I have the following folder structure:
/drive1/180204_somerandomtext/file.csv
/drive1/180504_somerandomtext/file.csv
/drive1/190101_somerandomtext/file.csv
/drive1/190305_somerandomtext/file.csv
...
Each file.txt has the same structure, but contains different data. From a file.txt I want to extract only a subset of lines using the following command:
grep -A5000 -m1 -e 'Sample_ID,' /drive1/180204_somerandomtext/file.csv | tail -n+2
This command works and prints the next 5000 lines following the line that starts with 'Sample_ID,'
I've extended this command
grep -A5000 -m1 -e 'Sample_ID,' /drive1/180204_somerandomtext/file.csv | tail -n+2 | sed 's/^/180204_somerandomtext,/'
Using the 'sed' I now add to the beginning of each line the pattern '180204_somerandomtext', which is actually the name of the folder that contains the file.csv
I'm now stuck at the following steps:
how to do this for all file.csv files in the subfolders of drive1
how to store this result in one large file called 'samples.csv'
I've tried something with xargs. It works with the grep command, but piping the sed, isn't working then.
find /drive1/ -maxdepth 1 -name '1*' | cut -d '/' -f2 | xargs -I {} grep -A5000 -m1 -e 'Sample_ID,' /drive1/{}/file.csv | sed 's/^/{},/'
I'm also not a big fan of xargs, I'm finding find -exec much clearer to use, let me explain:
Imagine I would like to do something with a file file1.txt:
Command -sw1 param1 -sw2 param2.1 param2.2 file1.txt
Launch a command, and use switches sw1, sw2 with parameters param1, param2.1 and param2.2.
When I want to perform this for all file1.txt within a directory structure, I do the following:
find . -name "file1.txt" -exec Command -sw1 param1 -sw2 param2.1 param2.2 {} \;
So I just put the find command (with some information on where and what to find), and afterwards comes the -exec. After that -exec I put the exact command, where I replace my original filename by {} and I end the whole thing by \;.
In your case, it would be something like:
find /drive1 -name file.csv -exec grep -A5000 -m1 -e 'Sample_ID,' {} \;
Related
Line1: .................
Line2: #hello1 #hello2 #hello3
Line3: .................
Line4: .................
Line5: #hello1 #hello4 #hello3
Line6: #hello1 #hello2 #hello3
Line7: .................
I have files that look similar in terms of lines on one of my project directories. I want to get the counts of all the lines that contain #hello1 and #hello2. In this case I would get 2 as a result only for this file. However, I want to do this recursively.
The canonical way to "do something recursively" is to use the find command. If you want to find lines that have two words on them, a simple regex will do:
grep -lr '#hello1.*#hello2' .
The option -l instructs grep to show us only filenames rather than file content, and the option -r tells grep to traverse the filesystem recursively. The start of the search is the path at the end of the line. Once you have the list of files, you can parse that list using commands run by xargs.
For example, this will count all the lines in files matching the pattern you specified.
grep -lr '#hello1.*#hello2' . | xargs -n 1 wc -l
This uses xargs to run the wc command on each of the files listed by grep. You could probably also run this without the -n 1, unless you're dealing with many many thousands of files that would exceed your maximum command line length.
Or, if I'm interpreting your question correctly, the following will count just the patterns in those files.
grep -lr '#hello1.*#hello2' . | xargs -n 1 grep -Hc '#hello1.*#hello2'
This runs a similar grep to the one used to generate your recursive list of files, and presents the output with filename (-H) and count (-c).
But if you want complex rules like finding two patterns possibly on different lines in the file, then grep probably is not the optimal tool, unless you use multiple greps launched by find:
find /path/to/base -type f \
-exec grep -q '#hello1' {} \; \
-exec grep -q '#hello2' {} \; \
-print
(Lines split for easier reading.)
This is somewhat costly, as find needs to launch up to two children for each file. So another approach would be to use awk instead:
find /path/to/base -type f \
-exec awk '/#hello1/{c++} /#hello2/{c++} c==2{r=1} END{exit 1-r}' {} \; \
-print
Alternately, if your shell is bash version 4 or above, you can avoid using find and use the bash option globstar:
$ shopt -s globstar
$ awk 'FNR=1{c=0} /#hello1/{c++} /#hello2/{c++} c==2{print FILENAME;nextfile}' **/*
Note: none of this is tested.
