Good general advice, but but profiling the OPs code won't tell you anything that isn't readily apparent from a cursory inspection.

Matching N elements from one file against M elements from a second, by iterating through an array containing the M elements--and respliting each element each time through--it is obvious enough where the problems lie.

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.
"Too many [] have been sedated by an oppressive environment of political correctness and risk aversion."

In reply to Re^2: tips on how to speed up a very slow perl script requested by BrowserUk
in thread tips on how to speed up a very slow perl script requested by Angharad

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