Print lines in one file matching patterns in another file
Here's how to do it in awk:
awk 'NR==FNR{pats[$0]; next} $2 in pats' File2 File1
Using a 60,000 line File1 (your File1 repeated 8000 times) and a 6,000 File2 (yours repeated 1200 times):
$ time grep -Fwf File2 File1 > ou2real 0m0.094suser 0m0.031ssys 0m0.062s$ time awk 'NR==FNR{pats[$0]; next} $2 in pats' File2 File1 > ou1real 0m0.094suser 0m0.015ssys 0m0.077s$ diff ou1 ou2
i.e. it's about as fast as the grep. One thing to note though is that the awk solution lets you pick a specific field to match on so if anything from File2 shows up anywhere else in File1 you won't get a false match. It also lets you match on a whole field at a time so if your target strings were various lengths and you didn't want "scign000003" to match "scign0000031" for example (though the -w for grep gives similar protection for that).
For completeness, here's the timing for the other awk solution posted elsethread:
$ time awk 'BEGIN{i=0}FNR==NR{a[i++]=$1;next}{for(j=0;j<i;j++)if(index($0,a[j]))print $0}' File2 File1 > ou3real 3m34.110suser 3m30.850ssys 0m1.263s
and here's the timing I get for the perl script Mark posted:
$ time ./go.pl > out2real 0m0.203suser 0m0.124ssys 0m0.062s
You could try with this awk:
awk 'BEGIN{i=0}FNR==NR { a[i++]=$1; next }{ for(j=0;j<i;j++) if(index($0,a[j])) {print $0;break}}' file2 file1
The FNR==NR
part specifies that the stuff following it in curly braces is only to be applied when processing the first input file (file2
). And it says to save all the words you are looking for in an array a[]
. The bit in the second set of curly braces applies to the processing of the second file... as each line is read in, it is compared with all elements of a[]
and if any are found, the line is printed. That's all folks!