Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Search multiple patterns in multiple files
Top Forums Shell Programming and Scripting Search multiple patterns in multiple files Post 302490046 by methyl on Sunday 23rd of January 2011 05:10:42 PM
Old 01-23-2011
What Operating System and version are you running? This is very important. I haven't seen the "fork" error in many years.
We gather that you have ksh.

Quote:
#!/usr/bin/ksh
for num in `cat file1.txt`
do
find . -name "*processed" -print | xargs gunzip -c | grep -q $num || echo "$num not found" >> outputfile.txt &
done
The script posted makes no sense because it does not search for zipped files.


If "file1.txt" contains 5,000,000 numbers this level of blunt processing is absurd in unix Shell when searching 5Gb of data.
You appear to want to search a specific field at a specific position within a record but have provided sample data in "file1.txt" which does not match the exact length of the highlighted field.


Do you have use of a professional Systems Analyst?
Do you have a database engine (e.g. Oracle) and use of professional Database Programmers?

IMHO you are way out of you depth. Hire a professional.



The background "&" within a 5,000,000 iteration loop is why you are getting "fork" errors. It would take a seriously special kernel build to create a unix which could cope with 5,000,000 concurrent processes (hmm. temptied to try it). I am surprised that you did not crash the computer with this irresponsible, uninformed and ignorant code.


Ps: Given a decent commercial database engine and some top-class Database Programmers this problem is solveable.
Last edited by methyl; 01-23-2011 at 06:46 PM.. Reason: Footnote:, layout and more layout
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

How to parameterize multiple search patterns and generate a new file

I have one file: 123*100*abcd*10 123*101*abcd*-29*def 123*100*abcd*-10 123*102*abcd*-105*asd I would like to parameterize the search patterns in the following way so that the user could dynamically change the search pattern. *100* and *- (ie *minus) *102* and *- The output that is... (6 Replies)
Discussion started by: augustinep
6 Replies

2. Shell Programming and Scripting

Perl: Match a line with multiple search patterns

Hi I'm not very good with the serach patterns and I'd need a sample how to find a line that has multiple patterns. Say I want to find a line that has "abd", "123" and "QWERTY" and there can be any characters or numbers between the serach patterns, I have a file that has thousands of lines and... (10 Replies)
Discussion started by: Juha
10 Replies

3. Shell Programming and Scripting

Perl - How to search a text file with multiple patterns?

Good day, great gurus, I'm new to Perl, and programming in general. I'm trying to retrieve a column of data from my text file which spans a non-specific number of lines. So I did a regexp that will pick out the columns. However,my pattern would vary. I tried using a foreach loop unsuccessfully.... (2 Replies)
Discussion started by: Sp3ck
2 Replies

4. Shell Programming and Scripting

search multiple patterns

I have two lists in a file that look like a b b a e f c d f e d c I would like a final list a b c d e f I've tried multiple grep and awk but can't get it to work (8 Replies)
Discussion started by: godzilla07
8 Replies

5. Shell Programming and Scripting

How to search Multiple patterns in unix

Hi, I tried to search multiple pattern using awk trans=1234 reason=LN MISMATCH rec=`awk '/$trans/ && /'"$reason"'/' file` whenevr i tried to run on command promt it is executing but when i tried to implment same logic in shell script,it is failing i.e $rec is empty ... (6 Replies)
Discussion started by: ns64110
6 Replies

6. Shell Programming and Scripting

Search & Replace: Multiple Strings / Multiple Files

I have a list of files all over a file system e.g. /home/1/foo/bar.x /www/sites/moose/foo.txtI'm looking for strings in these files and want to replace each occurrence with a replacement string, e.g. if I find: '#@!^\&@ in any of the files I want to replace it with: 655#@11, etc. There... (2 Replies)
Discussion started by: spacegoose
2 Replies

7. Shell Programming and Scripting

Grep from multiple patterns multiple file multiple output

Hi, I want to grep multiple patterns from multiple files and save to multiple outputs. As of now its outputting all to the same file when I use this command. Input : 108 files to check for 390 patterns to check for. output I need to 108 files with the searched patterns. Xargs -I {} grep... (3 Replies)
Discussion started by: Diya123
3 Replies

8. Shell Programming and Scripting

Search patterns in multiple logs parallelly.

Hi All, I am starting a service which will redirect its out put into 2 logs say A and B. Now for succesful startup of the service i need to search pattern1 in log A and pattern2 in log B which are writen continuosly. Now my requirement is to find the patterns in the increasing logs A and B... (19 Replies)
Discussion started by: Girish19
19 Replies

9. Shell Programming and Scripting

Search Multiple patterns and display

Hi, I have scenario like below and need to search for multiple patterns Eg: Test Time Started= secs Time Ended = secc Green test Test Time Started= secs Time Ended = secc Green test Output: I need to display the text starting with Test and starting with Time... (2 Replies)
Discussion started by: weknowd
2 Replies

10. UNIX for Beginners Questions & Answers

Issue with search and replacing multiple items in multiple files

Im having an issue when trying to replace the first column with a new set of values in multiple files. The results from the following code only replaces the files with the last set of values in val.txt. I want to replace all the files with all the values. for date in {1..31} do for val in... (1 Reply)
Discussion started by: ncwxpanther
1 Replies

LEARN ABOUT DEBIAN

bp_search2tribe

BP_SEARCH2TRIBE(1p)					User Contributed Perl Documentation				       BP_SEARCH2TRIBE(1p)

NAME

       search2tribe - Turn SearchIO parseable reports(s) into TRIBE matrix

SYNOPSIS

       Usage:
	 search2tribe [-o outputfile] [-f reportformat] [-w/--weight] file1 file2 ..

DESCRIPTION

       This script is probably too slow for most people's uses.  It is better to use something like scripts/searchio/fastam9_to_table, -m 9 output
       from BLAST, or the blast2table from the BLAST O'Reilly book to get a tabular output from these programs and then feed the table into MCL
       with the mcxdeblast script and the --m9 option.

       This script will turn a protein Search report (BLASTP, FASTP, SSEARCH) into a Markov Matrix for TribeMCL clustering.

       The options are:

	  -o filename	       - the output filename [default STDOUT]
	  -f format	       - search result format (blast, fasta)
				 (ssearch is fasta format). default is blast.
	  -w or --weight VALUE - Change the default weight for E(0.0) hits
				 to VALUE (default=200 (i.e. 1e-200) )
	  -h		       - this help menu

       Additionally specify the filenames you want to process on the command-line.  If no files are specified then STDIN input is assumed.  You
       specify this by doing: search2tribe < file1 file2 file3

AUTHOR

       Jason Stajich, jason-at-bioperl-dot-org

perl v5.14.2							    2012-03-02						       BP_SEARCH2TRIBE(1p)
All times are GMT -4. The time now is 03:03 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy