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Top Forums UNIX for Dummies Questions & Answers Use variables for cut command Post 302887781 by bakunin on Monday 10th of February 2014 06:22:58 PM
Old 02-10-2014
Quote:
Originally Posted by Gussifinknottle
#RudiC: I am just not getting an output as I ran it.
There is no output to expect. The script as you showed it writes a lot of output files and you will have to examine these for any output.

Quote:
Originally Posted by Gussifinknottle
#bakunin: I tried running your code as well; no output here either.
If there is no output (that is: none of the files to be expected) then your input file (matrix.pair.cols) isn't even read. Make sure the file is accessible, in the directory you expect it to be (in your script this is the current directory, regardless of where the script may be). Modify your script further to test this:

Code:
#!/bin/sh

input="matrix.pair.cols"

if [ ! -r $input ] ; then
     echo "ERROR: file $input not readable or not existing at all"
     exit 2
fi

while read p q r ; do
	echo p: \"$p\"    q: \"$q\"    r: \"$r\"
	echo "cut -f \"$q,$r\" matrix > $p.cols"
done < matrix.pair.cols

exit 0

I hope this helps.

bakunin
 

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SHELL-QUOTE(1p) 					User Contributed Perl Documentation					   SHELL-QUOTE(1p)

NAME
shell-quote - quote arguments for safe use, unmodified in a shell command SYNOPSIS
shell-quote [switch]... arg... DESCRIPTION
shell-quote lets you pass arbitrary strings through the shell so that they won't be changed by the shell. This lets you process commands or files with embedded white space or shell globbing characters safely. Here are a few examples. EXAMPLES
ssh preserving args When running a remote command with ssh, ssh doesn't preserve the separate arguments it receives. It just joins them with spaces and passes them to "$SHELL -c". This doesn't work as intended: ssh host touch 'hi there' # fails It creates 2 files, hi and there. Instead, do this: cmd=`shell-quote touch 'hi there'` ssh host "$cmd" This gives you just 1 file, hi there. process find output It's not ordinarily possible to process an arbitrary list of files output by find with a shell script. Anything you put in $IFS to split up the output could legitimately be in a file's name. Here's how you can do it using shell-quote: eval set -- `find -type f -print0 | xargs -0 shell-quote --` debug shell scripts shell-quote is better than echo for debugging shell scripts. debug() { [ -z "$debug" ] || shell-quote "debug:" "$@" } With echo you can't tell the difference between "debug 'foo bar'" and "debug foo bar", but with shell-quote you can. save a command for later shell-quote can be used to build up a shell command to run later. Say you want the user to be able to give you switches for a command you're going to run. If you don't want the switches to be re-evaluated by the shell (which is usually a good idea, else there are things the user can't pass through), you can do something like this: user_switches= while [ $# != 0 ] do case x$1 in x--pass-through) [ $# -gt 1 ] || die "need an argument for $1" user_switches="$user_switches "`shell-quote -- "$2"` shift;; # process other switches esac shift done # later eval "shell-quote some-command $user_switches my args" OPTIONS
--debug Turn debugging on. --help Show the usage message and die. --version Show the version number and exit. AVAILABILITY
The code is licensed under the GNU GPL. Check http://www.argon.org/~roderick/ or CPAN for updated versions. AUTHOR
Roderick Schertler <roderick@argon.org> perl v5.8.4 2005-05-03 SHELL-QUOTE(1p)
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