From 'rs#####' I suspect you're dealing with biology-related stuff, what is the file format if any, better still, show how the template looks like and how you want your output looking like, show your attempts, and then it will only be possible to provide you better guidance. The key is, clearly worded question with efforts displayed yield more accurate responses from the generous monks out here..
in reply to I need a perl script to make every instance of a repeated word unique
Go through How do I post a question effectively? and Perl and Bioinformatics ...
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