What I want:
In a bash script: Find all files in current directory that contain a certain string "teststring" and cop them into a subfolder "./testfolder"
Found this to find the filenames which im looking for
find . -type f -print0 | xargs -0 grep -l "teststring"
..and this to copy found files to another folder (here selecting by strings in filename):
find . -type f -iname "stringinfilename" -exec cp {} ./testfolder/ \;
Whats the best way to combine both commands to achieve what I described at the top?
Just let find do both:
find . -name subdir -prune -o -type f -exec \
grep -q teststring "{}" \; -exec cp "{}" subdir \;
Note that things like this are much easier if you don't try to add to the directory you're working in. In other words, write to a sibling dir instead of writing to a subdirectory. If you want to wind up with the data in a subdir, mv it when you're done. That way, you don't have to worry about the prune (ie, you don't have to worry about find descending into the subdir and attempting to duplicate the work).
Related
I want to copy all the log files from a directory which does not contain log files, but it contains other subdirectories with log files. These subdirectories also contain other subdirectories, so I need something recursive.
I tried
cp -R *.log /destination
But it doesn't work because the first directory does not contains log files. The response can be also a loop in bash.
find /path/to/logdir -type f -name "*.log" |xargs -I {} cp {} /path/to/destinationdir
Explanation:
find searches recursively
-type f tells you to search for files
-name specifies the name pattern
xargs executes commands
-I {} indicates an argument substitution symbol
Another version without xargs:
find /path/to/logdir -type f -name '* .log' -exec cp '{}' /path/to/destinationdir \;
I have files named test.txt in different directories like this
./222/test.txt
./111/test.txt
I want to rename all test.txt to info.txt
I've tried using this
find . -type f -iname 'test.txt' -exec mv {} {}info \;
I get test.txtinfo
Your idea is right, but you need to use -execdir instead of just -exec to simplify this.
find . -type f -iname 'test.txt' -execdir mv {} info.txt ';'
This works like -exec with the difference that the given shell command is executed with the directory of the found pathname as its current working directory and that {} will contain the basename of the found pathname without its path. Also note that the option is a non-standard one (non POSIX compliant).
I need to find subdirectories called "child" and copy the files in those folders to a new directory. Can't get it to work.
I can get as far as finding the subdirectories but I can't copy the files from them.
> find /Volumes/COMMON-LIC-PHOTO-1/STUDIO-COMPLETE/ISSUETRAK/2016/03_2016 -type d -iname child
The above will find all subdirectories in 03_2016 named "child" but how do I now copy the files inside those directories?
I tried this but the problem is that it seems to want to copy the directories themselves and not just the files:
> find /Volumes/COMMON-LIC-PHOTO-1/STUDIO-COMPLETE/ISSUETRAK/2016/03_2016 -type d -iname child | xargs cp '{}' /Volumes/COMMON-LIC-PHOTO-1/STUDIO-COMPLETE/ISSUETRAK/TEST \;
I can't get it to target only the files.
This might be a little cleaner than the above answer:
find $(find /Volumes/COMMON-LIC-PHOTO-1/STUDIO-COMPLETE/ISSUETRAK/2016/03_2016 -type d -iname child | xargs) -type f -exec cp {} /Volumes/COMMON-LIC-PHOTO-1/STUDIO-COMPLETE/ISSUETRAK/TEST \;
Two calls to find, one call to xargs. Like the other answer, this also will overwrite duplicate file names.
You're close:
> find $YOUR_PATH/03_2016/ -type d -iname child | xargs -I {} find -type f {} | xargs -I {} cp {} /Volumes/COMMON-LIC-PHOTO-1/STUDIO-COMPLETE/ISSUETRAK/TEST
Note: You might overwrite files that share the same name at the final destination
I have a Linux-System where some users put files with ftp in a Directory. In this Directory there are sub-directories which the users can create. Now I need a script that searches for all files in those subdirectories and moves them in a single Directory (for backup). The Problem: The Sub directories shouldn´t be removed.
the directory for the users is /files/media/documents/
and the files have to be moved in the Directory /files/dump/. I don´t care about files in /files/media/documents/, they are already handled by another script.
I already tried this script:
for dir in /files/media/documents/
do
find "$dir/" -iname '*' -print0 | xargs -0 mv -t /files/dump/
done
Instead of iterating, you could just use find. In man-page there is a "-type" option documented, so for moving only files you could do:
find "/files/media/documents/" -type f -print0 | xargs -0 mv -t /files/dump/
You also won't like to find files in /files/media/documents/, but all sub-directories? Simply add "-mindepth":
find "/files/media/documents/" -type f -mindepth 1 -print0 | xargs -0 mv -t /files/dump/
Alternatively you could also use "-exec" to skip a second command (xargs):
find "/files/media/documents/" -type f -mindepth 1 -exec mv {} /files/dump/ \;
I have the following directories:
P922_101
P922_102
.
.
Each directory, for instance P922_101 has following subdirectories:
140311_AH8MHGADXX 140401_AH8CU4ADXX
Each subdirectory, for instance 140311_AH8MHGADXX has the following files:
1_140311_AH8MH_P922_101_1.fastq.gz 1_140311_AH8MH_P922_101_2.fastq.gz
2_140311_AH8MH_P922_101_1.fastq.gz 2_140311_AH8MH_P922_101_2.fastq.gz
And files in 140401_AH8CU4ADXX are:
1_140401_AH8CU_P922_101_1.fastq.gz 1_140401_AH8CU_P922_4001_2.fastq.gz
2_140401_AH8CU_P922_101_1.fastq.gz 2_140401_AH8CU_P922_4001_2.fastq.gz
I want to do 'cat' for the files in the subdirectories in the following way:
cat 1_140311_AH8MH_P922_101_1.fastq.gz 2_140311_AH8MH_P922_101_1.fastq.gz
1_140401_AH8CU_P922_101_1.fastq.gz 2_140401_AH8CU_P922_101_1.fastq.gz > P922_101_1.fastq.gz
which means that files ending with _1.fastq.gz should be concatenated into a single file and files ending with _2.fatsq.gz into another file.
It should be run for all files in subdirectories in all directories. Could someone give a linux solution to do this?
Since they're compressed, you should probably use gzip -dc (decompress and write to stdout) -
find /somePath -type f -name "*.fastq.gz" -exec gzip -dc {} \; | \
tee -a /someOutFolder/out.txt
You can use find for this:
find /top/path -mindepth 2 -type f -name "*_1.fastq.gz" -exec cat {} \; > one_file
find /top/path -mindepth 2 -type f -name "*_2.fastq.gz" -exec cat {} \; > another_file
This will look for all the files starting from /top/path and having a name matching the pattern _1.fastq.gz / _2.fastq.gz and cat them into the desired file. -mindepth 2 makes find look for files that are at least under the current directory; this way, files in /top/path won't be matched.
Note that you will probably need zcat instead of cat, for gz files.
As you keep adding details in comments, let's see what else we can do:
Say you have the list of directories in a file directories_list, each line containing one:
while read directory
do
find $directory -mindepth 2 -type f -name "*_1.fastq.gz" -exec cat {} \; > $directory/output
done < directories_list