I'm with Belgarion -- you must have made some mistakes pasting the code into your post, because there are some real problems -- you're not only missing curly bracket here or there; you also have two copies of the "open" statements for reading "$qnum.tmp" and writing "$qnum.axe" (one outside a while loop, and another inexplicably inside the loop). And you have a regex like this:

    s/^col.//gi;
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Just a bit of a nit-pick, but when the regex is anchored to the start of the string (using "^"), the "g" modifier at the end is kinda pointless. The fact that you're using "g" everywhere makes me wonder if you understand its purpose. (browse through the "perlre" man page)

The whole two-pass design is a bit mysterious -- I'd be surprised if this cannot be done in a single pass (read .txt, write .axe, without the intermediary .tmp file). It might be instructive to provide a snippet of the "txt" input, and the equivalent snippet of intended output. (And if that output was really created by a perl script, post that script.)