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bzip2

to compress and decompress files

Examples


compress
files (original file will be removed after compression)

bzip2 myfile.txt
bzip2 *.txt


keep the original file (option -k)
bzip2 -k myfile.txt

as pipe
bzip2 -c myfile.txt > myfile.txt.bz2


extract/decompress
to view the compressed file (decompress to
standard output), original file keeps unchanged
bzcat myfile.txt.bz2

to decompress .bz2 files, use option -d (.bz2 file will be removed)
bzip2 -d myfile.txt.bz2 


more bz commands
bzgrep, bzcmp, bzdiff, bzcat, bzless, bzmore

Seq-Examples

compress all .fastq files
bzip2 *.fastq

to view the first 20 lines of a bzip2 compressed .fastq file
bzcat sample.fastq.bz2 | head -20

tar.bz2

compress all files of a directory in one compressed .tar.bz2 archive-file (option -j for bzip2 compression)
tar -jvcf compressedFiles.tar.bz2  directory_orig_files/  # -j for bz2
tar -zcvf compressedFiles.tar.gz directory_orig_files/    # -z for gzip
compress a set of files (without directory)
tar -jvcf compressedFiles.tar.bz2  file1.txt file2.txt file3.txt
tar -jvcf compressedFiles.tar.bz2  *.txt

join paired read sequence files into a single compressed sample file
tar -jvcf sample.tar.bz2  sample_1.fastq  sample_2.fastq

decompress .tar.bz2 files
tar -jvxf sample.tar.bz2

to decompress in a pipe, extract files to standard output (option -O)
tar -jxOf sample.tar.bz2 | head -20   # views the first 20 lines

list content (all files) of a .tar.bz2 archive
tar -tf sample.tar.bz2
sample_1.fastq 
sample_2.fastq


extract single file from .tar.bz2 archive
tar -jvxf sample.tar.bz2 sample_1.fastq

sample_1.fastq