Summary and Setup

The Unix shell has been around longer than most of its users have been alive. It has survived because it’s a powerful
tool that allows users to perform complex and powerful tasks, often with just a few keystrokes or lines of code. It
helps users automate repetitive tasks and easily combine smaller tasks into larger, more powerful workflows.

Use of the shell is fundamental to a wide range of advanced computing tasks, including high-performance
computing. These lessons will introduce you to this powerful tool.

PREREQUISITES

This lesson guides you through the basics of file systems and the shell. If you have stored files on a computer at all
and recognize the word “file” and either “directory” or “folder” (two common words for the same thing), you’re
ready for this lesson.

If you’re already comfortable manipulating files and directories, searching for files with grep and find, and
writing simple loops and scripts, you probably want to explore the next lesson: shell-extras.

Download files

You need to download some files to follow this lesson.

1. Download shell-lesson-data.zip and move the file to your Desktop.

2. Unzip/extract the file. Let your instructor know if you need help with this step. You should end up with
a new folder called shell-lesson-data on your Desktop.
Install software

If you do not already have the shell software installed, you will need to download and install it.

Open a new shell

After installing the software

3. Open a terminal. If you’re not sure how to open a terminal on your operating system, see the instructions
below.
4. In the terminal type cd then press the Return key. This step will make sure you start with your home folder
as your working directory.

In the lesson, you will find out how to access the data files in this folder.

WHERE TO TYPE COMMAN DS: HOW TO OPEN A NE W SHELL

The shell is a program that enables us to send commands to the computer and receive output. It is also referred to as
the terminal or command line.

Some computers include a default Unix Shell program. The steps below describe some methods for identifying and
opening a Unix Shell program if you already have one installed. There are also options for identifying and
downloading a Unix Shell program, a Linux/UNIX emulator, or a program to access a Unix Shell on a server.

If none of the options below address your circumstances, try an online search for: Unix shell [your computer model]
[your operating system].

Introducing the Shell

Last updated on 2023-06-09 | Edit this page

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OVERVIEW
Questions

 What is a command shell and why would I use one?

Objectives

 Explain how the shell relates to the keyboard, the screen, the operating system, and users’ programs.

 Explain when and why command-line interfaces should be used instead of graphical interfaces.
Background

Humans and computers commonly interact in many different ways, such as through a keyboard and mouse, touch
screen interfaces, or using speech recognition systems. The most widely used way to interact with personal
computers is called a graphical user interface (GUI). With a GUI, we give instructions by clicking a mouse and
using menu-driven interactions.

While the visual aid of a GUI makes it intuitive to learn, this way of delivering instructions to a computer scales
very poorly. Imagine the following task: for a literature search, you have to copy the third line of one thousand text
files in one thousand different directories and paste it into a single file. Using a GUI, you would not only be clicking
at your desk for several hours, but you could potentially also commit an error in the process of completing this
repetitive task. This is where we take advantage of the Unix shell. The Unix shell is both a command-line
interface (CLI) and a scripting language, allowing such repetitive tasks to be done automatically and fast. With the
proper commands, the shell can repeat tasks with or without some modification as many times as we want. Using the
shell, the task in the literature example can be accomplished in seconds.

The Shell

The shell is a program where users can type commands. With the shell, it’s possible to invoke complicated programs
like climate modeling software or simple commands that create an empty directory with only one line of code. The
most popular Unix shell is Bash (the Bourne Again SHell — so-called because it’s derived from a shell written by
Stephen Bourne). Bash is the default shell on most modern implementations of Unix and in most packages that
provide Unix-like tools for Windows. Note that ‘Git Bash’ is a piece of software that enables Windows users to use
a Bash like interface when interacting with Git.

Using the shell will take some effort and some time to learn. While a GUI presents you with choices to select, CLI
choices are not automatically presented to you, so you must learn a few commands like new vocabulary in a
language you’re studying. However, unlike a spoken language, a small number of “words” (i.e. commands) gets you
a long way, and we’ll cover those essential few today.

