In addition to what toolic says above, I'd point out you have a second instance of the bug he points out from line 17 on line 37 (%ref = ($1=>$2,); instead of $ref{$1} = $2;).

You also have a lot of nested loops - For each line in REF you cycle over all keys in %ref. This algorithm will result in a large number of identical lines in your output file. I cannot really judge whether this is appropriate, though, since I have a little difficulty following your description. To make it more clear, post an example of input and expected output (wrapped in <code> tags to maintain format). An example is worth 1,000 words. See How do I post a question effectively?.