Shell Scripts

Overview

Teaching: 30 min
Exercises: 15 min

Questions

How can I save and re-use commands?

Objectives

Write a shell script that runs a command or series of commands for a fixed set of files.

Run a shell script from the command line.

Write a shell script that operates on a set of files defined by the user on the command line.

Create pipelines that include shell scripts you, and others, have written.

We are finally ready to see what makes the shell such a powerful programming environment. We are going to take the commands we repeat frequently and save them in files so that we can re-run all those operations again later by typing a single command. For historical reasons, a bunch of commands saved in a file is usually called a shell script, but make no mistake: these are actually small programs.

Script File Format

$ nano myscript.sh

#!/bin/bash
# filename: myscript.sh
# This is our first script

echo "Hello world!" # This is a comment too

Comments

Comments start with the symbol #. Anything after the # is not get executed.

Then we save the file (Ctrl-O in nano), and exit the text editor (Ctrl-X in nano).

Once we have saved the file, we need to change the file permission to execute. This is done using chmod as:

$ chmod +x myscript.sh

Now, we run the following command:

$ ./myscript.sh
Hello world!

Variables

A variable is a placeholder for the data. In shell script, variables are as

variableName=variable value (Note: No spaces on either side of the = sign).

While calling the varible, $ sign must be called before the variable name.

Variable can be also called using curly braces,${}.

#!/bin/bash
# filename: myscript.sh
# This is our first script

echo "Hello world!" # This is a comment too

# Varaibles

name="John" # no spaces on either side of the = sign
echo Hello $name 
# OR
echo Hello ${name} 

$ ./myscript.sh
Hello world!
Hello John
Hello John

Let’s start by going back to molecules/ and creating a new file, middle.sh which will become our shell script:

$ cd molecules
$ nano middle.sh

The command nano middle.sh opens the file middle.sh within the text editor ‘nano’ (which runs within the shell). If the file does not exist, it will be created. We can use the text editor to directly edit the file – we’ll simply insert the following line:

#!/bin/bash
# filename: middle.sh

head -n 15 octane.pdb | tail -n 5

This is a variation on the pipe we constructed earlier: it selects lines 11-15 of the file octane.pdb. Remember, we are not running it as a command just yet: we are putting the commands in a file.

Then we save the file (Ctrl-O in nano), and exit the text editor (Ctrl-X in nano). Check that the directory molecules now contains a file called middle.sh.

Once we have saved the file, we need to change the file permission to execute. This is done using chmod as:

chmod +x middle.sh

Now, we can ask the shell to execute the commands it contains. so we run the following command:

$ ./middle.sh

ATOM      9  H           1      -4.502   0.681   0.785  1.00  0.00
ATOM     10  H           1      -5.254  -0.243  -0.537  1.00  0.00
ATOM     11  H           1      -4.357   1.252  -0.895  1.00  0.00
ATOM     12  H           1      -3.009  -0.741  -1.467  1.00  0.00
ATOM     13  H           1      -3.172  -1.337   0.206  1.00  0.00

Sure enough, our script’s output is exactly what we would get if we ran that pipeline directly.

Text vs. Whatever

We usually call programs like Microsoft Word or LibreOffice Writer “text editors”, but we need to be a bit more careful when it comes to programming. By default, Microsoft Word uses .docx files to store not only text, but also formatting information about fonts, headings, and so on. This extra information isn’t stored as characters, and doesn’t mean anything to tools like head: they expect input files to contain nothing but the letters, digits, and punctuation on a standard computer keyboard. When editing programs, therefore, you must either use a plain text editor, or be careful to save files as plain text.

In the above script, we have selected 11-15 line from the octane.pdb. What if we want to select lines from an arbitrary file? We could edit middle.sh each time to change the filename, but that would probably take longer than typing the command out again in the shell and executing it with a new file name. Instead, let’s edit middle.sh and make it more versatile:

$ nano middle.sh

Now, within “nano”, replace the text octane.pdb with the special variable called $1:

#!/bin/bash
# filename: middle.sh

head -n 15 "$1" | tail -n 5  # octane.pdb -> $1

Inside a shell script, $1 means ‘the first filename (or other argument) on the command line’.

