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you might use a shell wrapper, more fancy. And do all the shell processing you need, and then going back to perl with the final data.
Well if you only need to change |, why not:
$string=~ s/\|//g;
Assuming $string contains a text line of the file
The reason I am writing this in Perl because it will be part of other existing code that is written in Perl.
Which doesn't disprove what I've said - your solution has nothing to do with Perl. A solution in Perl would use Perl regular expressions or Perl built-in 'tr' or 'y' function.
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