One other use of the echo command is for displaying the contents of something known as environment variables. These contain user-specific or system-wide values that either reflect simple pieces of information (your username), or lists of useful locations on the file system. Some examples:
ubuntu@:~/Learning_unix$ echo $USER
ubuntu
ubuntu@:~/Learning_unix$ echo $HOME
/home/ubuntu
ubuntu@:~/Learning_unix$ echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
The last one shows the content of the $PATH environment variable, which displays a ‘colon separated’ list of directories that are expected to contain programs that you can run. This includes all of the Unix commands that you have seen so far. These are files that live in directories which are run like programs (e.g. ls is just a special type of file in the /bin directory).
Knowing how to change your $PATH to include custom directories can be necessary sometimes (e.g. if you install some new bioinformatics software in a non-standard location).
Use nano to add the following lines to opening_lines.txt:
Now is the winter of our discontent.
All children, except one, grow up.
The Galactic Empire was dying.
In a hole in the ground there lived a hobbit.
It was a pleasure to burn.
It was a bright, cold day in April, and the clocks were striking thirteen.
It was love at first sight.
I am an invisible man.
It was the day my grandmother exploded.
When he was nearly thirteen, my brother Jem got his arm badly broken at the elbow.
Marley was dead, to begin with.
You will often want to search files to find lines that match a certain pattern. The Unix command grep does this (and much more). The following examples show how you can use grep’s command-line options to:
-i)-w)-v)*, ., and [])grep was opening_lines.txt
The Galactic Empire was dying.
It was a pleasure to burn.
It was a bright, cold day in April, and the clocks were striking thirteen.
It was love at first sight.
It was the day my grandmother exploded.
When he was nearly thirteen, my brother Jem got his arm badly broken at the elbow.
Marley was dead, to begin with.
grep -v was opening_lines.txt
Call me Ishmael.
The primroses were over.
Now is the winter of our discontent.
All children, except one, grow up.
In a hole in the ground there lived a hobbit.
I am an invisible man.
grep all opening_lines.txt
Call me Ishmael.
grep -i all opening_lines.txt
Call me Ishmael.
All children, except one, grow up.
grep in opening_lines.txt
Now is the winter of our discontent.
The Galactic Empire was dying.
In a hole in the ground there lived a hobbit.
It was a bright, cold day in April, and the clocks were striking thirteen.
I am an invisible man.
Marley was dead, to begin with.
grep -w in opening_lines.txt
In a hole in the ground there lived a hobbit.
It was a bright, cold day in April, and the clocks were striking thirteen.
grep -w o.. opening_lines.txt
Now is the winter of our discontent.
All children, except one, grow up.
grep [aeiou]t opening_lines.txt
In a hole in the ground there lived a hobbit.
It was love at first sight.
It was the day my grandmother exploded.
When he was nearly thirteen, my brother Jem got his arm badly broken at the elbow.
Marley was dead, to begin with.
grep -w -i [aeiou]t opening_lines.txt
It was a pleasure to burn.
It was a bright, cold day in April, and the clocks were striking thirteen.
It was love at first sight.
It was the day my grandmother exploded.
When he was nearly thirteen, my brother Jem got his arm badly broken at the elbow.
One of the most powerful features of Unix is that you can send the output from one command or program to any other command (as long as the second command accepts input of some sort). We do this by using what is known as a pipe. This is implemented using the ‘|’ character (which is a character which always seems to be on different keys depending on the keyboard that you are using). Think of the pipe as simply connecting two Unix programs. Here’s an example which introduces some new Unix commands:
ubuntu@:~/Learning_unix$ grep was opening_lines.txt | wc -c
316
ubuntu@:~/Learning_unix$
grep was opening_lines.txt | sort | head -n 3 | wc -c
130
The first use of grep searches the specified file for lines matching ‘was’, it sends the lines that match through a pipe to the wc program. We use the -c option to just count characters in the matching lines (316).
The second example first sends the output of grep to the Unix sort command. This sorts a file alphanumerically by default. The sorted output is sent to the head command which by default shows the first 10 lines of a file. We use the -n option of this command to only show 3 lines. These 3 lines are then sent to the wc command as before.
Whenever making a long pipe, test each step as you build it!
The following examples introduce some other Unix commands, and show how they could be used to work on a fictional file called file.txt. Remember, you can always learn more about these Unix commands from their respective man pages with the man command. These are not all real world cases, but rather show the diversity of Unix command-line tools:
tail -n 20 file.txt | head
^ matches patterns at the start of a line):grep "^ATG" file.txt
cut -f 3 file.txt | sort -u
-c option of grep counts lines):grep -c '[bc]at' file.txt
cat file.txt | tr 'a-z' 'A-Z'
cat file.txt | sed 's/Chr1/Chromosome 1/' > file2.txt