I needed to scan some pretty massive gzipped text files, so my first try was the obvious "for line in gzip.open(...)." This worked but seemed way slower than expected. So I wrote "pyzcat" as a test and ran it against a file with 100k lines:
#!/usr/bin/python
import sys, gzip
for fname in sys.argv[1:]:
for line in gzip.open(fname):
print line,
Results:
$ time zcat testzcat.gz > /dev/null real 0m0.329s $ time ./pyzcat testzcat.gz > /dev/null real 0m3.792s
10x slower -- ouch! Well, if zcat is so much better, let's try using zcat to do the reads for us:
def gziplines(fname):
from subprocess import Popen, PIPE
f = Popen(['zcat', fname], stdout=PIPE)
for line in f.stdout:
yield line
for fname in sys.argv[1:]:
for line in gziplines(fname):
print line,
Results:
$ time ./pyzcat2 testzcat.gz |wc real 0m0.750s
So, reading from a zcat subprocess is 5x faster than using the gzip module. cGzipFile anyone?
Comments
Just increase the block size in which you do I/O to 1 MB and the performance will be close.
#pyzcat-large-block:
#!/usr/bin/env python
import sys
import gzip
BLOCK_SIZE = 2**20
f = gzip.open(sys.argv[1])
for i in iter(lambda: f.read(BLOCK_SIZE), ''):
sys.stdout.write(i)
# timing results on a 150 MB gzip file
$ /usr/bin/time zcat t.gz > /dev/null
2.12user 0.11system 0:02.68elapsed 83%CPU (0avgtext+0avgdata 0maxresident)k
/usr/bin/time ./pyzcat t.gz > /dev/null
2.40user 0.57system 0:03.02elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k
0inputs+0outputs (2major+90189minor)pagefaults 0swaps
feeding your 1MB chunks to a cStringIO for turning into individual lines might speed things up vs the python code in GzipFile, but it's going to take some work when lines span your chunks.
zcat doesn't give you a line-oriented interface but your pyzcat is doing buffering and scanning to make that happen.
#!/usr/bin/python
import sys, gzip, shutil
for fname in sys.argv[1:]:
shutil.copyfileobj(gzip.open(fname), sys.stdout))
That gives me 0.369s for zcat and 0.530 for a more similar pyzcat.
I guess most people commenting here didn't read past the first block of code.