I am trying to grep 40k files in the current directory and i am getting this error.
for i in $(cat A01/genes.txt); do grep $i *.kaks; done > A01/A01.result.txt
-bash: /usr/bin/grep: Argument list too long
How do one normally grep thousands of files?
Thanks
Upendra
This makes David sad...
Everyone so far is wrong (except for anubhava).
Shell scripting is not like any other programming language because much of the interpretation of lines comes from the power of the shell interpolating them before the command is actually executed.
Let's take something simple:
$ set -x
$ ls
+ ls
bar.txt foo.txt fubar.log
$ echo The text files are *.txt
echo The text files are *.txt
> echo The text files are bar.txt foo.txt
The text files are bar.txt foo.txt
$ set +x
$
The set -x allows you to see how the shell actually interpolates the glob and then passes that back to the command as input. The > points to the line that is actually being executed by the command.
You can see that the echo command isn't interpreting the *. Instead, the shell grabs the * and replaces it with the names of the matching files. Then and only then does the echo command actually executes the command.
When you have 40K plus files, and you do grep *, you're expanding that * to the names of those 40,000 plus files before grep even has a chance to execute, and that's where the error message /usr/bin/grep: Argument list too long is coming from.
Fortunately, Unix has a way around this dilemma:
$ find . -name "*.kaks" -type f -maxdepth 1 | xargs grep -f A01/genes.txt
The find . -name "*.kaks" -type f -maxdepth 1 will find all of your *.kaks files, and the -depth 1 will only include files in the current directory. The -type f makes sure you only pick up files and not a directory.
The find command pipes the names of the files into xargs and xargs will append the names of the file to the grep -f A01/genes.txtcommand. However, xargs has a trick up it sleeve. It knows how long the command line buffer is, and will execute the grep when the command line buffer is full, then pass in another series of file to the grep. This way, grep gets executed maybe three or ten times (depending upon the size of the command line buffer), and all of our files are used.
Unfortunately, xargs uses whitespace as a separator for the file names. If your files contain spaces or tabs, you'll have trouble with xargs. Fortunately, there's another fix:
$ find . -name "*.kaks" -type f -maxdepth 1 -print0 | xargs -0 grep -f A01/genes.txt
The -print0 will cause find to print out the names of the files not separated by newlines, but by the NUL character. The -0 parameter for xargs tells xargs that the file separator isn't whitespace, but the NUL character. Thus, fixes the issue.
You could also do this too:
$ find . -name "*.kaks" -type f -maxdepth 1 -exec grep -f A01/genes.txt {} \;
This will execute the grep for each and every file found instead of what xargs does and only runs grep for all the files it can stuff on the command line. The advantage of this is that it avoids shell interference entirely. However, it may or may not be less efficient.
What would be interesting is to experiment and see which one is more efficient. You can use time to see:
$ time find . -name "*.kaks" -type f -maxdepth 1 -exec grep -f A01/genes.txt {} \;
This will execute the command and then tell you how long it took. Try it with the -exec and with xargs and see which is faster. Let us know what you find.
You can combine find with grep like this:
find . -maxdepth 1 -name '*.kaks' -exec grep -H -f A01/genes.txt '{}' \; > A01/A01.result.txt
you can use recursive feature of grep:
for i in $(cat A01/genes.txt); do
grep -r $i .
done > A01/A01.result.txt
though if you want to select only kaks files:
for i in $(cat A01/genes.txt); do
find . -iregex '.*\.kaks$' -exec grep $i \;
done > A01/A01.result.txt
Put another for loop inside your outer one:
for f in *.kaks; do
grep -H $i "$f"
done
By the way, are you interested in finding EVERY occurrence in each file, or merely if the search string exists in there one or more times? If it is "good enough" to know the string occurs in there one or more times you can specify "-n 1" to grep and it will not bother reading/searching the rest of the file after finding the first match, which could potentially save lots of time.
The following solution has worked for me:
Problem:
grep -r "example\.com" *
-bash: /bin/grep: Argument list too long
Solution:
grep -r "example\.com" .
