I have a directory with unknown number of subdirectories and unknown level of sub*directories within them. How do I copy all the file swith the same suffix to a new directory?
E.g. from this directory:
> some-dir
>> foo-subdir
>>> bar-sudsubdir
>>>> file-adx.txt
>> foobar-subdir
>>> file-kiv.txt
Move all the *.txt files to:
> new-dir
>> file-adx.txt
>> file-kiv.txt
One option is to use find:
find some-dir -type f -name "*.txt" -exec cp \{\} new-dir \;
find some-dir -type f -name "*.txt" would find *.txt files in the directory some-dir. The -exec option builds a command line (e.g. cp file new.txt) for every matching file denoted by {}.
Use find with xargs as shown below:
find some-dir -type f -name "*.txt" -print0 | xargs -0 cp --target-directory=new-dir
For a large number of files, this xargs version is more efficient than using find some-dir -type f -name "*.txt" -exec cp {} new-dir \; because xargs will pass multiple files at a time to cp, instead of calling cp once per file. So there will be fewer fork/exec calls with the xargs version.
Related
Am trying to write a script that finds the files that are older than 10 hours from the sub-directories that are in the "HS_client_list". And send the Output to a file "find.log".
#!/bin/bash
while IFS= read -r line; do
echo Executing cd /moveit/$line
cd /moveit/$line
#Find files less than 600 minutes old.
find $PWD -type f -iname "*.enc" -mmin +600 -execdir basename '{}' ';' | xargs ls > /home/infa91punv/find.log
done < HS_client_list
However, the script is able to cd to the folders from HS_client_list(this file contents the name of the subdirectories) but, the find command (find $PWD -type f -iname "*.enc" -mmin +600 -execdir basename '{}' ';' | xargs ls > /home/infa91punv/find.log) is not working. The Output file is empty. But when I run find $PWD -type f -iname "*.enc" -mmin +600 -execdir basename '{}' ';' | xargs ls > /home/infa91punv/find.log as a command it works and from the script it doesn't.
You are overwriting the file in each iteration.
You can use xargs to perform find on multiple directories; but you have to use an alternate delimiter to avoid having xargs populate the {} in the -execdir command.
sed 's%^%/moveit/%' HS_client_list |
xargs -I '<>' find '<>' -type f -iname "*.enc" -mmin +600 -execdir basename {} \; > /home/infa91punv/find.log
The xargs ls did not seem to perform any useful functionality, so I took it out. Generally, don't use ls in scripts.
With GNU find, you could avoid the call to an external utility, and use the -printf predicate to print just the part of the path name that you care about.
For added efficiency, you could invoke a shell to collect the arguments:
sed 's%^%/moveit/%' HS_client_list |
xargs sh -c 'find "$#" -type f -iname "*.enc" -mmin +600 -execdir basename {} \;' _ >/home/infa91punv/find.log
This will run as many directories as possible in a single find invocation.
If you want to keep your loop, the solution is to put the redirection after done. I would still factor out the cd, and take care to quote the variable interpolation.
while IFS= read -r line; do
find /moveit/"$line" -type f -iname "*.enc" -mmin +600 -execdir basename '{}' ';'
done < HS_client_list >/home/infa91punv/find.log
I need to get all the texts in the matching file in the folder. However, at the same time need to get the matching file path as well. How can I get the matching file path as well using the following command.
find . -type f -name release.txt | xargs cat
try
find . -type f -name release.txt -exec grep -il {} \; | xargs cat
Skip xargs, just do:
find . -type f -name release.txt -exec sh -c 'echo "$1"; cat "$1"' _ {} \;
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 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
In Unix, what is the single cmd that lets me search and locate a file recursively and then retrieve the file instead of just the path of the file?
What do you mean by retrieve?
You can simply use -exec argument to find.
$ find /path/to/search -type f -name '*.txt' -exec cat {} \;
$ find /path/to/search -type f -name 'pattern' -exec cp {} /path/to/new \;
The second one should work.
cat `find /wherever/you/want/to/start/from -name name_of_file`
Note those quotes are backquotes (`).