The grammar of a shell allows you to combine existing tools into powerful pipelines and handle large volumes of
data automatically. Sequences of commands can be written into a script, improving the reproducibility of
workflows.

In addition, the command line is often the easiest way to interact with remote machines and supercomputers.
Familiarity with the shell is near essential to run a variety of specialized tools and resources including high-
performance computing systems. As clusters and cloud computing systems become more popular for scientific data
crunching, being able to interact with the shell is becoming a necessary skill. We can build on the command-line
skills covered here to tackle a wide range of scientific questions and computational challenges.

Let’s get started.

When the shell is first opened, you are presented with a prompt, indicating that the shell is waiting for input.

BASH
$
The shell typically uses $ as the prompt, but may use a different symbol. In the examples for this lesson, we’ll show
the prompt as $. Most importantly, do not type the prompt when typing commands. Only type the command that
follows the prompt. This rule applies both in these lessons and in lessons from other sources. Also note that after
you type a command, you have to press the Enter key to execute it.

The prompt is followed by a text cursor, a character that indicates the position where your typing will appear. The
cursor is usually a flashing or solid block, but it can also be an underscore or a pipe. You may have seen it in a text
editor program, for example.

Note that your prompt might look a little different. In particular, most popular shell environments by default put
your user name and the host name before the $. Such a prompt might look like, e.g.:

BASH

nelle@localhost $
The prompt might even include more than this. Do not worry if your prompt is not just a short $. This lesson does
not depend on this additional information and it should also not get in your way. The only important item to focus
on is the $ character itself and we will see later why.

So let’s try our first command, ls, which is short for listing. This command will list the contents of the current
directory:

BASH

$ ls

OUTPUT

Desktop Downloads Movies Pictures

Documents Library Music Public
COMMAND NOT FOUND

If the shell can’t find a program whose name is the command you typed, it will print an error message such as:

BASH

$ ks
OUTPUT

ks: command not found

This might happen if the command was mis-typed or if the program corresponding to that command is not installed.

Nelle’s Pipeline: A Typical Problem

Nelle Nemo, a marine biologist, has just returned from a six-month survey of the North Pacific Gyre, where she has
been sampling gelatinous marine life in the Great Pacific Garbage Patch. She has 1520 samples that she’s run
through an assay machine to measure the relative abundance of 300 proteins. She needs to run these 1520 files
through an imaginary program called goostats.sh. In addition to this huge task, she has to write up results by
the end of the month, so her paper can appear in a special issue of Aquatic Goo Letters.

If Nelle chooses to run goostats.sh by hand using a GUI, she’ll have to select and open a file 1520 times.
If goostats.sh takes 30 seconds to run each file, the whole process will take more than 12 hours of Nelle’s
attention. With the shell, Nelle can instead assign her computer this mundane task while she focuses her attention on
writing her paper.

The next few lessons will explore the ways Nelle can achieve this. More specifically, the lessons explain how she
can use a command shell to run the goostats.sh program, using loops to automate the repetitive steps of
entering file names, so that her computer can work while she writes her paper.

As a bonus, once she has put a processing pipeline together, she will be able to use it again whenever she collects
more data.

In order to achieve her task, Nelle needs to know how to:

 navigate to a file/directory
 create a file/directory
 check the length of a file
 chain commands together
 retrieve a set of files
 iterate over files
 run a shell script containing her pipeline

KEYPOINTS

 A shell is a program whose primary purpose is to read commands and run other programs.

 This lesson uses Bash, the default shell in many implementations of Unix.

 Programs can be run in Bash by entering commands at the command-line prompt.

  The shell’s main advantages are its high action-to-keystroke ratio, its support for automating
repetitive tasks, and its capacity to access networked machines.

 A significant challenge when using the shell can be knowing what commands need to be run and
how to run them.