["In newer versions of grep you can omit the “.“, as the current directory is implied."]
Source:
Reinlick, J. https://www.saotn.org/bash-grep-through-large-number-files-argument-list-too-long/
Related
Trying to find a word/pattern contained within the resulting file names of the find command.
For instance, I have this command:
find . -name Gruntfile.js that returns several file names.
How do I grep within these for a word pattern?
Was thinking something along the lines of:
find . -name Gruntfile.js | grep -rnw -e 'purifycss'
However, this is doesn't work..
Use the -exec {} + option to pass the list of filenames that are found as arguments to grep:
find -name Gruntfile.js -exec grep -nw 'purifycss' {} +
This is the safest and most efficient approach, as it doesn't break when the path to the file isn't "well-behaved" (e.g. contains a space). Like an approach using xargs, it also minimises the number of calls to grep by passing multiple filenames at once.
I have removed the -e and -r switches, as I don't think that they're useful to you here.
An excerpt from man find:
-exec command {} +
This variant of the -exec action runs the specified command on the selected files, but the command line is built by appending each selected file name at the end; the total number of invocations of the command will be much less than the number of matched files.
While this doesn't strictly answer your question, provided you have globstar turned on (shopt -s globstar), you could filter the results in bash like this:
grep something **/Gruntfile.js
I was using religiously the approach used by Tom Fenech until I switched to zsh, which handles such things much better. Now all I do is:
grep text **/*(.)
which greps text through all regular files in current directory.
I believe this to be much cleaner syntax especially for day-to-day work in shell.
When too many files exist for the * expansion to run:
$ grep -o 'xxmaj\|xxbos\|xxfld' train/* | wc -l
-bash: /bin/grep: Argument list too long
0
Then this code fixes the “too long” problem:
$ find junk -maxdepth 1 -type f | xargs grep -o 'TVDetails\|xxmaj\|xxbos\|xxfld'
junk/gum-.doc.out:TVDetails
junk/Zv0n.doc.out:TVDetails
$ find junk -maxdepth 1 -type f | xargs grep -o 'TVDetails\|xxmaj\|xxbos\|xxfld' | wc -l
2
It runs faster on my system, and maybe yours, when using the -P 0 option:
$ /usr/bin/time -f "%E Elapsed Real Time" find train -maxdepth 1 -type f | xargs -P 0 grep -o 'TVDetails\|xxmaj\|xxbos\|xxfld' | wc -l
0:02.45 Elapsed Real Time
358
$ /usr/bin/time -f "%E Elapsed Real Time" find train -maxdepth 1 -type f | xargs grep -o 'TVDetails\|xxmaj\|xxbos\|xxfld' | wc -l
0:11.96 Elapsed Real Time
358
Hope this helps.
I want to make a search for all .fits files that contain a certain text in their name and then copy them to a directory.
I can use a command called fetchKeys to list the files that contain say 'foo'
The command looks like this : fetchKeys -t 'foo' -F | grep .fits
This returns a list of .fits files that contain 'foo'. Great! Now I want to copy all of these to a directory /path/to/dir. There are too many files to do individually , I need to copy them all using one command.
I'm thinking something like:
fetchKeys -t 'foo' -F | grep .fits > /path/to/dir
or
cp fetchKeys -t 'foo' -F | grep .fits /path/to/dir
but of course neither of these works. Any other ideas?
If this is on Linux/Unix, can you use the find command? That seems very much like fetchkeys.
$ find . -name "*foo*.fit" -type f -print0 | while read -r -d $'\0' file
do
basename=$(basename $file)
cp "$file" "$fits_dir/$basename"
done
The find command will find all files that match *foo*.fits in their name. The -type f says they have to be files and not directories. The -print0 means print out the files found, but separate them with the NUL character. Normally, the find command will simply return a file on each line, but what if the file name contains spaces, tabs, new lines, or even other strange characters?
