Re: python vs. grep

2008-05-13 Thread Ville M. Vainio
Ricardo Aráoz [EMAIL PROTECTED] writes:

 The easy/simple (too easy/simple?) way I see out of it is to read THE
 WHOLE file into memory and don't worry. But what if the file is too

The easiest and simplest approach is often the best with
Python. Reading in the whole file is rarely too heavy, and you omit
the python object overhead entirely - all the code executes in the
fast C extensions.

If the file is too big, you might want to look up mmap:

http://effbot.org/librarybook/mmap.htm
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Re: python vs. grep

2008-05-13 Thread Ricardo Aráoz

Ville M. Vainio wrote:

Ricardo Aráoz [EMAIL PROTECTED] writes:


The easy/simple (too easy/simple?) way I see out of it is to read THE
WHOLE file into memory and don't worry. But what if the file is too


The easiest and simplest approach is often the best with
Python. 


Keep forgetting that!



If the file is too big, you might want to look up mmap:

http://effbot.org/librarybook/mmap.htm


Thanks!
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Re: python vs. grep

2008-05-12 Thread Ricardo Aráoz

Ville Vainio wrote:

On May 8, 8:11 pm, Ricardo Aráoz [EMAIL PROTECTED] wrote:


All these examples assume your regular expression will not span multiple
lines, but this can easily be the case. How would you process the file
with regular expressions that span multiple lines?


re.findall/ finditer, as I said earlier.



Hi, sorry took so long to answer. Too much work.

findall/finditer do not address the issue, they merely find ALL the 
matches in a STRING. But if you keep reading the files a line at a time 
(as most examples given in this thread do) then you are STILL in trouble 
when a regular expression spans multiple lines.
The easy/simple (too easy/simple?) way I see out of it is to read THE 
WHOLE file into memory and don't worry. But what if the file is too 
heavy? So I was wondering if there is any other way out of it. Does grep 
read the whole file into memory? Does it ONLY process a line at a time?


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Re: python vs. grep

2008-05-12 Thread Kam-Hung Soh
On Tue, 13 May 2008 00:03:08 +1000, Ricardo Aráoz [EMAIL PROTECTED]  
wrote:



Ville Vainio wrote:

On May 8, 8:11 pm, Ricardo Aráoz [EMAIL PROTECTED] wrote:

All these examples assume your regular expression will not span  
multiple

lines, but this can easily be the case. How would you process the file
with regular expressions that span multiple lines?

 re.findall/ finditer, as I said earlier.



Hi, sorry took so long to answer. Too much work.

findall/finditer do not address the issue, they merely find ALL the  
matches in a STRING. But if you keep reading the files a line at a time  
(as most examples given in this thread do) then you are STILL in trouble  
when a regular expression spans multiple lines.
The easy/simple (too easy/simple?) way I see out of it is to read THE  
WHOLE file into memory and don't worry. But what if the file is too  
heavy? So I was wondering if there is any other way out of it. Does grep  
read the whole file into memory? Does it ONLY process a line at a time?


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Standard grep can only match a line at a time.  Are you thinking about  
sed, which has a sliding window?


See http://www.gnu.org/software/sed/manual/sed.html, Section 4.13

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Re: python vs. grep

2008-05-09 Thread Ville Vainio
On May 8, 8:11 pm, Ricardo Aráoz [EMAIL PROTECTED] wrote:

 All these examples assume your regular expression will not span multiple
 lines, but this can easily be the case. How would you process the file
 with regular expressions that span multiple lines?

re.findall/ finditer, as I said earlier.


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Re: python vs. grep

2008-05-08 Thread Alan Isaac

Anton Slesarev wrote:

I've read great paper about generators:
http://www.dabeaz.com/generators/index.html 
Author say that it's easy to write analog of common linux tools such 
as awk,grep etc. He say that performance could be even better. 
But I have some problem with writing performance grep analog. 



https://svn.enthought.com/svn/sandbox/grin/trunk/

hth,
Alan Isaac
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Re: python vs. grep

2008-05-08 Thread Robert Kern

Alan Isaac wrote:

Anton Slesarev wrote:

I've read great paper about generators:
http://www.dabeaz.com/generators/index.html Author say that it's easy 
to write analog of common linux tools such as awk,grep etc. He say 
that performance could be even better. But I have some problem with 
writing performance grep analog. 


https://svn.enthought.com/svn/sandbox/grin/trunk/


As the author of grin I can definitively state that it is not at all competitive 
with grep in terms of speed. grep reads files really fast. awk is probably 
beatable, though.


