Bash syntax error Post: 302917443

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Top Forums Shell Programming and Scripting Bash syntax error Post 302917443 by chrisjorg on Tuesday 16th of September 2014 05:05:09 PM

09-16-2014

Registered User

Bash syntax error

Code:

while read line
do
    mkdir $line
    scp -r Docking_results/docking_$line.pdb $line/
    cd /$line/
    set a=`grep ENDMDL docking_'$line'.pdb | wc -l`
    set b=`expr $a - 2`
    csplit -k -s -n 3 -f docking_'$line'. docking'$line'.pdb '/^ENDMDL/+1' '{'$b'}'
    foreach f ( docking'$line'.[0-9][0-9][0-9] )
      mv $f $f.pdb
    end
    cd ..
done<file

When I run the above script I get an error in the foreach line:

Code:

./docking_cluster.sh: line 9: syntax error near unexpected token `('
./docking_cluster.sh: line 9: `    foreach f ( docking'$line'.[0-9][0-9][0-9] )'

I'm not sure how to pass the $line variable correctly.

File is a file containing a list of strings
$line is a particular string in file

chrisjorg

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