The -print0 will separate out files with nulls (\0), and the read -d $'\0' file means to read in each file separating by these null characters. If your files don't contain whitespace or strange characters, you could do this:
$ find . -name "*foo*.fit" -type f | while read file
do
basename=$(basename $file)
cp "$file" "$fits_dir/$basename"
done
Basically, you read each file found with your find command into the shell variable file. Then, you can use that to copy that file into your $fits_dir or where ever you want.
Again, maybe there's a reason to use fetchKeys, and it is possible to replace that find with fetchKeys, but I don't know that fetchKeys command.
Copy all files with the name containing foo to a certain directory:
find . -name "*foo*.fit" -type f -exec cp {} "/path/to/dir/" \;
Copy all files themselves containing foo to a certain directory (solution without xargs):
for f in `find . -type f -exec grep -l foo {} \;`; do cp "$f" /path/to/dir/; done
The find command has very useful arguments -exec, -print, -delete. They are very robust and eliminate the need to manually process the file names. The syntax for -exec is: -exec (what to do) \;. The name of the file currently processed will be substituted instead of the placeholder {}.
Other commands that are very useful for such tasks are sed and awk.
The xargs tool can execute a command for every line what it gets from stdin. This time, we execute a cp command:
fetchkeys -t 'foo' -F | grep .fits | xargs -P 1 -n 500 --replace='{}' cp -vfa '{}' /path/to/dir
xargs is a very useful tool, although its parametrization is not really trivial. This command reads in 500 .fits files, and calls a single cp command for every group. I didn't tested it to deep, if it doesn't go, I'm waiting your comment.
In the current directory, I'd like to print the filename and contents in it.
I can print filenames or contents separately by
find . | grep "file_for_print" | xargs echo
find . | grep "file_for_print" | xargs cat
but what I want is printing them together like this:
file1
line1 inside file1
line2 inside file1
file2
line1 inside file2
line2 inside file2
I read xargs with multiple commands as argument
and tried
find . | grep "file_for_print" | xargs -I % sh -c 'echo; cat;'
but doesn't work.
I'm not familiar with xargs, so don't know what exactly "-I % sh -c" means.
could anyone help me? thank you!
find . | grep "file_for_print" | xargs -I % sh -c 'echo %; cat %;' (OP was missing %s)
To start with, there is virtually no difference between:
find . | grep "file_for_print" | xargs echo
and
find . -name "file_for_print*"
except that the second one will not match filenames like this_is_not_the_file_for_print, and it will print the filenames one per line. It will also be a lot faster, because it doesn't need to generate and print the entire recursive directory structure just in order for grep to toss most of it away.
find . -name "file_for_print*"
is actually exactly the same as
find . -name "file_for_print*" -print
where the -print action prints each matched filename followed by a newline. If you don't provide find with any actions, it assumes you wanted -print. But it has more tricks up its sleeve than that. For example:
find . -name "file_for_print*" -exec cat {} \;
The -exec action causes find to execute the following command, up to the \;, replacing {} with each matching file name.
find does not limit itself to a single action. You can tell it to do however many you want. So:
find . -name "file_for_print*" -print -exec cat {} \;
will probably do pretty well what you want.
For lots more information on this very useful utility, type:
man find
or
info find
and read all about It.
Since it's not been said yet: -I % tells xargs to replace '%' with the arguments in the command you give it. The sh -c '...' just means run the commands '...' in a new shell.
So
xargs -I % sh -c 'echo %; cat %;'
will run echo [filename] followed by cat [filename] for every filename given to xargs. The echo and cat commands will be executed inside a different shell process but this usually doesn't matter. Your version didn't work because it was missing the % signs inside the command passed to xargs.
For what it's worth I would use this command to achieve the same thing:
find -name "*file_for_print*" | parallel 'echo {}; cat {};'
because it's simpler (parallel automatically uses {} as the substitution character and can take multiple commands by default).
In this specific case, each command is executed for each individual file anyway, so there's no advantage in using xargs. You may just append -exec twice to your 'find':
find . -name "*file_for_print*" -exec echo {} \; -exec cat {} \;
In this case-print could be used instead of the first echo as pointed out by rici, but this example shows the ability to execute two arbitrary commands with a single find
What about writing your own bash function?