--
Robert Kern

I have come to believe that the whole world is an enigma, a harmless enigma
 that is made terrible by our own mad attempt to interpret it as though it had
 an underlying truth.
  -- Umberto Eco

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Re: python vs. grep

2008-05-08 Thread Ricardo Aráoz

Anton Slesarev wrote:

I try to save my time not cpu cycles)

I've got file which I really need to parse:
-rw-rw-r--  1 xxx  xxx  3381564736 May  7 09:29 bigfile

That's my results:

$ time grep python bigfile | wc -l
2470

real0m4.744s
user0m2.441s
sys 0m2.307s

And python scripts:

import sys

if len(sys.argv) != 3:
   print 'grep.py pattern file'
   sys.exit(1)

f = open(sys.argv[2],'r')

print ''.join((line for line in f if sys.argv[1] in line)),

$ time python grep.py python bigfile | wc -l
2470

real0m37.225s
user0m34.215s
sys 0m3.009s

Second script:

import sys

if len(sys.argv) != 3:
   print 'grepwc.py pattern file'
   sys.exit(1)

f = open(sys.argv[2],'r',1)

print sum((1 for line in f if sys.argv[1] in line)),


time python grepwc.py python bigfile
2470

real0m39.357s
user0m34.410s
sys 0m4.491s

40 sec and 5. This is really sad...

That was on freeBSD.



On windows cygwin.

Size of bigfile is ~50 mb

$ time grep python bigfile | wc -l
51

real0m0.196s
user0m0.169s
sys 0m0.046s

$ time python grepwc.py python bigfile
51

real0m25.485s
user0m2.733s
sys 0m0.375s

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All these examples assume your regular expression will not span multiple 
lines, but this can easily be the case. How would you process the file 
with regular expressions that span multiple lines?






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Re: python vs. grep

2008-05-07 Thread Anton Slesarev
I try to save my time not cpu cycles)

I've got file which I really need to parse:
-rw-rw-r--  1 xxx  xxx  3381564736 May  7 09:29 bigfile

That's my results:

$ time grep python bigfile | wc -l
2470

real0m4.744s
user0m2.441s
sys 0m2.307s

And python scripts:

import sys

if len(sys.argv) != 3:
   print 'grep.py pattern file'
   sys.exit(1)

f = open(sys.argv[2],'r')

print ''.join((line for line in f if sys.argv[1] in line)),

$ time python grep.py python bigfile | wc -l
2470

real0m37.225s
user0m34.215s
sys 0m3.009s

Second script:

import sys

if len(sys.argv) != 3:
   print 'grepwc.py pattern file'
   sys.exit(1)

f = open(sys.argv[2],'r',1)

print sum((1 for line in f if sys.argv[1] in line)),


time python grepwc.py python bigfile
2470

real0m39.357s
user0m34.410s
sys 0m4.491s

40 sec and 5. This is really sad...

That was on freeBSD.



On windows cygwin.

Size of bigfile is ~50 mb

$ time grep python bigfile | wc -l
51

real0m0.196s
user0m0.169s
sys 0m0.046s

$ time python grepwc.py python bigfile
51

real0m25.485s
user0m2.733s
sys 0m0.375s

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Re: python vs. grep

2008-05-07 Thread Ville Vainio
On May 6, 10:42 pm, Anton Slesarev [EMAIL PROTECTED] wrote:

 flines = (line for line in f if pat.search(line))

What about re.findall() / re.finditer() for the whole file contents?

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Re: python vs. grep

2008-05-07 Thread Pop User

Anton Slesarev wrote:


But I have some problem with writing performance grep analog.



I don't think you can ever catch grep.  Searching is its only purpose in 
life and its very good at it.  You may be able to come closer, this 
thread relates.


http://groups.google.com/group/comp.lang.python/browse_thread/thread/2f564523f476840a/d9476da5d7a9e466

This relates to the speed of re.  If you don't need regex don't use re. 
 If you do need re an alternate re library might be useful but you 
aren't going to catch grep.



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Re: python vs. grep

2008-05-07 Thread Anton Slesarev
On May 7, 7:22 pm, Pop User [EMAIL PROTECTED] wrote:
 Anton Slesarev wrote:

  But I have some problem with writing performance grep analog.

