I cannot use CPAN or any other libraries.
Actually, Yes, even you can use CPAN. If nothing else, you could copy code from a module and put it directly in your script, although you would not benefit from potential bug fixes, etc. (I would question why this artificial limitation exists, however.)
As to the main question, it seems like the easiest thing would be to first remove comment lines (using either regexes or, more likely, a state machine), then process the remainder.
Hope that helps.
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