One of the things that might go wrong is that you only read one line of $B_file, is this intensional?

Another potential problem is that you don't strip line endings from the line you read (no chomp) but write a \n to the output file nevertheless, so you may have an end-of-line too many.

And as pointed out above, the read operation might fail without you noticing since you don't check for errors after attempting to open $B_file.

Hope this helps, but yes, mentioning what kind of problems you have might help you even more ;) -gjb-