Like pERL CALLING lINUX COMMANDS SEQUENTIALLY your title messed up, are you having problems with you caps and shift keys? Here (like previous posts) you're not actually asking a question. If all you want to do is call linux commands why involve Perl at all, since you seeming don't want to use any of it's features? Again, please read and understand How do I post a question effectively?. Since you don't seem to know basic perl I suggest spending time learning from the following:

• perlintro
• http://learn.perl.org
• http://perldoc.perl.org
• The tutorials section of this site

Nothing wrong with cut or calling unix commands in general but may as well use the normal Perl commands once you've started. In particular, look into split so for each file you could do something like:

@a = split(/\t/);
print "$a[0]\t$a[1]\t$a[12]\t$a[11]\n";
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Hi, let's suppose we have tab-separated data like that in the lines after the __DATA__ token and we want to swap columns two and three:

use strict;
use warnings;

while (<DATA>) {    # go through data line by line
    chomp;          # don't forget to remove newline character
    my @fields = split /\t+/;
    print join "\t",           # join fields with tab
          @fields[ 0, 2, 1 ],  # select fields using array slice
          "\n";
}

__DATA__
Col1    Col2    Col3
a       b       c
1       2       3
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To work with files, just

• add $^I = ".bak"; before the while loop to edit files in place keeping backups
• replace <DATA> with <> (diamond operator)

and then run the program like this:

$ perl script.pl *.dat
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