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use strict;
open sourcefile, '<', "source.cbl" or die "Can't open: $!";
...
        print targetfile $line;
    } elsif ($line =~ s/PROGRAM -BEGIN\./begin/) {
        print targetfile $line;

use strict;
use warnings;
...
    $line =~ s/$_-[0]/$_->[1]/ for @pairs;
    print targetfile $line;
}