CODEWITHSUNDEEP
awk
sara
sara

Reputation: 93

compare two columns of two files and give conditional

File 1:

chr pos1 sample Gene
chr1 123 sample1 x
chr1 234 sample2 Y
chr2 345 sample2 z

File 2:

sample Gene chr pos1 
sample1 x chr1 123 
sample2 A chr1 234 
sample2 c chr3 123 
sample2 z chr2 345

I used awk 'NR==FNR{A[$1,$2]++;next}A[$3,$4]'file1 file2 to get the common result, like wise i tried 

awk 'NR==FNR{A[FNR]=[$1,$2]++;next}{print A[$3,$4]==A[FNR] ? $0"\t"1 :$0"\t"0}' file1 file2

but getting error.

Upvotes: 0

Views: 248

Answers (1)

nu11p01n73R
nu11p01n73R

Reputation: 26667

print A[$3,$4]==A[FNR]`

is wrong as in the firest action you used FNR as index and here you are using `$3,$4

`A[FNR]=[$1,$2]++;`

i didnt understand you use ++ here??

You should be using something line

awk 'NR==FNR{A[FNR]=$0;}NR!=FNR{split(A[FNR],line); if (line[1] == $3 && line[2]==$4) print $0 1; else print $0 0}' file1 file2

which will give an output as 

sample Gene chr pos1 1
sample1 x chr1 123 1
sample2 A chr1 234 1
sample2 c chr3 123 0
sample2 z chr2 345 0

Here for the first file, NR==FNR the entire line is copied to arrray A and for the second file when NR!=FNR the array is splited split and checked with $3 and $4

Upvotes: 1

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