Chapter 5 Achiving and compressing files

5.1 Common compressed file format

If you download open source software, like bwa and ViewBS, you will encouther archived files very often.

The common compressed file usually have the the suffix of tar.gz (equaivalent of tgz), gz, zip and tar.bz2.

For example, if we want to use bowtie2 in Linux, we need to download the bowtie2 software. Bowtie2 file for Linux can be downloaded form the link below:

https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.3.1/bowtie2-2.3.3.1-linux-x86_64.zip

In side the zip file, there are files and sub folders.

The files for samtools v1.6 are archived in to a file named samtools-1.6.tar.bz2`. From the link below you can download the link:

https://gigenet.dl.sourceforge.net/project/samtools/samtools/1.6/samtools-1.6.tar.bz2

5.2 How to work with different format

5.2.1 *.gz

5.2.1.1 How to check the file

zcat file.gz |less

5.2.1.2 How to test if a gzip file is valid

gzip -t file.gz

5.2.1.3 How decompress a *.gz file

  • Decompress a *.gz file
mkdir tmp
cp tmp
cp ../data/Arabidopsis_thaliana.TAIR10.37.gff3.gz ./
gunzip Arabidopsis_thaliana.TAIR10.37.gff3.gz
  • Decompress a file and keep the original copy
gunzip -c file.gz > file

5.2.2 *.tar.gz

5.2.2.1 How to decompress the *.tar.gz file

tar zxvf file.tar.gz
  • z means (un)z̲ip.
  • x means ex̲tract files from the archive.
  • v means print the filenames v̲erbosely.
  • f means the following argument is a f̱ilename.

5.2.2.2 How to view the content without extract the files

tar -tf file.tar.gz
tar -tvf file.tar.gz

5.2.2.3 How to create a *.tar.gz file

tar zcvf file_new.tar.gz file1 file2 folder1 folder2

5.2.2.4 How to extract a specific file from a *.tar.gz file

#tar -xvf {tarball.tar} {path/to/file}
tar -zxvf config.tar.gz etc/default/sysstat

5.2.3 *.zip

5.2.3.1 How to unzip a *.zip file

unzip file.zip

5.2.3.2 How to create a *.zip file

zip file_new.zip file1 file2 folder1 folder2

5.2.4 *.tar.bz2

5.2.4.1 How to decompress a *.tar.bz2 file

mkdir tmp
cd tmp
pwd
ls 
wget https://downloads.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2
ls
tar -jxvf bwa-0.7.17.tar.bz2

5.2.4.2 How to create a *.tar.bz2 file

tar -cvjSf folder.tar.bz2 file1 file2 folder1 folder2