Shell Programming and Scripting

I meant A[1] = $0 for the mapping part as I thought A is the array from split(). So that later A[$2] will get what I want by $2 as the key/subscript of the array. What did I miss?

Hello yifangt,

So here A[1] means array named A whose index is 1(digit one) and value is A[1]=current line of Input_file1. So now when you try to print A[$2] or A[$1] then it means it will look for $2/$1's value from current line from Input_file2 into array A(eg-->A[S00739A]) which is NOT present at all in array A. Thus it will NOT print anything then. Kindly do let me know if I was NOT clear, will try to explain more on same then.

Thanks,
R. Singh

split makes A[1] A[2] ...
Nothing that you can lookup via a column.
Your initial attempt would need a second array that is string-addressed.

Code:

awk 'FNR==NR {split($1, A, "_"); B[A[1]]=$0; next} {print B[$1], $2}' file1 file2

But now the output corresponds to file2.

Code:

awk 'FNR==NR {split($1, A, "_"); A[1]=$0; next} {print A[$1], $2}' file1 file2

Yes, A is the receiving array of the split() function. It has index values 1 .. 4 (which never will match $1 nor $2 in file2) and is overwritten for every line read from the input file, so after reading the entire file1 it will hold the last line in A[1] and the residual fields in A[2] till A[4], never to be matched by following records from file2.
Plus, with file2 being the last file worked upon, the output - should it be generated at all - would have four lines only.

I figured out the problem which should be:

Code:

awk 'FNR==NR {split($1, A, "_"); B[A[1]]=$0; next} {print B[$1],$2} ' file1 file2

Thanks again!
Aha, I am soooooo glad I got the same as MadeInGermany!

Thanks for all your input!

Are you aware that you don't get your desired output from post#1 with your approach in post#12?
It would yield four lines only, and all R1.fq.gz would have disappeared

Thanks RudiC!
I was too excited to notice the problem, which is a serious bug for sure.
Seems the files order must be changed because of the similarity of the _R1/R2.fq.gz file names.

Code:

awk 'FNR==NR {B[$1]=$2; next} split($1, A, "_"){print $0, B[A[1]]}' file2 file1

However, if I do not change the files order, how to fix this bug if possible, Please?
Thanks again!