If you are not nterested in the number of files also,
then just something along:
find $BASEDIRECTORY -type f -print0 | xargs -0 grep -h PATTERN | wc -l
If you want to count lines containing #hello1 and #hello2 separated by space in a specific file you can:
$ grep -c '#hello1 #hello2' file
If you want to count in more than one file:
$ grep -c '#hello1 #hello2' file1 file2 ...
And if you want to get the gran total:
$ grep -c '#hello1 #hello2' file1 file2 ... | paste -s -d+ - | bc
of course you can let your shell expanding file names. So, for example:
$ grep -c '#hello1 #hello2' *.txt | paste -s -d+ - | bc
or so...
find . -type f | xargs -1 awk '/#hello1/ && /#hello2/{c++} END{print FILENAME, c+0}'
I have a statement which
Finds a set of files
Cats their contents out
Then greps their contents
It is this pipeline:
find . | grep -i "Test_" | xargs cat | grep -i "start-node name="
produces an output such as:
<start-node name="Start" secure="false"/>
<start-node name="Run" secure="false"/>
What I was hoping to get is something like:
filename1-<start-node name="Start" secure="false"/>
filename2-<start-node name="Run" secure="false"/>
An easier may be to execute grep on the result of find, without xargs and cat:
grep -i "Test_" `find .` | grep -i "start-node name="
Because you cat all the files into a single stream, grep doesn't have any filename information. You want to give all the filenames to grep as arguments:
find ... | xargs grep "<start-node name=" /dev/null
Note two additional changes - I've dropped the -i flag, as it appears you're inspecting XML, and that's not case-insensitive; I've added /dev/null to the list of files, so that grep always has at least two files of input, even if find only gives one result. That's the portable way to get grep to print filenames.
Now, let's look at the find command. Instead of finding all files, then filtering through grep, we can use the -iregex predicate of GNU grep:
find . -iregex '.*Test_.*' \( -type 'f' -o -type 'l' \) | xargs grep ...
The mixed-case pattern suggests your filenames aren't really case-insensitive, and you might not want to grep symlinks (I'm sure you don't want directories and special files passed through), in which case you can simplify (and can use portable find again):
find . -name '*Test_*' -type 'f' | xargs grep ...
Now protect against the kind of filenames that trip up pipelines, and you have
find . -name '*Test_*' -type 'f' -print0 \
| xargs -0 grep -e "<start-node name=" -- /dev/null
Alternatively, if you have GNU grep, you don't need find at all:
grep --recursive --include '*[Tt]est_*' -e "<start-node name=" .
If you just need to count them:
find . | grep -i "Test_" | xargs cat | grep -i "start-node name=" | awk 'BEGIN{n=0}{n=n+1;print "filename" n "-" $0}'
From man grep:
-H Always print filename headers with output lines.
How do I recursively view a list of files that has one string and specifically doesn't have another string? Also, I mean to evaluate the text of the files, not the filenames.
Conclusion:
As per comments, I ended up using:
find . -name "*.html" -exec grep -lR 'base\-maps' {} \; | xargs grep -L 'base\-maps\-bot'
This returned files with "base-maps" and not "base-maps-bot". Thank you!!
Try this:
grep -rl <string-to-match> | xargs grep -L <string-not-to-match>
Explanation: grep -lr makes grep recursively (r) output a list (l) of all files that contain <string-to-match>. xargs loops over these files, calling grep -L on each one of them. grep -L will only output the filename when the file does not contain <string-not-to-match>.
The use of xargs in the answers above is not necessary; you can achieve the same thing like this:
find . -type f -exec grep -q <string-to-match> {} \; -not -exec grep -q <string-not-to-match> {} \; -print
grep -q means run quietly but return an exit code indicating whether a match was found; find can then use that exit code to determine whether to keep executing the rest of its options. If -exec grep -q <string-to-match> {} \; returns 0, then it will go on to execute -not -exec grep -q <string-not-to-match>{} \;. If that also returns 0, it will go on to execute -print, which prints the name of the file.
As another answer has noted, using find in this way has major advantages over grep -Rl where you only want to search files of a certain type. If, on the other hand, you really want to search all files, grep -Rl is probably quicker, as it uses one grep process to perform the first filter for all files, instead of a separate grep process for each file.
These answers seem off as the match BOTH strings. The following command should work better:
grep -l <string-to-match> * | xargs grep -c <string-not-to-match> | grep '\:0'
Here is a more generic construction:
find . -name <nameFilter> -print0 | xargs -0 grep -Z -l <patternYes> | xargs -0 grep -L <patternNo>
This command outputs files whose name matches <nameFilter> (adjust find predicates as you need) which contain <patternYes>, but do not contain <patternNo>.