Command line arguments

$0: The name of the script.

$1-$9:$1 is the first argument, $2 is the second and so on.

$#: How many command line arguments were given to the script.

$*: All of the command line arguments.

We can now run our script like this:

$ ./middle.sh octane.pdb

ATOM      9  H           1      -4.502   0.681   0.785  1.00  0.00
ATOM     10  H           1      -5.254  -0.243  -0.537  1.00  0.00
ATOM     11  H           1      -4.357   1.252  -0.895  1.00  0.00
ATOM     12  H           1      -3.009  -0.741  -1.467  1.00  0.00
ATOM     13  H           1      -3.172  -1.337   0.206  1.00  0.00

or on a different file like this:

$ ./middle.sh pentane.pdb

ATOM      9  H           1       1.324   0.350  -1.332  1.00  0.00
ATOM     10  H           1       1.271   1.378   0.122  1.00  0.00
ATOM     11  H           1      -0.074  -0.384   1.288  1.00  0.00
ATOM     12  H           1      -0.048  -1.362  -0.205  1.00  0.00
ATOM     13  H           1      -1.183   0.500  -1.412  1.00  0.00

Double-Quotes Around Arguments

For the same reason that we put the loop variable inside double-quotes, in case the filename happens to contain any spaces, we surround $1 with double-quotes.

We still need to edit middle.sh each time we want to adjust the range of lines, though. Let’s fix that by using the special variables $2 and $3 for the number of lines to be passed to head and tail respectively:

$ nano middle.sh

#!/bin/bash
# filename: middle.sh

# head -n 15 octane.pdb | tail -n 5

head -n "$2" "$1" | tail -n "$3"  # $1 = filename,   line-range=($2-$3) to $2

We can now run:

$ ./middle.sh pentane.pdb 15 5

ATOM      9  H           1       1.324   0.350  -1.332  1.00  0.00
ATOM     10  H           1       1.271   1.378   0.122  1.00  0.00
ATOM     11  H           1      -0.074  -0.384   1.288  1.00  0.00
ATOM     12  H           1      -0.048  -1.362  -0.205  1.00  0.00
ATOM     13  H           1      -1.183   0.500  -1.412  1.00  0.00

By changing the arguments to our command we can change our script’s behaviour:

$ bash middle.sh pentane.pdb 20 5

ATOM     14  H           1      -1.259   1.420   0.112  1.00  0.00
ATOM     15  H           1      -2.608  -0.407   1.130  1.00  0.00
ATOM     16  H           1      -2.540  -1.303  -0.404  1.00  0.00
ATOM     17  H           1      -3.393   0.254  -0.321  1.00  0.00
TER      18              1

This works, but it may take the next person who reads middle.sh a moment to figure out what it does. We can improve our script by adding some comments at the top:

$ nano middle.sh

#!/bin/bash
# filename: middle.sh

# Select lines from the middle of a file.
# Usage: bash middle.sh filename end_line num_lines

head -n "$2" "$1" | tail -n "$3"

A comment starts with a # character and runs to the end of the line. The computer ignores comments, but they’re invaluable for helping people (including your future self) understand and use scripts. The only caveat is that each time you modify the script, you should check that the comment is still accurate: an explanation that sends the reader in the wrong direction is worse than none at all.

