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Old 04-16-2009, 07:50 AM   #1
bioinformatics_guy
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Bash test if pattern match of file exists


So I have an if loop which iterates through all files of form cluster_*

The problem is, if there are not files that match that pattern, my script trips up. What I'd like to do is, test whether any files match the pattern cluster_* and if so, continue.

What I was thinking is:

if [ -f cluster_* ] ; then
...
...
fi

but since it does not recognize cluster_* as a pattern, it searches exactly cluster_* . Any suggestions?
 
Old 04-16-2009, 07:59 AM   #2
colucix
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Maybe I don't get the exact problem. Are you trying to see if there are files whose name begins with "cluster_" inside specific directories? Why don't you use ls, if this is the case?
Code:
if ls cluster_* > /dev/null 2>&1
then
  echo cluster files found
else
  echo cluster files not found
fi
 
Old 04-16-2009, 09:16 AM   #3
bioinformatics_guy
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Maybe I don't get the exact problem. Are you trying to see if there are files whose name begins with "cluster_" inside specific directories? Why don't you use ls, if this is the case?

Yes, downstream in my script, I use the files in a for loop:

for zzCLUSTERS in cluster_*; do

cat "${zzCLUSTERS}" | tr '/' ' ' | awk '{print $1}' | sort | uniq | cat > reads."${zzCLUSTERS}"

done

But if there are no matches for cluster_*, it enters cluster_\* into ${zzCLUSTERS} , which throws off my script which is why I wanted this test.

Would you mind explaining the syntax to me?

if ls cluster_* > /dev/null 2>&1

I'm use to seeing if statements as

if [ ] ;

and > as a redirect

what does /dev/null mean and what does

2>&1 mean?
 
Old 04-16-2009, 11:17 AM   #4
colucix
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Ok. The if statement can be used to test an expression enclosed in square bracket or to test the result of a command, as in my example. You know about the exit code of a command? Any command in linux has an exit code, which is usually 0 if the command had success, a value different than 0 (in most cases 1) if the command failed.

You can retrieve the exit code explicitly using
Code:
$ command
$ echo $?
where $? is a special variable storing the exit code of the previous command.

The if ls statement test the result of the ls command based on its exit code: if it is successful the commands inside the if/then block are executed, otherwise they are skipped. The
Code:
> /dev/null 2>&1
just redirect the standard output to /dev/null, which is a sort of black hole in unix systems. This prevent the output to be shown in the terminal, since you're not really intersted to visualize the list of files. The 2>&1 just redirect the standard error to the standard output, so that even the error message (when no file is found) is not displayed. Hope it is clear now.
 
Old 04-17-2009, 06:42 AM   #5
Valery Reznic
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Quote:
Originally Posted by bioinformatics_guy View Post
So I have an if loop which iterates through all files of form cluster_*

The problem is, if there are not files that match that pattern, my script trips up. What I'd like to do is, test whether any files match the pattern cluster_* and if so, continue.

What I was thinking is:

if [ -f cluster_* ] ; then
...
...
fi

but since it does not recognize cluster_* as a pattern, it searches exactly cluster_* . Any suggestions?
Code:
shopt nullglob
In this case filename expansion for noon-exist filenames will be empty string
 
  


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