The enhancements are:
It works with filenames containing whitespace.
It lets you filter files by name.
If you don't need to filter by name (one often wants to consider all the files in current directory), you can strip find and add -R to the first grep:
grep -R -Z -l <patternYes> | xargs -0 grep -L <patternNo>
find . -maxdepth 1 -name "*.py" -exec grep -L "string-not-to-match" {} \;
This Command will get all ".py" files that don't contain "string-not-to-match" at same directory.
To match string A and exclude strings B & C being present in the same line I use, and quotes to allow search string to contain a space
grep -r <string A> | grep -v -e <string B> -e "<string C>" | awk -F ':' '{print $1}'
Explanation: grep -r recursively filters all lines matching in output format
filename: line
To exclude (grep -v) from those lines the ones that also contain either -e string B or -e string C. awk is used to print only the first field (the filename) using the colon as fieldseparator -F
After a few searches from Google, what I come up with is:
find my_folder -type f -exec grep -l "needle text" {} \; -exec file {} \; | grep text
which is very unhandy and outputs unneeded texts such as mime type information. Any better solutions? I have lots of images and other binary files in the same folder with a lot of text files that I need to search through.
I know this is an old thread, but I stumbled across it and thought I'd share my method which I have found to be a very fast way to use find to find only non-binary files:
find . -type f -exec grep -Iq . {} \; -print
The -I option to grep tells it to immediately ignore binary files and the . option along with the -q will make it immediately match text files so it goes very fast. You can change the -print to a -print0 for piping into an xargs -0 or something if you are concerned about spaces (thanks for the tip, #lucas.werkmeister!)
Also the first dot is only necessary for certain BSD versions of find such as on OS X, but it doesn't hurt anything just having it there all the time if you want to put this in an alias or something.
EDIT: As #ruslan correctly pointed out, the -and can be omitted since it is implied.
Based on this SO question :
grep -rIl "needle text" my_folder
Why is it unhandy? If you need to use it often, and don't want to type it every time just define a bash function for it:
function findTextInAsciiFiles {
# usage: findTextInAsciiFiles DIRECTORY NEEDLE_TEXT
find "$1" -type f -exec grep -l "$2" {} \; -exec file {} \; | grep text
}
put it in your .bashrc and then just run:
findTextInAsciiFiles your_folder "needle text"
whenever you want.
EDIT to reflect OP's edit:
if you want to cut out mime informations you could just add a further stage to the pipeline that filters out mime informations. This should do the trick, by taking only what comes before :: cut -d':' -f1:
function findTextInAsciiFiles {
# usage: findTextInAsciiFiles DIRECTORY NEEDLE_TEXT
find "$1" -type f -exec grep -l "$2" {} \; -exec file {} \; | grep text | cut -d ':' -f1
}
find . -type f -print0 | xargs -0 file | grep -P text | cut -d: -f1 | xargs grep -Pil "search"
This is unfortunately not space save. Putting this into bash script makes it a bit easier.
This is space safe:
#!/bin/bash
#if [ ! "$1" ] ; then
echo "Usage: $0 <search>";
exit
fi
find . -type f -print0 \
| xargs -0 file \
| grep -P text \
| cut -d: -f1 \
| xargs -i% grep -Pil "$1" "%"
Another way of doing this:
# find . |xargs file {} \; |grep "ASCII text"
If you want empty files too:
# find . |xargs file {} \; |egrep "ASCII text|empty"
How about this:
$ grep -rl "needle text" my_folder | tr '\n' '\0' | xargs -r -0 file | grep -e ':[^:]*text[^:]*$' | grep -v -e 'executable'
If you want the filenames without the file types, just add a final sed filter.
$ grep -rl "needle text" my_folder | tr '\n' '\0' | xargs -r -0 file | grep -e ':[^:]*text[^:]*$' | grep -v -e 'executable' | sed 's|:[^:]*$||'
You can filter-out unneeded file types by adding more -e 'type' options to the last grep command.
EDIT:
If your xargs version supports the -d option, the commands above become simpler:
$ grep -rl "needle text" my_folder | xargs -d '\n' -r file | grep -e ':[^:]*text[^:]*$' | grep -v -e 'executable' | sed 's|:[^:]*$||'
Here's how I've done it ...
1 . make a small script to test if a file is plain text
istext:
#!/bin/bash
[[ "$(file -bi $1)" == *"file"* ]]
2 . use find as before
find . -type f -exec istext {} \; -exec grep -nHi mystring {} \;
Here's a simplified version with extended explanation for beginners like me who are trying to learn how to put more than one command in one line.