#!/bin/bash
myFunction() {
while read -r file; do
echo "$file"
cat "$file"
done
}
find . -name "file_for_print*" | myFunction
So after a lot of searching and trying to interpret others' questions and answers to my needs, I decided to ask for myself.
I'm trying to take a directory structure full of images and place all the images (regardless of extension) in a single folder. In addition to this, I want to be able to remove images matching certain filenames in the process. I have a find command working that outputs all the filepaths for me
find -type f -exec file -i -- {} + | grep -i image | sed 's/\:.*//'
but if I try to use that to copy files, I have trouble with the spaces in the filenames.
cp `find -type f -exec file -i -- {} + | grep -i image | sed 's/\:.*//'` out/
What am I doing wrong, and is there a better way to do this?
With the caveat that it won't work if files have newlines in their names:
find . -type f -exec file -i -- {} + |
awk -vFS=: -vOFS=: '$NF ~ /image/{NF--;printf "%s\0", $0}' |
xargs -0 cp -t out/
(Based on answer by Jonathan Leffler and subsequent comments discussion with him and #devnull.)
The find command works well if none of the file names contain any newlines. Within broad limits, the grep command works OK under the same circumstances. The sed command works fine as long as there are no colons in the file names. However, given that there are spaces in the names, the use of $(...) (command substitution, also indicated by back-ticks `...`) is a disaster. Unfortunately, xargs isn't readily a part of the solution; it splits on spaces by default. Because you have to run file and grep in the middle, you can't easily use the -print0 option to (GNU) find and the -0 option to (GNU) xargs.
In some respects, it is crude, but in many ways, it is easiest if you write an executable shell script that can be invoked by find:
#!/bin/bash
for file in "$#"
do
if file -i -- "$file" | grep -i -q "$file:.*image"
then cp "$file" out/
fi
done
This is a little painful in that it invokes file and grep separately for each name, but it is reliable. The file command is even safe if the file name contains a newline; the grep is probably not.
If that script is called 'copyimage.sh', then the find command becomes:
find . -type f -exec ./copyimage.sh {} +
And, given the way the grep command is written, the copyimage.sh file won't be copied, even though its name contains the magic word 'image'.
Pipe the results of your find command to
xargs -l --replace cp "{}" out/
Example of how this works for me on Ubuntu 10.04:
atomic#atomic-desktop:~/temp$ ls
img.png img space.png
atomic#atomic-desktop:~/temp$ mkdir out
atomic#atomic-desktop:~/temp$ find -type f -exec file -i \{\} \; | grep -i image | sed 's/\:.*//' | xargs -l --replace cp -v "{}" out/
`./img.png' -> `out/img.png'
`./img space.png' -> `out/img space.png'
atomic#atomic-desktop:~/temp$ ls out
img.png img space.png
atomic#atomic-desktop:~/temp$
This is the command I've been using for finding matches (queryString) in php files, in the current directory, with grep, case insensitive, and showing matching results in line:
find . -iname "*php" -exec grep -iH queryString {} \;
Is there a way to also pipe just the file name of the matches to another script?
I could probably run the -exec command twice, but that seems inefficient.
What I'd love to do on Mac OS X is then actually to "reveal" that file in the finder. I think I can handle that part. If I had to give up the inline matches and just let grep show the files names, and then pipe that to a third script, that would be fine, too - I would settle.
But I'm actually not even sure how to pipe the output (the matched file names) to somewhere else...
Help! :)
Clarification
I'd like to reveal each of the files in a finder window - so I'm probably not going to using the -q flag and stop at the first one.
I'm going to run this in the console, ideally I'd like to see the inline matches printed out there, as well as being able to pipe them to another script, like oascript (applescript, to reveal them in the finder). That's why I have been using -H - because I like to see both the file name and the match.
If I had to settle for just using -l so that the file name could more easily be piped to another script, that would be OK, too. But I think after looking at the reply below from #Charlie Martin, that xargs could be helpful here in doing both at the same time with a single find, and single grep command.
