Piping search term (not filename) to grep

Question

I want to pick out certain lines containing a given number from a file. The file I want to search is called os_clusters/piRNA_clusters.bed.

awk '{if (a[$0]++ == 0) {split($0,b,"."); ;split(b[1],c,"r"); print c[3]}};' test_non_enriched | xargs grep {} os_clusters/piRNA_clusters.bed

The first part, before the pipe, works- it produces the terms to search for, such as 8707, 8824 etc. However, the latter part does not.

awk '' ... | xargs grep {} os_clusters/piRNA_clusters.bed

Instead of searching the target file for the terms produced by the pipe, it considers the search terms as the input file. Hence, I get error messages like:

grep: 8707: No such file or directory
grep: 8824: No such file or directory

What do I need to change to search the file os_clusters/piRNA_clusters.bed for the terms produced by the pipe?

Answer 1

I think you want

... | grep -f - os_clusters/piRNA_clusters.bed

-f tells grep to obtain its search pattern from a file and - tells it that this file is actually stdin (the output of the pipe in your case).

Thanks to @rici's comment, for non-GNU grep use

... | grep -f /dev/stdin os_clusters/piRNA_clusters.bed