If you were to write out the problem in steps, it would look like this:
// For every file in this directory
// Check the filetype
// If it's an ASCII file, then print out the filename
To achieve this, we can use three UNIX commands: find, file, and grep.
find will check every file in the directory.
file will give us the filetype. In our case, we're looking for a return of 'ASCII text'
grep will look for the keyword 'ASCII' in the output from file
So how can we string these together in a single line? There are multiple ways to do it, but I find that doing it in order of our pseudo-code makes the most sense (especially to a beginner like me).
find ./ -exec file {} ";" | grep 'ASCII'
Looks complicated, but not bad when we break it down:
find ./ = look through every file in this directory. The find command prints out the filename of any file that matches the 'expression', or whatever comes after the path, which in our case is the current directory or ./
The most important thing to understand is that everything after that first bit is going to be evaluated as either True or False. If True, the file name will get printed out. If not, then the command moves on.
-exec = this flag is an option within the find command that allows us to use the result of some other command as the search expression. It's like calling a function within a function.
file {} = the command being called inside of find. The file command returns a string that tells you the filetype of a file. Regularly, it would look like this: file mytextfile.txt. In our case, we want it to use whatever file is being looked at by the find command, so we put in the curly braces {} to act as an empty variable, or parameter. In other words, we're just asking for the system to output a string for every file in the directory.
";" = this is required by find and is the punctuation mark at the end of our -exec command. See the manual for 'find' for more explanation if you need it by running man find.
| grep 'ASCII' = | is a pipe. Pipe take the output of whatever is on the left and uses it as input to whatever is on the right. It takes the output of the find command (a string that is the filetype of a single file) and tests it to see if it contains the string 'ASCII'. If it does, it returns true.
NOW, the expression to the right of find ./ will return true when the grep command returns true. Voila.
I have two issues with histumness' answer:
It only list text files. It does not actually search them as
requested. To actually search, use
find . -type f -exec grep -Iq . {} \; -and -print0 | xargs -0 grep "needle text"
It spawns a grep process for every file, which is very slow. A better solution is then
find . -type f -print0 | xargs -0 grep -IZl . | xargs -0 grep "needle text"
or simply
find . -type f -print0 | xargs -0 grep -I "needle text"
This only takes 0.2s compared to 4s for solution above (2.5GB data / 7700 files), i.e. 20x faster.
Also, nobody cited ag, the Silver Searcher or ack-grep¸as alternatives. If one of these are available, they are much better alternatives:
ag -t "needle text" # Much faster than ack
ack -t "needle text" # or ack-grep
As a last note, beware of false positives (binary files taken as text files). I already had false positive using either grep/ag/ack, so better list the matched files first before editing the files.
Although it is an old question, I think this info bellow will add to the quality of the answers here.
When ignoring files with the executable bit set, I just use this command:
find . ! -perm -111
To keep it from recursively enter into other directories:
find . -maxdepth 1 ! -perm -111
No need for pipes to mix lots of commands, just the powerful plain find command.
Disclaimer: it is not exactly what OP asked, because it doesn't check if the file is binary or not. It will, for example, filter out bash script files, that are text themselves but have the executable bit set.
That said, I hope this is useful to anyone.
I do it this way:
1) since there're too many files (~30k) to search thru, I generate the text file list daily for use via crontab using below command:
find /to/src/folder -type f -exec file {} \; | grep text | cut -d: -f1 > ~/.src_list &
2) create a function in .bashrc:
findex() {
cat ~/.src_list | xargs grep "$*" 2>/dev/null
}
Then I can use below command to do the search:
findex "needle text"
HTH:)
I prefer xargs
find . -type f | xargs grep -I "needle text"
if your filenames are weird look up using the -0 options:
find . -type f -print0 | xargs -0 grep -I "needle text"
bash example to serach text "eth0" in /etc in all text/ascii files
grep eth0 $(find /etc/ -type f -exec file {} \; | egrep -i "text|ascii" | cut -d ':' -f1)
If you are interested in finding any file type by their magic bytes using the awesome file utility combined with power of find, this can come in handy:
$ # Let's make some test files
$ mkdir ASCII-finder
$ cd ASCII-finder
$ dd if=/dev/urandom of=binary.file bs=1M count=1
1+0 records in
1+0 records out
1048576 bytes (1.0 MB, 1.0 MiB) copied, 0.009023 s, 116 MB/s
$ file binary.file
binary.file: data
$ echo 123 > text.txt
$ # Let the magic begin
$ find -type f -print0 | \
xargs -0 -I ## bash -c 'file "$#" | grep ASCII &>/dev/null && echo "file is ASCII: $#"' -- ##
Output:
file is ASCII: ./text.txt
Legend: $ is the interactive shell prompt where we enter our commands
You can modify the part after && to call some other script or do some other stuff inline as well, i.e. if that file contains given string, cat the entire file or look for a secondary string in it.
