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Bash syntax error

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# 1  
Old 09-16-2014
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
# 2  
Old 09-16-2014
The 'foreach f' looks like you're trying to translate an MSDOS 'foreach /f' loop.

Code:
for f in docking"$line".[0-9][0-9][0-9]
do
        echo "$f"
done

# 3  
Old 09-16-2014
Code:
  set a=`grep ENDMDL my_docking.pdb | wc -l`
    set b=`expr $a - 2`
    csplit -k -s -n 3 -f my_docking. mydocking.pdb '/^ENDMDL/+1' '{'$b'}'
    foreach f ( mydocking.[0-9][0-9][0-9] )
      mv $f $f.pdb
    end

This is a code I know works.

The only thing I changed was to add a loop over the strings in file file.

So I think the problem is the way $line is passed through.

What's the difference between

Code:
$line, "$line" and '$line'

?
# 4  
Old 09-16-2014
Quote:
Originally Posted by chrisjorg
Code:
  set a=`grep ENDMDL my_docking.pdb | wc -l`
    set b=`expr $a - 2`
    csplit -k -s -n 3 -f my_docking. mydocking.pdb '/^ENDMDL/+1' '{'$b'}'
    foreach f ( mydocking.[0-9][0-9][0-9] )
      mv $f $f.pdb
    end

This is a code I know works.

The only thing I changed was to add a loop over the strings in file file.

So I think the problem is the way $line is passed through.

What's the difference between

Code:
$line, "$line" and '$line'

?
Sorry, but we don't believe you. The foreach is not valid bash syntax. Are you sure you didn't run the above code which a csh derivative instead of with bash?

And, yes, you also need to change single quotes in '$line' to double quotes "$line" throughout your script (as Corona688 suggested in his replacement for your foreach loop).
# 5  
Old 09-16-2014
The first thing I've noticed is the missing shebang/hashbang (something like #!/bin/bash) in the very first line.

cd /$line/ I think the first slash should be removed, unless you're running this script from the root "/" directory.

set a=`grep ENDMDL my_docking.pdb | wc -l` should not work in bash. Try a=`grep ENDMDL my_docking.pdb | wc -l` instead.

Demonstration:
Code:
$ set a=`uname`
$ echo $a

$ a=`uname`
$ echo $a
Linux
$

Quote:
Originally Posted by chrisjorg
What's the difference ...
$line: variable will expand
"$line": variable will expand safely, e.g. preserving whitespaces in filenames (good practice + recommended)
'$line': variable will *not* expand, it's treated as a *literal* string $line

Demonstration:
Code:
$ test -d "VirtualBox VMs"
$ echo $?
0
$ 
$ for name in "VirtualBox VMs"; do ls $name; done
ls: cannot access VirtualBox: No such file or directory
ls: cannot access VMs: No such file or directory
$ 
$ for name in "VirtualBox VMs"; do ls "$name"; done
testvm1
$ 
$ for name in "VirtualBox VMs"; do ls '$name'; done
ls: cannot access $name: No such file or directory
$

Most likely, '{'$b'}' also needs to be replaced by either ${b} or "$b"

HTH
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