Navigating Files and Directories

Last updated on 2023-06-18 | Edit this page

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OVERVIEW
Questions

 How can I move around on my computer?

 How can I see what files and directories I have?

 How can I specify the location of a file or directory on my computer?

Objectives

 Explain the similarities and differences between a file and a directory.

 Translate an absolute path into a relative path and vice versa.

 Construct absolute and relative paths that identify specific files and directories.

 Use options and arguments to change the behaviour of a shell command.

 Demonstrate the use of tab completion and explain its advantages.

The part of the operating system responsible for managing files and directories is called the file
system. It organizes our data into files, which hold information, and directories (also called
‘folders’), which hold files or other directories.

Several commands are frequently used to create, inspect, rename, and delete files and directories.
To start exploring them, we’ll go to our open shell window.

First, let’s find out where we are by running a command called pwd (which stands for ‘print
working directory’). Directories are like places — at any time while we are using the shell, we
are in exactly one place called our current working directory. Commands mostly read and
write files in the current working directory, i.e. ‘here’, so knowing where you are before running
a command is important. pwd shows you where you are:

BASH

$ pwd

OUTPUT

/Users/nelle
Here, the computer’s response is /Users/nelle, which is Nelle’s home directory:

HOME DIRECTORY VARIA TION

The home directory path will look different on different operating systems. On Linux, it may
look like /home/nelle, and on Windows, it will be similar to C:\Documents and
Settings\nelle or C:\Users\nelle. (Note that it may look slightly different for different
versions of Windows.) In future examples, we’ve used Mac output as the default - Linux and
Windows output may differ slightly but should be generally similar.

We will also assume that your pwd command returns your user’s home directory. If pwd returns
something different, you may need to navigate there using cd or some commands in this lesson
will not work as written. See Exploring Other Directories for more details on the cd command.

To understand what a ‘home directory’ is, let’s have a look at how the file system as a whole is
organized. For the sake of this example, we’ll be illustrating the filesystem on our scientist
Nelle’s computer. After this illustration, you’ll be learning commands to explore your own
filesystem, which will be constructed in a similar way, but not be exactly identical.

On Nelle’s computer, the filesystem looks like this:

The filesystem looks like an upside down tree. The topmost directory is the root directory that
holds everything else. We refer to it using a slash character, /, on its own; this character is the
leading slash in /Users/nelle.

Inside that directory are several other directories: bin (which is where some built-in programs
are stored), data (for miscellaneous data files), Users (where users’ personal directories are
located), tmp (for temporary files that don’t need to be stored long-term), and so on.

We know that our current working directory /Users/nelle is stored

inside /Users because /Users is the first part of its name. Similarly, we know that /Users is
stored inside the root directory / because its name begins with /.

SLASHES
Notice that there are two meanings for the / character. When it appears at the front of a file or
directory name, it refers to the root directory. When it appears inside a path, it’s just a separator.

Underneath /Users, we find one directory for each user with an account on Nelle’s machine, her
colleagues imhotep and larry.

The user imhotep’s files are stored in /Users/imhotep, user larry’s in /Users/larry, and
Nelle’s in /Users/nelle. Nelle is the user in our examples here; therefore, we
get /Users/nelle as our home directory. Typically, when you open a new command prompt,
you will be in your home directory to start.

Now let’s learn the command that will let us see the contents of our own filesystem. We can see
what’s in our home directory by running ls:

BASH

$ ls

OUTPUT

Applications Documents Library Music Public

Desktop Downloads Movies Pictures
(Again, your results may be slightly different depending on your operating system and how you
have customized your filesystem.)

ls prints the names of the files and directories in the current directory. We can make its output
more comprehensible by using the -F option which tells ls to classify the output by adding a
marker to file and directory names to indicate what they are:

 a trailing / indicates that this is a directory

 @ indicates a link
 * indicates an executable
Depending on your shell’s default settings, the shell might also use colors to indicate whether
each entry is a file or directory.

