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use strict;
use warnings;
...
  or warn "Could not close input file 1 '$input_file': $!";
close $out_fh
  or warn "Could not close output file '$output_file': $!";

perl -wlpe 'if(!/^2/){substr($_,99,1,"9");substr($_,148,1,"Z");}' <in.
+dat >out.dat