I am trying to create a script for linux that will make a list with all files inside all zip files from a directory.
#! /bin/bash
for file in `find /home -iname "*.zip*" -type f`
do
unzip -l $(echo ${file}) >> /home/list.txt
done
It works, but only when there are no white spaces in filename.
What can I do to make it work ?
You can use the find command to execute a command for each file it finds. Perhaps try something like:
find /home -iname "*.zip*" -type f -exec unzip -l {} \; > /home/list.txt
Related
find -name archive.zip -exec unzip {} file.txt \;
This command finds all files named archive.zip and unzips file.txt to the folder that I execute the command from, is there a way to unzip the file to the same folder where the .zip file was found? I would like file.txt to be unzipped to folder1.
folder1\archive.zip
folder2\archive.zip
I realize $dirname is available in a script but I'm looking for a one line command if possible.
#iheartcpp - I successfully ran three alternatives using the same base command...
find . -iname "*.zip"
... which is used to provide the list of / to be passed as an argument to the next command.
Alternative 1: find with -exec + Shell Script (unzips.sh)
File unzips.sh:
#!/bin/sh
# This will unzip the zip files in the same directory as the zip are
for f in "$#" ; do
unzip -o -d `dirname $f` $f
done
Use this alternative like this:
find . -iname '*.zip' -exec ./unzips.sh {} \;
Alternative 2: find with | xargs _ Shell Script (unzips)
Same unzips.sh file.
Use this alternative like this:
find . -iname '*.zip' | xargs ./unzips.sh
Alternative 3: all commands in the same line (no .sh files)
Use this alternative like this:
find . -iname '*.zip' | xargs sh -c 'for f in $#; do unzip -o -d `dirname $f` $f; done;'
Of course, there are other alternatives but hope that the above ones can help.
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
I have a main directory with 361 subdirectories. Within the each subdirectory, there is a parameter file and one executable program file. The executable file is coded to look for the parameter file in the directory where the executable is located. (The same executable file is in all subdirectories. The parameter files all have the same file name in all subdirectories)
Instead of executing the program file individually, is there a cshell command for terminal to run them all at once?
UPDATED
If your Linux is so old it doesn't have -execdir, you could try this:
find $(pwd) -name YourProgram -exec dirname {} \; | while read d; do cd "$d" && pwd; done
If that correctly prints the names of the directories where your program needs to be run, just remove the pwd and replace with whatever you want done in tha directory - presumably something like this:
find $(pwd) -name YourProgram -exec dirname {} \; | while read d; do cd "$d" && ./YourPrgram; done
ORIGINAL ANSWER
Like this maybe:
find . -type f -name YourProgramName -execdir ./YourProgramName YourParameterFile \;
But backup first and check it looks right before using.
The -execdir causes find to change to the directory it has found before running the commands there.
If your command is more complicated, you can do this:
find . -type f -name YourProgramName -execdir sh -c "command1; command2; command3" \;
Check it does what you want like this:
find . -type f -name YourProgramName -execdir pwd \;
Maybe this will help. Suppose you have in each folder a file named params_file and an executable named exec_file, then:
for dir in `find . -maxdepth 1 -mindepth 1 -type d` ; do
cd $dir
cat params_file | xargs ./exec_file
cd ..
done
I have a folder in ~/Downloads with lots of
files and folders scattered. This consists of various files of different
extensions. I need to copy only the
.pdf files within various directories to ~/pdfs
Use find:
find ~/Downloads -type f -name "*.pdf" -exec cp {} ~/pdfs \;
if ~/pdfs exists in your system use the following command
cd ~/Downloads ; cp -r *.pdf ~/pdfs
if ~/pdfs does not exists in your system use the following command
cd ~/Downloads ; mkdir ~/pdfs ; cp -r *.pdf ~/pdfs
In order to deal with potential file names with spaces, etc., I would recommend this approach:
find ~/Downloads/. -type f -name "*.pdf" -print0 | xargs -0 -I_ cp _ ~/pdfs/.
I have a project in Linux. I want to create a file named index.html in all folders.
So I have used the following command:
find . -type d -exec touch {}/index.html \;
It's working! Now I'm trying to copy the existing file from a given location and it to be automatically replaced into all the folders of my project.
This should actually work exactly in the same way:
find . -type d -exec cp $sourcedir/index.html {}/index.html \;
If I understand your question correctly, what you want is to copy a given file in all the directories.
You can use a similar find command :
find . -type d -exec cp -f /tmp/index.html {} \;
where /tmp/index.html is path to the original file (replace it with your own path).
Also, you don't need to create the files if your final objective is to replace them with the original file.
tar -cvzf index.tar.gz `find . -type f -iname 'index.html'` && scp index.tar.gz USER#SERVER:/your/projec/root/on/SERVER && ssh USER#SERVER "tar -xvzf index.tar.gz"
Or if you're in the proper directory localhost, and rsync is available:
rsync -r --exclude='**' --include='**/index.html' . USER#SERVER:/your/projec/root/on/SERVER
HTH