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Old 02-19-2009, 10:31 AM   #1
bioinformatics_guy
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For loop in bash using ls to get array of file names


So I have a group of files of the form:

cluster_1 cluster_2 cluster_3 etc


CLUSTERS="ls cluster_*"

for zzCLUSTER in $CLUSTERS
do
cat "${zzCLUSTERS}" | tr '/' ' ' | uniq | cat > "${zzCLUSTERS}".reads
done

but for some reason this isent working? I've looked at like 50 examples and I can't seem to get it to work. It says that I can't redirect
 
Old 02-19-2009, 10:35 AM   #2
bioinformatics_guy
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Correction, this is the code I have essentially

clusterlist="ls cluster_*"

for zzCLUSTERS in "$clusterlist"
do
cat "${zzCLUSTERS}" | tr '/' ' '| cat > "${zzCLUSTERS}".reads
done

the error I'm getting is

cat: ls cluster_*: No such file or directory
 
Old 02-19-2009, 10:36 AM   #3
jschiwal
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Location: Fargo, ND
Distribution: SuSE AMD64
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You can use:
for zzCLUSTER in cluster_*; do
...
done

instead of
CLUSTERS=$(ls cluster_*)

You used double quotes instead of backticks or the $(...) form.
 
Old 02-19-2009, 10:41 AM   #4
bioinformatics_guy
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Thank you thank you thank you!

So what is the difference between " " , ' ' , and ` ` in bash? When should each be used?
 
Old 02-19-2009, 10:49 AM   #5
schneidz
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Code:
schneidz@lq /sp> ls temp
hello/        hello-c.s     hello-cc.s    hello-cpp.C   hello-cpp.x*
hello-c.C     hello-c.x*    hello-cc.x*   hello-cpp.s
schneidz@lq /sp> dir=temp
schneidz@lq /sp> echo "ls $dir"
ls temp
schneidz@lq /sp> echo 'ls $dir'
ls $dir
schneidz@lq /sp> echo `ls $dir`
hello/ hello-c.s hello-cc.s hello-cpp.C hello-cpp.x* hello-c.C hello-c.x* hello-cc.x* hello-cpp.s

Last edited by schneidz; 02-19-2009 at 10:50 AM.
 
Old 02-19-2009, 10:49 AM   #6
jschiwal
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Registered: Aug 2001
Location: Fargo, ND
Distribution: SuSE AMD64
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You can use:
for zzCLUSTER in cluster_*; do
...
done

instead of
CLUSTERS=$(ls cluster_*)

You used double quotes instead of backticks or the $(...) form.
 
  


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