Thanks a bunch for everyones comments.  Really appreciate it.  Here is what I am going to use:

The Ascii.txt looks something like this:

"X[6]" + "XM7"  + "Z_data[17]" + "Z[18][20]"
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Then the user supplied the mapping file

X[6] X_6_
XM7 X_7_
Z_data[17] Z_17_
Z[18][20] Z_18__20_
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Then my perl script looked like this:

#use strict;
#use warnings;
$regexp = table2;
$i =0;

open RE, $regexp;
while (<RE>) {
  chop;
  ($search[$i], $replace[$i]) = split(/ /, $_ );
  $search[$i] =~ s/\[/\\[/g;
  $search[$i] =~ s/\]/\\]/g;
  $i++;
}
  

while (<>) {
  for($i=0; $i < $#search; $i++) {
    s{$search[$i]}{$replace[$i]}g;
  }
  print;
}
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