How to gunzip all the files with a given extension and send to another folder?-CodePudding

I have a folder with 28 gz files with the extension .gz and 28 files with the extension .gz.bam.

I would like to unzip all the 28 .gz files and send them to another folder. I was doing one by one as follows:

gunzip -c file1.gz > /mnt/s3/data_transfer/file1

How can I specify I want the .gz and not the .gz.bam?

CodePudding user response：

This might be what you're looking for:

for f in *.gz; do gunzip -c "$f" > /mnt/s3/data_transfer/"${f%.gz}"; done

You may remove the .gz files by rm *.gz after that, if you want. Or, alternatively

cp *.gz /mnt/s3/data_transfer/ && cd /mnt/s3/data_transfer && gunzip *.gz

Note that the latter command will gunzip all .gz files in the directory /mnt/s3/data_transfer, including the ones that exist, if any, before the cp command is executed. If you want to remove the original .gz files, replace cp with mv.

CodePudding user response：

First, let's find the files:

find . -type f -name "*.gz" > foo.sh

We find the files whose name ends with gz and save them into foo.sh. Let's open it:

vim foo.sh

Now, we prepend the gunzip command to each line. Let's hit the : key, so at the bottom of the file you can enter a command. Now, let's enter this command:

%s/^/gunzip -c /

this replaces the start of each line with the text we want to prepend.

Then we append the destination path, by pressing : again and pasting the following:

%s/$/ \/some\/path/

of course, instead of \/some\/path you will need to use your own path.

Finally, add

cd /some/path
rename 's/\.gz//' *

to remove all the gz extensions from the files in /some/path (replace this with your actual path)

Note that you may need to install rename and here I assumed that the target path already existed.