 I don't think you can ever catch grep.  Searching is its only purpose in
 life and its very good at it.  You may be able to come closer, this
 thread relates.

 http://groups.google.com/group/comp.lang.python/browse_thread/thread/...

 This relates to the speed of re.  If you don't need regex don't use re.
   If you do need re an alternate re library might be useful but you
 aren't going to catch grep.

In my last test I dont use re. As I understand the main problem in
reading file.
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python vs. grep

2008-05-06 Thread Anton Slesarev
I've read great paper about generators:
http://www.dabeaz.com/generators/index.html

Author say that it's easy to write analog of common linux tools such
as awk,grep etc. He say that performance could be even better.

But I have some problem with writing performance grep analog.


It's my script:

import re
pat = re.compile(sometext)

f = open(bigfile,'r')

flines = (line for line in f if pat.search(line))
c=0
for x in flines:
c+=1
print c

and bash:
grep sometext bigfile | wc -l

Python code 3-4 times slower on windows. And as I remember on linux
the same situation...

Buffering in open even increase time.

Is it possible to increase file reading performance?
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Re: python vs. grep

2008-05-06 Thread Ian Kelly
On Tue, May 6, 2008 at 1:42 PM, Anton Slesarev [EMAIL PROTECTED] wrote:
  Is it possible to increase file reading performance?

Dunno about that, but this part:

  flines = (line for line in f if pat.search(line))
  c=0
  for x in flines:
 c+=1
  print c

could be rewritten as just:

print sum(1 for line in f if pat.search(line))
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Re: python vs. grep

2008-05-06 Thread Arnaud Delobelle
Anton Slesarev [EMAIL PROTECTED] writes:

 f = open(bigfile,'r')

 flines = (line for line in f if pat.search(line))
 c=0
 for x in flines:
 c+=1
 print c

It would be simpler (and probably faster) not to use a generator expression:

search = re.compile('sometext').search

c = 0
for line in open('bigfile'):
if search(line):
 c += 1

Perhaps faster (because the number of name lookups is reduced), using
itertools.ifilter:

from itertools import ifilter

c = 0
for line in ifilter(search, 'bigfile'):
c += 1


If 'sometext' is just text (no regexp wildcards) then even simpler:

...
for line in ...:
if 'sometext' in line:
 c += 1

I don't believe you'll easily beat grep + wc using Python though.

Perhaps faster?

sum(bool(search(line)) for line in open('bigfile'))
sum(1 for line in ifilter(search, open('bigfile')))

...etc...

All this is untested!
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Re: python vs. grep

2008-05-06 Thread Wojciech Walczak
2008/5/6, Anton Slesarev [EMAIL PROTECTED]:
  But I have some problem with writing performance grep analog.
[...]
  Python code 3-4 times slower on windows. And as I remember on linux
  the same situation...

  Buffering in open even increase time.

  Is it possible to increase file reading performance?

The best advice would be not to try to beat grep, but if you really
want to, this is the right place ;)

Here is my code:
$ cat grep.py
import sys

if len(sys.argv) != 3:
   print 'grep.py pattern file'
   sys.exit(1)

f = open(sys.argv[2],'r')

print ''.join((line for line in f if sys.argv[1] in line)),

$ ls -lh debug.0
-rw-r- 1 gminick root 4,1M 2008-05-07 00:49 debug.0

---
$ time grep nusia debug.0 |wc -l
26009

real0m0.042s
user0m0.020s
sys 0m0.004s
---

---
$ time python grep.py nusia debug.0 |wc -l
26009

real0m0.077s
user0m0.044s
sys 0m0.016s
---

---
$ time grep nusia debug.0

real0m3.163s
user0m0.016s
sys 0m0.064s
---

---
$ time python grep.py nusia debug.0
[26009 lines here...]
real0m2.628s
user0m0.032s
sys 0m0.064s
---

So, printing the results take 2.6 secs for python and 3.1s for original grep.
Suprised? The only reason for this is that we have reduced the number
of write calls in the python example:

$ strace -ooriggrep.log grep nusia debug.0
$ grep write origgrep.log |wc -l
26009


$ strace -opygrep.log python grep.py nusia debug.0
$ grep write pygrep.log |wc -l
12


Wish you luck saving your CPU cycles :)

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Wojtek Walczak
http://www.stud.umk.pl/~wojtekwa/
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