Use the IO::InSitu module:

use IO::InSitu;

my ( $src, $dest ) = open_rw( 'my_file', 'my_file' );

while ( my $line = <$src> ) {
   # If this is the line you want to modify
   # Call a routine to modify either the minor or
   # major version, depending on the case in question
   # by modifying $line
   print {$dest} $line;
}
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Thanks to the Damian for this one!