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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?

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up vote 14 down vote accepted

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
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Thanks for the tip, but it just produced: grep: -: No such file or directory – The Unfun Cat Aug 4 '13 at 6:20
@TheUnfunCat Try it without xargs – Joseph R. Aug 4 '13 at 6:22
Didn't work unfortunately. Same error. – The Unfun Cat Aug 4 '13 at 6:24
If you're not using gnu grep, try -f /dev/stdin instead of -f - – rici Aug 4 '13 at 6:30
You can also use bash's <() syntax: grep -f <(awk ...) os_clusters/piRNA_clusters.bed – rici Aug 4 '13 at 6:33

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