Shell Programming and Scripting

Hello,

I am using Awk in UBUNTU 12.04.

I have a file like following with three fields and 44706 rows.
F1 A A
F2 G G
F3 A T

I have another file like this:

AL_1 F1 A A
AL_2 F1 A T
AL_3 F1 A A
AL_1 F2 G G
AL_2 F2 G A
AL_3 F2 G G
BO_1 F1 A A
BO_2 F1 A T
BO_1 F2 G A
BO_2 F2 G G
CO_1 F1 A T
CO_2 F1 T T
CO_1 F2 G G
CO_2 F2 G A

( I didn't write for F3 anymore but it contains F3 as well)

This sounds a bit complex. What I want to have is like this:

F1 A T
F2 G A
F3 A T

Sorry as this sounds complex. So, what I want to do is to look in the second file for a "F1" whose 3rd and 4th fields are not the same (i.e. A T instead of A A) and replace it in the first file for "F1".

So, for F2, F3 and the rest.

Thank you very much for any help.

Try this,

Code:

awk 'NR==FNR{Ar[$1$2$3]=1; next} !($2$3$4 in Ar){Ar[$2$3$4]=1;print $2,$3,$4}' file1 file2
F1 A T
F2 G A
F1 T T

Try:

Code:

awk 'NR==FNR&&$3!=$4{a[$2]=$3" "$4}NR==FNR{next}$1 in a{$2=a[$1];$3="";}1' file2 file1

Try

Code:

awk 'NR==FNR{X[$1]=$2" "$3;next}{if(X[$2]){split(X[$2],P," ")
if(P[1] == P[2]){if($3 != $4){print $2,$3,$4;delete X[$2]}}else{print $2,X[$2];delete X[$2]}}}' file1 file2

Sorry, but both bartus11's and pamu's code are missing the F1 T T record in your sample file.

But the output with bartus11 code is correct. I don't want all the lines of my second file and particularly, I don't want to have the same columns for a given F.

For example, I don't want to have T T for F1 but in stead if there is A T for F1, I want to have that in my output.

Thank you.

If your all file1 entries are present in file2 then my script will produce correct output as what you need.