You've got two nested loops, and you're reading the *entire* second file before reading the next line of the first file. But since the second file has been read in its entirety, the second loop will fail from that point on.
There are a good few approaches you could use:
- Read both files into an array and iterate over the arrays. (Easy, but "inelegant".)
- Sort both input files by the matching column and then use a single loop, consuming the line having the lowest key value. (A *little* tricky.)
- Rewind/reopen the second file each iteration. (Ugly.)
- Read both files into hashes using your key column as the hash key, and then process the hashes. (Usually a good way, but your data has duplicate keys, so it wouldn't be very helpful in this case.)
In this case, I'm thinking you'll probably be best off with the first suggestion.
Update: You may want to put a few print statements in your program so you can see what's happening.
When your only tool is a hammer, all problems look like your thumb.
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