or so it appears.
Is there a way to create a text file in Lua that can later be accessed with io.read/write? Additionally, do I need to call io.close() before opening or creating a new text file? I appreciate any help given. Thanks!
You need to open the file for writing as follows: f=io.open("textfile.txt","w"). Then use f:write() to write stuff to it. When finished writing, call f:close().
I have doubt in the following scenario
Scenario:
A process or program starts with opening a file in a write mode and entering a infinite loop say example: while(1) whose body has logic to write to the opened file.
Problem: What if i delete the opened or created file soon after the process enters the infinite loop
In Unix, users really cannot delete files, they only can drop references to files. The kernel deletes the file when there are no references (hard links and open file descriptors) left.
From what you're saying, it sounds like in reality you don't want an infinite loop, but rather a while loop with some flag, something to the effect of
while (file exists)
perform operation
Add a line that checks to see if the file exists during the while loop. If it doesn't exist, kill the loop.
It appears that what happens is that your file disappears (basically).
Try this, create a file test.py and put the following in it:
import os
f = open('out.txt', 'w') # Open file for writing
f.write("Hi Mom!") # Write something
os.remove('out.txt') # Delete the file
try:
while True: # Do forever
f.write("Silly English Kanighit!")
except:
f.close()
then $ python test.py and hit enter. Ctrl-C should stop the execution. This will open, then delete the file, then continue writing to the file that no longer exists, for the reasons that have previously been mentioned.
However, if you really have a different question such as "How can I prevent my file from being accidentally deleted while I'm writing to it?" or something else, it's probably better to ask that question.