Hi jvoot,
The code in the other thread I pointed to in post #2 in this thread had to keep a counter of the number of lines in a file that had the same keys. As long as you treat both fields of a line from File 1 as a single key (the two subscripts I used in the Keys[] array), it should correctly deal with the problem you were having in your code. Your problem seems to be caused by the fact that you're using two arrays (A[], and B[]) instead of just one array to keep track of the fact that you need an entry from $1 in File 1 and an entry from $2 in File 1 that come from the same line.

Did you try running the code I suggested in post #5? Didn't it give you the output you want? If you tried the different portion of File 2 you showed us in post #6, didn't the code I suggested in post #5 still give you the output you wanted?

Since you have changed the code you originally showed us (based on MadeInGermany's suggestions) without showing us your modified code, I can't comment on what else might need to be done to make it work with your updated requirements.

Note that since your original sample File 2 contents included the "record":

Code:

 PS005,012 [W-<Cj>] [L-<LM <Ti>] [NCBXWN-<Pr>] [K <Ob>]
 Lexeme     W      # L <LM      # CBX         # K      #
 PhraseType  6(6) 5(5,2.2) 1(1:1) 7(7)
 PhraseLab  509[0]   506[0]       501[0]        503[0]
 ClauseType WxY0 PS005,013 [>JK SKR> MQBLT> <Aj>] [T<VP-<Pr>] [NJ <Ob>]
 Lexeme     >JK SKR QBL          # <VP       # NJ      #
 PhraseType  5(5,2.3,13:62.3) 1(1:1) 7(7)
 PhraseLab  505[0]                 501[0]      503[0]
 ClauseType xYq0

which contains two lines starting with Cl and two lines matching $1=="Lexeme", I chose to make my code trigger off of the empty line between records instead of off of the ClauseType keyword that appears on multiple lines in some of your records. That may have made my code more difficult to understand and it led me to create a function to print selected output "record"s since I assume that there is no empty line after the last "record" in File 2. Calling that function when NF==0 happens on the empty line between records and calling that function in the END clause handles the case of the last record in an input file not being followed by an empty line.

If my code does what you want with your new sample input file, I'll be happy to try to explain how it works. If it doesn't work for you, then I still don't understand what you're trying to do and I won't be able to help you until I can understand requirements (i.e. specifications) for the software you're trying to write.

We could also look at the code Scrutinizer suggested, but we'd have to make it a little more complex to be sure that it looks for "<Co>" on the first line (and only on the first line) of each multi-line record and to be sure that it only looks for a match for field 2 from File 1 on lines that have "Lexeme" as the first word on a line (his code is currently looking for a match on any word in the entire multi-line record; not just on the "Lexeme" line).

Please understand that we know you have a non-computer science background and we respect that. But to write software that does what you want it to, a computer expects extremely picky details about the data it is asked to process to be clearly specified. If you can't do that, a computer will be very happy giving you results that match what you said you wanted instead of results that match what you really want. I tried to point out a couple of cases where what you said you wanted might not be what you really want, but only you can tell us whether some fields can appear anywhere or only in certain places, whether lines containing "Lexeme" can appear more than once (as in the example from you sample input above) or can only appear as the 2nd line of a multi-line "record" in your real data, etc., etc., etc.

P.S. If you'd like to play around with genes to find a cure for Type 1 diabetes, I'll be happy to write awk scripts for you to help you reach your goal.