The following assumes the entire text in a single scalar, and leaves lines starting with four >'s alone as well. 
s/^>>>(?!>)(?![^\n]*\n>>(?!>))/PYTHON_PROMPT/gm;

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Also, I'd prefer to avoid $1 if possible, for performance reasons.
That's a strange remark. You're willing to use regexes, and even Perl, but not $1, "for performance reasons". Apparently, performance is very important to you. In that case, you ought to use C - what you want to do isn't too hard in C.

In reply to Re: Using a regex to catch interpreters by Anonymous Monk
in thread Using a regex to catch interpreters by eastcoastcoder

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