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Bioinformatics Solutions in Ecology and Evolution

14 May 2015

Unix cheat sheet

Tagged: Commandline






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Being familiar with the Unix commandline is essential for bioinformatics data analysis but it might seem complex or tedious at the beginning. However, you will get already quite far with only a few commands. Here, I provide a cheat sheet that gives a quick overview of the most essential commands which will increase your efficiency in data analysis and file handling drastically - promised! You will find more details on most of these commands in my previous blog posts that were marked with the ‘Commandline’ tag. The cheat sheet can also be downloaded as a PDF file (click here).

FILE system

Command Meaning
cd DIR change directory to DIR
cd .. go up one directory
cd ~ to to your home directory
pwd show present working directory
ls list items in current directory
ls -a list all items, including hidden ones
ls -lhcrt list all items in long, human-readable format and sort in reverse order by modification time
ls -F list all items in current directory and show directories with a slash and executables with a star
tree -C print hierarchical structure of your FILEs and directories (color-coded)
tree -d print hierarchical structure of all subdirectories
tree -sh print hierarchical structure of FILEs and directories with sizes (-s) in a human-readable format (-h)
mkdir directoryname make new directory named directoryname
mv FILE1 FILE2 rename FILE1 to FILE2
mv FILE1 ../FILE2 move FILE1 one directory up
cp FILE1 FILE2 copy FILE1 and save it as FILE2
rm FILE remove FILE
rm -r DIRECTORY remove directory and all of its contents

Opening FILEs and extracting information

Command Meaning
less FILE open FILE and scroll through it line by line
wc -l -w -m FILE counting lines, words, and characters in FILE
grep "pattern" FILE print lines from FILE that contain “pattern”
grp -v "pattern" FILE print lines from FILE that do not contain “pattern”
cat FILE > FILE2 write the content of FILE to FILE2
cat FILE >> FILE2 append the content of FILE to FILE2
sed -n 11,12p FILE extract lines 11 to 12 from FILE
awk -F "\t" '$1 > 20 {print $0}' FILE Print all columns of a line ($0) in FILE if the value in column 1 ($1) is bigger than 20
unzip FILE.zip unzip the zip-compressed FILE
gunzip FILE.gz unzip the gz-compressed FILE
sort -n NUMBERS sort a row of NUMBERS numerically
uniq -c FILE count unique lines in FILE
nano FILE open FILE on the command-line
xdg-open FILE open FILE with the standard program for its file type
eog FILE open FILE (which is a figure) with the Eye of Gnome graphics viewer program

Data transfer

Command Meaning
rsync --progress -avz SRC DEST transfer from SRC to DEST, show the progress while FILEs are compressed during the transfer in archive mode (including recursing into directories)
rsync FILE user@host://home/usr/ transfer FILE to the folder /home/usr on the remote server user@host
rsync -avz directory/ DEST transfer all FILEs saved in directory to DEST
rsync -avz directory DEST create the folder directory in DEST and transfer all FILEs in this directory
scp -r SRC DEST transfer all FILEs in SRC to DEST
scp FILE DEST transfer FILE to DEST

Executing scripts and programs

Command Meaning
nohup ... & execute … in the background
nohup ... > FILE.txt & execute … in the background and redirect output to FILE.txt
ps -p ID print the status of a process with the specified process-ID
kill ID stop the process witht the specified process-ID
pkill NAME stop all processes with NAME (NAME could be for example ‘R’ or ‘python’)
top provides an ongoing look at processor activity in real time

Networking

Command Meaning
ssh user@host connect to host as user
ssh -X user@host connect to host as user with X11 forwarding enabled (you can open programs with graphical user interface)

Help

Command Meaning
command --help Lists the options for command
man command opens the manual page for command (exit with ‘q’)

Tricks

Pipe output from one command with | as input to another command.

Command Meaning
TAB key auto-completion of commands, FILE names etc.
UP or DOWN arrows move through the history of your commands
history Get overview of the commands you have used
* Allows to generalize file names. For example, *fasta refers to all fasta files in a directory