Say I have a 10GB HDD Ubuntu VPS in the USA (and I live in some where else), and I have a 9GB text file on the hard drive. I have 512MB of RAM, and about the same amount of swap.
Given the fact that I cannot add more HDD space and cannot move the file to somewhere else to process, is there an efficient method to remove some lines from the file using Python (preferably, but any other language will be acceptable)?
How about this? It edits the file in place. I've tested it on some small text files (in Python 2.6.1), but I'm not sure how well it will perform on massive files because of all the jumping around, but still...
I've used a indefinite while loop with a manual EOF check, because for line in f: didn't work correctly (presumably all the jumping around messes up the normal iteration). There may be a better way to check this, but I'm relatively new to Python, so someone please let me know if there is.
Also, you'll need to define the function isRequired(line).
writeLoc = 0
readLoc = 0
with open( "filename" , "r+" ) as f:
while True:
line = f.readline()
#manual EOF check; not sure of the correct
#Python way to do this manually...
if line == "":
break
#save how far we've read
readLoc = f.tell()
#if we need this line write it and
#update the write location
if isRequired(line):
f.seek( writeLoc )
f.write( line )
writeLoc = f.tell()
f.seek( readLoc )
#finally, chop off the rest of file that's no longer needed
f.truncate( writeLoc )
Try this:
currentReadPos = 0
removedLinesLength = 0
for line in file:
currentReadPos = file.tell()
if remove(line):
removedLinesLength += len(line)
else:
file.seek(file.tell() - removedLinesLength)
file.write(line + "\n")
file.flush()
file.seek(currentReadPos)
I have not run this, but the idea is to modify the file in place by overwriting the lines you want to remove with lines you want to keep. I am not sure how the seeking and modifying interacts with the iterating over the file.
Update:
I have tried fileinput with inplace by creating a 1GB file. What I expected was different from what happened. I read the documentation properly this time.
Optional in-place filtering: if the keyword argument inplace=1 is passed to fileinput.input() or to the FileInput constructor, the file is moved to a backup file and standard output is directed to the input file (if a file of the same name as the backup file already exists, it will be replaced silently).
from docs/fileinput
So, this doesn't seem to be an option now for you. Please check other answers.
Before Edit:
If you are looking for editing the file inplace, then check out Python's fileinput module - Docs.
I am really not sure about its efficiency when used with a 10gb file. But, to me, this seemed to be the only option you have using Python.
Just sequentially read and write to the files.
f.readlines() returns a list containing all the lines of data in the file. If given an optional parameter sizehint, it reads that many bytes from the file and enough more to complete a line, and returns the lines from that. This is often used to allow efficient reading of a large file by lines, but without having to load the entire file in memory. Only complete lines will be returned.
Process the file getting 10/20 or more MB of chunks. This would be the fastest way.
Other way of doing this is to stream this file and filter it using AWK for example.
example pseudo code:
file = open(rw)
linesCnt=50
newReadOffset=0
tmpWrtOffset=0
rule=1
processFile()
{
while(rule)
{
(lines,newoffset)=getLines(file, newReadOffset)
if lines:
[x for line in lines if line==cool: line]
tmpWrtOffset = writeBackToFile(file, x, tmpWrtOffset) #should return new offset to write for the next time
else:
rule=0
}
}
To resize file at the end use truncate(size=None)
