Bash/Shell Tutorial

The ability to navigate the filesystem using bash is a very important skill in statistical genetics. Bash is a programming language commonly used to navigate the terminal and manipulate files and folders. Some terminals run "bash-like" scripting languages like "zsh". For the purposes of this tutorial, they are indistinguishable from bash. There are approximately 50 bash commands that are used 95% of the time. Here we will review some common commands and do some simple file analysis.

Common Commands

cd

This command is used to change our directory, in the following manner:

   cd $PATH

where $PATH represents the path to the target directory. Common usage of cd includes:

   cd ~/ # will bring you to your home directory

   cd $HOME # will bring you to your home directory

   cd ../ # will bring you to the parent directory (up one level)

   cd Downloads # will bring you to the Downloads directory, provided that you are in the home directory

   cd ~/Downloads # will bring you to Downloads, no matter where you are in the filesystem

ls

This command allows you to look at the contents of a directory:

ls

Some common usage of ls includes:

ls # list the contents of the current directory 
ls ~ # list the contents of the home directory 
ls ~/Desktop # Will list the contents of the Desktop

For ls, there are a number of additional Unix command options that you can append to it to get additional information, for example:

    ls -l  # shows files as list

    ls -lh  # shows files as a list with human readable format

    ls -lt  # shows the files as a list sorted by time-last-edited

    ls -lS  # shows the files as a list sorted by size

mkdir

This command to create a new directory in your home folder:

mkdir ~/test_directory

cd ~/test_directory wsl                                                                                                                                                                                        

echo

echo prints to screen:

echo "Hello"

touch

touch creates a new (empty) file:

touch foo

rm

rm deletes a file:

rm foo

^

The carrot sign ^ sends the output to a file:

echo "Hello" > output.txt

cat

cat prints the entire contents of a file to the screen:

cat output.txt

less

less can be used to view a file:

less output.txt

to return to the terminal press q

cp

cp copies a file:

cat output.txt output2.txt

nano

nano can be used to edit a file:

nano data1.txt

Will bring up an editor window:

Starting from the top line type:

bob   1
fred  2 
mary  3
noah  4 
sally 5

And then save the file using Ctrl-O and press enter, and quit using Ctrl-X.

wc

The word count command wc can be used to count the number of lines or words in a file:

    wc -l data1.txt

grep

Can be used to search a file for a string:

grep "noah" data1.txt

will return all the lines in data1.txt containing the string "noah".

File Analysis

A very powerful feature of the terminal is the awk programming language, which allows us to extract subsets of a data file, filter data according to some criteria or perform arithmetic operations on the data. awk manipulates a data file by performing operations on its columns - this is extremely useful for scientific data sets because typically the columns are features or variables of interest.

For example, we can use awk to produce a new file that squares the data in our previous file:

awk '{print $1,$2*$2}' data1.txt > data2.txt

We can also use awk to add up all the squared data values:

awk 'BEGIN{total=0} {total+=$2} END{print total}' data2.txt