BASH

$ ls -F

OUTPUT

Applications/ Documents/ Library/ Music/ Public/

Desktop/ Downloads/ Movies/ Pictures/
Here, we can see that the home directory contains only sub-directories. Any names in the output
that don’t have a classification symbol are files in the current working directory.

CLEARING YOUR TERMIN AL

If your screen gets too cluttered, you can clear your terminal using the clear command. You
can still access previous commands using ↑ and ↓ to move line-by-line, or by scrolling in your
terminal.

Getting help

ls has lots of other options. There are two common ways to find out how to use a command and
what options it accepts — depending on your environment, you might find that only one of
these ways works:

1. We can pass a --help option to any command (available on Linux and Git Bash), for
example:

BASH

$ ls --help
 2. We can read its manual with man (available on Linux and macOS):

BASH

$ man ls
We’ll describe both ways next.

HELP FOR BUILT -IN COMMANDS

Some commands are built in to the Bash shell, rather than existing as separate programs on the
filesystem. One example is the cd (change directory) command. If you get a message like No
manual entry for cd, try help cd instead. The help command is how you get usage
information for Bash built-ins.

The --help option

Most bash commands and programs that people have written to be run from within bash, support
a --help option that displays more information on how to use the command or program.

BASH

$ ls --help

OUTPUT

Usage: ls [OPTION]... [FILE]...

List information about the FILEs (the current directory by default).
Sort entries alphabetically if neither -cftuvSUX nor --sort is specified.

Mandatory arguments to long options are mandatory for short options, too.
-a, --all do not ignore entries starting with .
-A, --almost-all do not list implied . and ..
 --author with -l, print the author of each file
-b, --escape print C-style escapes for nongraphic characters
--block-size=SIZE scale sizes by SIZE before printing them; e.g.,
'--block-size=M' prints sizes in units of
1,048,576 bytes; see SIZE format below
-B, --ignore-backups do not list implied entries ending with ~
-c with -lt: sort by, and show, ctime (time of
last
modification of file status information);
with -l: show ctime and sort by name;
otherwise: sort by ctime, newest first
-C list entries by columns
--color[=WHEN] colorize the output; WHEN can be 'always'
(default
if omitted), 'auto', or 'never'; more info
below
-d, --directory list directories themselves, not their contents
-D, --dired generate output designed for Emacs' dired mode
-f do not sort, enable -aU, disable -ls --color
-F, --classify append indicator (one of */=>@|) to entries
... ... ...
UNSUPPORTED COMMAND -LINE OPTIONS

If you try to use an option that is not supported, ls and other commands will usually print an
error message similar to:

BASH

$ ls -j

ERROR
ls: invalid option -- 'j'
Try 'ls --help' for more information.

The man command

The other way to learn about ls is to type

BASH

$ man ls
This command will turn your terminal into a page with a description of the ls command and its
options.

To navigate through the man pages, you may use ↑ and ↓ to move line-by-line, or
try B and Spacebar to skip up and down by a full page. To search for a character or word in
the man pages, use / followed by the character or word you are searching for. Sometimes a search
will result in multiple hits. If so, you can move between hits using N (for moving forward)
and Shift+N (for moving backward).

To quit the man pages, press Q.

MANUAL PAGES ON THE WEB

Of course, there is a third way to access help for commands: searching the internet via your web
browser. When using internet search, including the phrase unix man page in your search query
will help to find relevant results.

GNU provides links to its manuals including the core GNU utilities, which covers many
commands introduced within this lesson.

EXPLORING MORE l s OPTIONS

You can also use two options at the same time. What does the command ls do when used with
the -l option? What about if you use both the -l and the -h option?
Some of its output is about properties that we do not cover in this lesson (such as file permissions
and ownership), but the rest should be useful nevertheless.

Show me the solution

The -l option makes ls use a long listing format, showing not only the file/directory names but
also additional information, such as the file size and the time of its last modification. If you use
both the -h option and the -l option, this makes the file size ‘human readable’, i.e. displaying
something like 5.3K instead of 5369.