Explanation:
find items that are files
Make xargs feed each item as a line into one liner bash
command/script
file checks type of file by magic byte, grep checks if ASCII
exists, if so, then after && your next command executes.
find prints results null separated, this is good to escape
filenames with spaces and meta-characters in it.
xargs , using -0 option, reads them null separated, -I ##
takes each record and uses as positional parameter/args to bash
script.
-- for bash ensures whatever comes after it is an argument even
if it starts with - like -c which could otherwise be interpreted
as bash option
If you need to find types other than ASCII, simply replace grep ASCII with other type, like grep "PDF document, version 1.4"
find . -type f | xargs file | grep "ASCII text" | awk -F: '{print $1}'
Use find command to list all files, use file command to verify they are text (not tar,key), finally use awk command to filter and print the result.
How about this
find . -type f|xargs grep "needle text"
I am trying to delete erroneous emails based on finding the email address in the file via Linux CLI.
I can get the files with
find . | xargs grep -l email#example.com
But I cannot figure out how to delete them from there as the following code doesn't work.
rm -f | xargs find . | xargs grep -l email#example.com
Solution for your command:
grep -l email#example.com * | xargs rm
Or
for file in $(grep -l email#example.com *); do
rm -i $file;
# ^ prompt for delete
done
For safety I normally pipe the output from find to something like awk and create a batch file with each line being "rm filename"
That way you can check it before actually running it and manually fix any odd edge cases that are difficult to do with a regex
find . | xargs grep -l email#example.com | awk '{print "rm "$1}' > doit.sh
vi doit.sh // check for murphy and his law
source doit.sh
You can use find's -exec and -delete, it will only delete the file if the grep command succeeds. Using grep -q so it wouldn't print anything, you can replace the -q with -l to see which files had the string in them.
find . -exec grep -q 'email#example.com' '{}' \; -delete
I liked Martin Beckett's solution but found that file names with spaces could trip it up (like who uses spaces in file names, pfft :D). Also I wanted to review what was matched so I move the matched files to a local folder instead of just deleting them with the 'rm' command:
# Make a folder in the current directory to put the matched files
$ mkdir -p './matched-files'
# Create a script to move files that match the grep
# NOTE: Remove "-name '*.txt'" to allow all file extensions to be searched.
# NOTE: Edit the grep argument 'something' to what you want to search for.
$ find . -name '*.txt' -print0 | xargs -0 grep -al 'something' | awk -F '\n' '{ print "mv \""$0"\" ./matched-files" }' > doit.sh
Or because its possible (in Linux, idk about other OS's) to have newlines in a file name you can use this longer, untested if works better (who puts newlines in filenames? pfft :D), version:
$ find . -name '*.txt' -print0 | xargs -0 grep -alZ 'something' | awk -F '\0' '{ for (x=1; x<NF; x++) print "mv \""$x"\" ./matched-files" }' > doit.sh
# Evaluate the file following the 'source' command as a list of commands executed in the current context:
$ source doit.sh
NOTE: I had issues where grep could not match inside files that had utf-16 encoding.
See here for a workaround. In case that website disappears what you do is use grep's -a flag which makes grep treat files as text and use a regex pattern that matches any first-byte in each extended character. For example to match Entité do this:
grep -a 'Entit.e'
and if that doesn't work then try this:
grep -a 'E.n.t.i.t.e'
Despite Martin's safe answer, if you've got certainty of what you want to delete, such as in writing a script, I've used this with greater success than any other one-liner suggested before around here:
$ find . | grep -l email#example.com | xargs -I {} rm -rf {}
But I rather find by name:
$ find . -iname *something* | xargs -I {} echo {}
rm -f `find . | xargs grep -li email#example.com`
does the job better. Use `...` to run the command to offer the file names containing email.#example.com (grep -l lists them, -i ignores case) to remove them with rm (-f forcibly / -i interactively).
find . | xargs grep -l email#example.com
how to remove:
rm -f 'find . | xargs grep -l email#example.com'
Quick and efficent. Replace find_files_having_this_text with the text you want to search.
grep -Ril 'find_files_having_this_text' . | xargs rm