In general, when you want to use keys from one file to lookup values in another file, you load the keys from one file into a hash as its keys, then loop through the other file checking to see if each line's key exists in the hash, and doing something with it if it is. Unless there's a reason to do otherwise, it's usually best to load the smaller file (in this case your 5K one) into the hash, then loop through the other file. So in pseudo-code:

open 5k file
foreach line
  get key from line and put it in hash as key=1
close 5k file

open 100M file
foreach line
  get key from line
  if key is in hash from other file
    do stuff with the line
close 100M file
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Once you have some code which attempts to do that, show it to us along with a few lines of sample input and output data, and we can guide you further if you need it.