LISTING IN REVERSE C HRONOLOGICAL ORDER

By default, ls lists the contents of a directory in alphabetical order by name. The command ls
-t lists items by time of last change instead of alphabetically. The command ls -r lists the
contents of a directory in reverse order. Which file is displayed last when you combine the -
t and -r options? Hint: You may need to use the -l option to see the last changed dates.

Show me the solution

The most recently changed file is listed last when using -rt. This can be very useful for finding
your most recent edits or checking to see if a new output file was written.

Exploring Other Directories

Not only can we use ls on the current working directory, but we can use it to list the contents of
a different directory. Let’s take a look at our Desktop directory by running ls -F Desktop,
i.e., the command ls with the -F option and the argument Desktop. The
argument Desktop tells ls that we want a listing of something other than our current working
directory:

BASH

$ ls -F Desktop

OUTPUT
shell-lesson-data/
Note that if a directory named Desktop does not exist in your current working directory, this
command will return an error. Typically, a Desktop directory exists in your home directory,
which we assume is the current working directory of your bash shell.

Your output should be a list of all the files and sub-directories in your Desktop directory,
including the shell-lesson-data directory you downloaded at the setup for this lesson. (On
most systems, the contents of the Desktop directory in the shell will show up as icons in a
graphical user interface behind all the open windows. See if this is the case for you.)

Organizing things hierarchically helps us keep track of our work. While it’s possible to put
hundreds of files in our home directory just as it’s possible to pile hundreds of printed papers on
our desk, it’s much easier to find things when they’ve been organized into sensibly-named
subdirectories.

Now that we know the shell-lesson-data directory is located in our Desktop directory, we
can do two things.

First, using the same strategy as before, we can look at its contents by passing a directory name
to ls:

BASH

$ ls -F Desktop/shell-lesson-data

OUTPUT

exercise-data/ north-pacific-gyre/
Second, we can actually change our location to a different directory, so we are no longer located
in our home directory.

The command to change locations is cd followed by a directory name to change our working
directory. cd stands for ‘change directory’, which is a bit misleading. The command doesn’t
change the directory; it changes the shell’s current working directory. In other words it changes
the shell’s settings for what directory we are in. The cd command is akin to double-clicking a
folder in a graphical interface to get into that folder.

Let’s say we want to move into the exercise-data directory we saw above. We can use the
following series of commands to get there:

BASH

$ cd Desktop
$ cd shell-lesson-data
$ cd exercise-data
These commands will move us from our home directory into our Desktop directory, then into
the shell-lesson-data directory, then into the exercise-data directory. You will notice
that cd doesn’t print anything. This is normal. Many shell commands will not output anything to
the screen when successfully executed. But if we run pwd after it, we can see that we are now
in /Users/nelle/Desktop/shell-lesson-data/exercise-data.

If we run ls -F without arguments now, it lists the contents

of /Users/nelle/Desktop/shell-lesson-data/exercise-data, because that’s where we
now are:

BASH

$ pwd

OUTPUT

/Users/nelle/Desktop/shell-lesson-data/exercise-data

BASH
$ ls -F

OUTPUT

animal-counts/ creatures/ numbers.txt alkanes/ writing/

We now know how to go down the directory tree (i.e. how to go into a subdirectory), but how do
we go up (i.e. how do we leave a directory and go into its parent directory)? We might try the
following:

BASH

$ cd shell-lesson-data

ERROR

-bash: cd: shell-lesson-data: No such file or directory

But we get an error! Why is this?

With our methods so far, cd can only see sub-directories inside your current directory. There are
different ways to see directories above your current location; we’ll start with the simplest.

