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Best way to search for patterns in huge text files

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# 1  
Old 01-08-2010
Bug Best way to search for patterns in huge text files
I have the following situation:

a text file with 50000 string patterns:

Code:
abc2344536
gvk6575556
klo6575556
....

and 3 text files each with more than 1 million lines:

Code:
...
000000 abc2344536      46575 0000
000000 abc2344536      46575 4444
000000 abc2344555      46575 1234
...

I have to extract all lines from the 3 files that match all patterns from the pattern file :-)

Any ideas, please!!!

Andy
Last edited by radoulov; 01-08-2010 at 05:32 PM.. Reason: Please use code tags!
# 2  
Old 01-08-2010
If I understand correctly ("all patterns" is a bit confusing) ...
Try this:

Code:
awk 'NR == FNR { p[$1]; next } $2 in p' pattern_file input_file1 input_file2 ...

Use gawk, nawk or /usr/xpg4/bin/awk on Solaris.
# 3  
Old 01-08-2010
thank u for your quick replay...but it does not work ..

I need something faster than the following solution:
Code:
for i in `cat pattern_file`
do
  grep $i  input_file1 >> output_file1
  grep $i  input_file2 >> output_file2  
  grep $i  input_file3 >> output_file3
done

Any ideas please!!!
Last edited by Scott; 01-08-2010 at 06:32 PM.. Reason: Please use code tags
# 4  
Old 01-08-2010
Hi.

Is:
Code:
grep -f pattern_file input_file[123] > output_fileX

quicker?

Also, please say WHAT doesn't work with the awk solution.

Like radoulov, I don't know what you mean by "all patterns".
Last edited by Scott; 01-08-2010 at 06:41 PM..
# 5  
Old 01-08-2010
scottn ,
Code:
grep -f pattern_file input_file[123] > output_fileX

I get out of memory :-)

"all patterns" means: returns every line that contains any string pattern from the pattern file. And the results of each file should be separatly..excuse me my english :-(
Last edited by Scott; 01-09-2010 at 07:26 PM.. Reason: Added code tags
# 6  
Old 01-08-2010
Hi Andy.

You're English is not an issue - it's rather good Smilie.

You didn't say what was wrong with the original awk (why it didn't work).

You can try:
Code:
cat input_file1 input_file2 etc | grep -f pattern_file

A slight change to the awk:
Code:
awk 'NR == FNR { p[$1]; next } $0 ~ p[$2]' pattern_file input_file*

(changing the filenames to suit your requirements)
# 7  
Old 01-09-2010
scottn,

thank you for your Patience.

The first solution:

Code:
cat input_file1 input_file2 etc | grep -f pattern_file

returns virtual memory exhausted :-(

The second one:

Code:
awk 'NR == FNR { p[$1]; next } $0 ~ p[$2]' pattern_file input_file*

Does not work!! It returns all the lines of "input_file". A second bad thing is that, the searched pattern is NOT always at the second position, e.g.
Code:
...
000000 abc2344536      46575 0000
000000 89798798798    abc2344536
000000 abc2344555      46575 1234
000000 7777777777     abc2344536
...

:-(
Last edited by radoulov; 01-09-2010 at 11:50 AM.. Reason: Please use code tags!
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