awk,compare,match,mismatch , Compare two files and append the values, leave the mismatches as such in the output file


Compare two files and append the values, leave the mismatches as such in the output file

Question:

Tag: awk,compare,match,mismatch

I'm trying to match two files,file1.txt(50,000 lines), file2.txt(55,000 lines). I want to campare file2 to file 1 extract the values of column 2 and 3 and leave the mismatches as such. Output file must contain all the ids from file2 i.e., it should have 55000 lines. Note: All the ids in file 1 are not present in file2. i.e the actual matches could be less than 50,000.

file1.txt

ab1 12 345  
ab2 9 456  
gh67 6 987  

file2.txt

ab2 0 0  
ab1 0 345  
nh7 0 0  
gh67 6 987  

Output

ab2 9 456  
ab1 12 345  
nh7 0 0  
gh67 6 987 

This is what i tried but it only print the matches (so instead of 55,000 lines i have 49,000 lines in my output file)

awk "NR==FNR {f[$1]=$0;next}$1 in f{print f[$1],$0}" file1.txt file2.txt >output.txt

Answer:

This awk script will work

NR == FNR {
    a[$1] = $0
    next
}
$1 in a {
    split(a[$1], b)
    print $1, (b[2] == $2 ? $2 : b[2]), (b[3] == $3 ? $3 : b[3])
}
!($1 in a)

If you save this as a.awk and run

awk -f a.awk foo.txt foo1.txt

This will output

ab2 9 456
ab1 12 345
nh7 0 0
gh67 6 987

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