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  $myfile =~ s!([A-Z]+)!<i>$1</i>!g;

  $ perl -lwe '$_="hi MOM and DAD"; print;
               s!([A-Z]+)!<i>$1</i>!g; print'
  hi MOM and DAD
  hi <i>MOM</i> and <i>DAD</i>

  $myfile =~ s!\b([A-Z]+)\b!<i>$1</i>!g;

  perl -i~ -plwe 's/mom/dad/g' *.txt

  open my $fh, "source-data.txt"
    or die "opening source-data.txt: $!";
...
  print $fh "</blockquote>\n";
  close $fh
    or die "closing source-data.txt: $!";

  while ( <$fh> )
  {
...
      # output the result
      print $fh $_;
  }