#!/bin/sh
for A in file.txt
do
egrep 'pattern1' ${A}.txt > ${A}_p1.temp
egrep 'pattern2' ${A}.txt > ${A}_p2.temp
for B in *_p*.temp
do
C=`basename ${B} .temp`
D=`cut -c 5-15 ${C}`
awk '{print '"${D}"',$0}' ${A}_p1.temp >> allresults.tab
awk '{print '"${D}"',$0}' ${A}_p1.temp >> allresults.tab
done
exit;
1. egrep 'pattern1' ${A}.txt > ${A}_p1.temp --> Why have you given ${A}.txt? Is there a file by name "file.txt.txt"?
2. Why do you want to use for-loop for just one file "file.txt"?
3. Your first for-loop has a "do" but doesn't have a corresponding "done".
4. "exit" is really not required at the end because your script will end anyway. Use exit only if you want to abruptly terminate the program after some conditional check.
5. And please indent your script.
------------------------
Ah, methyl has already replied!
Last edited by balajesuri; 12-15-2011 at 07:03 AM..
Reason: Late reply
@lucasvs regarding post #3. Is it safe to assume that your error message has gone?
Read post #4 first. There are useful comments about filenames and whether the first "for" is needed.
It is quite difficult to advise on a script which is failing unless we know what the script is intended to achieve. It always helps to post sample input (blotting anything confidential) , brief description of the process, sample expected output.
I've just realised the second awk command has to look in ${A}_p2.temp (not p1).
Sorry methyl, I should have explained before.
Briefly, I try to:
1) find different patterns (more than 50 in total) in a text file (called file.txt),
2) extract them,
3) and put them in a same file called allresults.tab.
After adding the second "done", I don't have "unexpected end of file" error message.
Now it seems there is a problem with the cut command,
Code:
cut: file_p1: No such file or directory
and with the awk command:
Code:
awk: syntax error at source line 1
context is
{print >>> , <<<
awk: illegal statement at source line 1
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