How to recursively search directories for a pattern and just print out file names and line numbers

grep

Currently I am using grep as follows:

grep -lr <PATTERN> .

This gives me the following output, containing a list of all files whose contents (not name) contain :

./path/to/file1
./path/to/file2
...

This is okay but knowing the line numbers would be useful. The following output would be ideal but having gone through the man page for grep, I can't seem to figure out the right switches:

./path/to/file1 15, 22, 54
./path/to/file2 16, 17
...

Is this possible with grep or some other tool?

Best Answer

ack does something similar by default. you can use

$ ack blah
path/to/blah
16: blah blah
19: blah blah blah

path/to/more/blah
21: blahness

If you just want the file names that match you can say ack -l. ack -lc will give you number of matches per file.

Using grep

Why can't you just use the -r switch to grep to recurse the filesystem instead of making use of find? There are 2 additional switches I'd use too, instead of the -n switch.

$ grep -rHn PATTERN <DIR> | cut -d":" -f1-2

Example #1

$ grep -rHn PATH ~/.bashrc | cut -d":" -f1-2
/home/saml/.bashrc:25

Details

-r - recursively search through files + directories
-H - prints the name of the file if it matches (less restrictive than -l) i.e. it works with grep's other switches
-n - display the line number of the match

Example #2

$ grep -rHn PATH ~/.bash* | cut -d":" -f1-2
/home/saml/.bash_profile:10
/home/saml/.bash_profile:12
/home/saml/.bash_profile_askapache:99
/home/saml/.bash_profile_askapache:101
/home/saml/.bash_profile_askapache:118
/home/saml/.bash_profile_askapache:166
/home/saml/.bash_profile_askapache:218
/home/saml/.bash_profile_askapache:250
/home/saml/.bash_profile_askapache:314
/home/saml/.bash_profile_askapache:2317
/home/saml/.bash_profile_askapache:2323
/home/saml/.bashrc:25

Using find

$ find . -exec sh -c 'grep -Hn PATTERN "$@" | cut -d":" -f1-2' {}  +

Example

$ find ~/.bash* -exec sh -c 'grep -Hn PATH "$@" | cut -d":" -f1-2' {}  +
/home/saml/.bash_profile:10
/home/saml/.bash_profile:12
/home/saml/.bash_profile_askapache:99
/home/saml/.bash_profile_askapache:101
/home/saml/.bash_profile_askapache:118
/home/saml/.bash_profile_askapache:166
/home/saml/.bash_profile_askapache:218
/home/saml/.bash_profile_askapache:250
/home/saml/.bash_profile_askapache:314
/home/saml/.bash_profile_askapache:2317
/home/saml/.bash_profile_askapache:2323
/home/saml/.bashrc:25

If you truly want to use find you can do something like this to exec grep upon finding the files using find.

Grep Command – Troubleshooting Grep Errors

Since your gene names are always in the 2nd column of the file, you can use awk for this:

awk '
    {   ## while reading the first file, save name in the array a
        if(NR==FNR){a[$1]++;} 

        ## If this is the 2nd file
        else{
            ## print if the value of the second column is defined in the array 
            if($2 in a){print}
        }
    }' file1 file2

The same, condensed:

awk '{if(NR==FNR){a[$1]++;}else{if($2 in a){print}}}' file1 file2

more condensed:

awk '(NR==FNR){a[$1]++}($2 in a){print}' file1 file2

and truly minimalist (in answer to @Awk):

awk 'NR==FNR{a[$1]}$2 in a' file1 file2