What if we want to process many files in a single pipeline? For example, if we want to sort our .pdb files by length, we would type:

$ wc -l *.pdb | sort -n

because wc -l lists the number of lines in the files (recall that wc stands for ‘word count’, adding the -l option means ‘count lines’ instead) and sort -n sorts things numerically. We could put this in a file, but then it would only ever sort a list of .pdb files in the current directory. If we want to be able to get a sorted list of other kinds of files, we need a way to get all those names into the script. We can’t use $1, $2, and so on because we don’t know how many files there are. Instead, we use the special variable $@, which means, ‘All of the command-line arguments to the shell script’. We also should put $@ inside double-quotes to handle the case of arguments containing spaces ("$@" is equivalent to "$1" "$2" …) Here’s an example:

$ nano sorted.sh

#!/bin/bash
#filename: sorted.sh
# Sort files by their length.
# Usage: bash sorted.sh one_or_more_filenames
wc -l "$@" | sort -n

$ bash sorted.sh *.pdb ../creatures/*.dat

methane.pdb
ethane.pdb
propane.pdb
cubane.pdb
pentane.pdb
octane.pdb
../creatures/basilisk.dat
../creatures/minotaur.dat
../creatures/unicorn.dat
total

List Unique Species

Leah has several hundred data files, each of which is formatted like this:
2013-11-05,deer,5
2013-11-05,rabbit,22
2013-11-05,raccoon,7
2013-11-06,rabbit,19
2013-11-06,deer,2
2013-11-06,fox,1
2013-11-07,rabbit,18
2013-11-07,bear,1
An example of this type of file is given in data-shell/data/animal-counts/animals.txt.

We can use the command cut -d , -f 2 animals.txt | sort | uniq to produce the unique species in animals.txt. In order to avoid having to type out this series of commands every time, a scientist may choose to write a shell script instead.

Write a shell script called species.sh that takes any number of filenames as command-line arguments, and uses a variation of the above command to print a list of the unique species appearing in each of those files separately.
Solution
# Script to find unique species in csv files where species is the second data field
# This script accepts any number of file names as command line arguments

# Loop over all files
for file in $@
do
	echo "Unique species in $file:"
	# Extract species names
	cut -d , -f 2 $file | sort | uniq
done

Variables in Shell Scripts

In the molecules directory, imagine you have a shell script called script.sh containing the following commands:
head -n $2 $1
tail -n $3 $1
While you are in the molecules directory, you type the following command:
bash script.sh '*.pdb' 1 1
Which of the following outputs would you expect to see?

All of the lines between the first and the last lines of each file ending in .pdb in the molecules directory

The first and the last line of each file ending in .pdb in the molecules directory

The first and the last line of each file in the molecules directory

An error because of the quotes around *.pdb
Solution

The correct answer is 2.

The special variables $1, $2 and $3 represent the command line arguments given to the script, such that the commands run are:
$ head -n 1 cubane.pdb ethane.pdb octane.pdb pentane.pdb propane.pdb
$ tail -n 1 cubane.pdb ethane.pdb octane.pdb pentane.pdb propane.pdb
The shell does not expand '*.pdb' because it is enclosed by quote marks. As such, the first argument to the script is '*.pdb' which gets expanded within the script by head and tail.

Find the Longest File With a Given Extension

Write a shell script called longest.sh that takes the name of a directory and a filename extension as its arguments, and prints out the name of the file with the most lines in that directory with that extension. For example:
$ bash longest.sh /tmp/data pdb
would print the name of the .pdb file in /tmp/data that has the most lines.
Solution
# Shell script which takes two arguments:
#    1. a directory name
#    2. a file extension
# and prints the name of the file in that directory
# with the most lines which matches the file extension.

wc -l $1/*.$2 | sort -n | tail -n 2 | head -n 1

Key Points

Save commands in files (usually called shell scripts) for re-use.

bash filename runs the commands saved in a file.

$@ refers to all of a shell script’s command-line arguments.

$1, $2, etc., refer to the first command-line argument, the second command-line argument, etc.

Place variables in quotes if the values might have spaces in them.

Letting users decide what files to process is more flexible and more consistent with built-in Unix commands.

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The Unix Shell

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Shell Scripts

Overview

Script File Format

Comments

Variables

Text vs. Whatever

Command line arguments

Double-Quotes Around Arguments

List Unique Species

Solution

Variables in Shell Scripts

Solution

Find the Longest File With a Given Extension

Solution

Key Points

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