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#!/usr/bin/perl

...

close $rfh or die "Can't close $filename : $!";
close $wfh or die "Can't close $newfile : $!";

perl -pi -e 'chomp;s/^(HEADER.*)$/${1}42/;s/^(REMARK.*)$/Extra line\n$
+1/;$_.="\n"' whateveryourfileiscalled.txt