I did say bash but I don't really mind if this needs to be ran as /bin/sh instead - I don't know too much about the differences yet, but I do know there are some important ones.
Thank you all for the responses, I'm going to try some of them at the command line and see if I can get any of them to work and then I think I can choose the best answer. Leave a comment if you want me to clarify anything more.
Thanks again!
You bet. The usual thing is something like
$ find /path -name pattern -print | xargs command
So you might for example do
$ find . -name '*.[ch]' -print | xargs grep -H 'main'
(Quiz: why -H?)
You can carry on with this farther; for example. you might use
$ find . -name '*.[ch]' -print | xargs grep -H 'main' | cut -d ':' -f 1
to get the vector of file names for files that contain 'main', or
$ find . -name '*.[ch]' -print | xargs grep -H 'main' | cut -d ':' -f 1 |
xargs growlnotify -
to have each name become a Growl notification.
You could also do
$ grep pattern `find /path -name pattern`
or
$ grep pattern $(find /path -name pattern)
(in bash(1) at least these are equivalent) but you can run into limits on the length of a command line that way.
Update
To answer your questions:
(1) You can do anything in bash you can do in sh. The one thing I've mentioned that would be any different is the use of $(command) in place of using backticks around command, and that works in the version of sh on Macs. The csh, zsh, ash, and fish are different.
(2) I think merely doing $ open $(dirname arg) will opena finder window on the containing directory.
It sounds like you want to open all *.php files that contain querystring from within a Terminal.app session.
You could do it this way:
find . -name '*.php' -exec grep -li 'querystring' {} \; | xargs open
With my setup, this opens MacVim with each file on a separate tab. YMMV.
Replace -H with -l and you will get a list of those filenames that matched the pattern.
if you have bash4, simply do
grep pattern /path/**/*.php
the ** operator is like
grep pattern `find -name \*.php -print`
find /home/aaronmcdaid/Code/ -name '*.cpp' -exec grep -q -iH boost {} \; -exec echo {} \;
The first change I made is to add -q to your grep command. This is "Exit immediately with zero status if any match is found".
The good news is that this speeds up grep when a file has many matching lines. You don't care how many matches there are. But that means we need another exec on the end to actually print the filenames when grep has been successful
The grep result will be sent to stdout, so another -exec predicate is probably the best solution here.
Pipe to another script:
find . -iname "*.php" | myScript
File names will come into the stdin of myScript 1 line at a time.
You can also use xargs to form/execute commands to act on each file:
find . -iname "*.php" | xargs ls -l
act on files you find that match:
find . -iname "*.php" | xargs grep -l pattern | myScript
act that don't match pattern
find . -iname "*.php" | xargs grep -L pattern | myScript
In general using multiple -exec's and grep -q will be FAR faster than piping, since find has implied short circuits -a's separating each juxtaposed pair of expressions that's not separated with an explicit operator. The main problem here, is that you want something to happen if grep matches something AND for matches to be printed. If the files are reasonably sized then this should be faster (because grep -q exits after finding a single match)
find . -iname "*php" -exec grep -iq queryString {} \; -exec grep -iH queryString {} \; -exec otherprogram {} \;
If the files are particularly big, encapsulating it in a shell script may be faster then running multiple grep commands
find . -iname "*php" -exec bash -c \
'out=$(grep -iH queryString "$1"); [[ -n $out ]] && echo "$out" && exit 0 || exit 1' \
bash {} \; -print
Also note, if the matches are not particularly needed, then
find . -iname "*php" -exec grep -iq queryString {} \; -exec otherprogram {} \;
Will virtually always be faster than then a piped solution like
find . -iname "*php" -print0 | xargs -0 grep -iH | ...
Additionally, you should really have -type f in all cases, unless you want to catch *php directories
Regarding the question of which is faster, and you actually care about the minuscule time difference, which maybe you might if you are trying to see which will save your processor some time... perhaps testing using the command as a suffix to the "time" command, and see which one performs better.