There is a shortcut in the shell to move up one directory level. It works as follows:

BASH

$ cd ..
.. is a special directory name meaning “the directory containing this one”, or more succinctly,
the parent of the current directory. Sure enough, if we run pwd after running cd .., we’re back
in /Users/nelle/Desktop/shell-lesson-data:
BASH

$ pwd

OUTPUT

/Users/nelle/Desktop/shell-lesson-data
The special directory .. doesn’t usually show up when we run ls. If we want to display it, we
can add the -a option to ls -F:

BASH

$ ls -F -a

OUTPUT

./ ../ exercise-data/ north-pacific-gyre/

-a stands for ‘show all’ (including hidden files); it forces ls to show us file and directory names
that begin with ., such as .. (which, if we’re in /Users/nelle, refers to the /Users directory).
As you can see, it also displays another special directory that’s just called ., which means ‘the
current working directory’. It may seem redundant to have a name for it, but we’ll see some uses
for it soon.

Note that in most command line tools, multiple options can be combined with a single - and no
spaces between the options; ls -F -a is equivalent to ls -Fa.

OTHER HIDDEN FILES

In addition to the hidden directories .. and ., you may also see a file called .bash_profile.
This file usually contains shell configuration settings. You may also see other files and
directories beginning with .. These are usually files and directories that are used to configure
different programs on your computer. The prefix . is used to prevent these configuration files
from cluttering the terminal when a standard ls command is used.

These three commands are the basic commands for navigating the filesystem on your
computer: pwd, ls, and cd. Let’s explore some variations on those commands. What happens if
you type cd on its own, without giving a directory?

BASH

$ cd
How can you check what happened? pwd gives us the answer!

BASH

$ pwd

OUTPUT

/Users/nelle
It turns out that cd without an argument will return you to your home directory, which is great if
you’ve got lost in your own filesystem.

Let’s try returning to the exercise-data directory from before. Last time, we used three
commands, but we can actually string together the list of directories to move to exercise-
data in one step:

BASH

$ cd Desktop/shell-lesson-data/exercise-data
Check that we’ve moved to the right place by running pwd and ls -F.
If we want to move up one level from the data directory, we could use cd ... But there is
another way to move to any directory, regardless of your current location.

So far, when specifying directory names, or even a directory path (as above), we have been
using relative paths. When you use a relative path with a command like ls or cd, it tries to find
that location from where we are, rather than from the root of the file system.

However, it is possible to specify the absolute path to a directory by including its entire path
from the root directory, which is indicated by a leading slash. The leading / tells the computer to
follow the path from the root of the file system, so it always refers to exactly one directory, no
matter where we are when we run the command.

This allows us to move to our shell-lesson-data directory from anywhere on the filesystem
(including from inside exercise-data). To find the absolute path we’re looking for, we can
use pwd and then extract the piece we need to move to shell-lesson-data.

BASH

$ pwd

OUTPUT

/Users/nelle/Desktop/shell-lesson-data/exercise-data

BASH

$ cd /Users/nelle/Desktop/shell-lesson-data
Run pwd and ls -F to ensure that we’re in the directory we expect.

TWO MORE SHORTCUTS

The shell interprets a tilde (~) character at the start of a path to mean “the current user’s home
directory”. For example, if Nelle’s home directory is /Users/nelle, then ~/data is equivalent
to /Users/nelle/data. This only works if it is the first character in the
path; here/there/~/elsewhere is not here/there/Users/nelle/elsewhere.

Another shortcut is the - (dash) character. cd will translate - into the previous directory I was in,
which is faster than having to remember, then type, the full path. This is a very efficient way of
moving back and forth between two directories – i.e. if you execute cd - twice, you end up back
in the starting directory.

The difference between cd .. and cd - is that the former brings you up, while the latter brings
you back.

Try it! First navigate to ~/Desktop/shell-lesson-data (you should already be there).

BASH

$ cd ~/Desktop/shell-lesson-data
Then cd into the exercise-data/creatures directory

BASH

$ cd exercise-data/creatures
Now if you run

BASH

$ cd -
you’ll see you’re back in ~/Desktop/shell-lesson-data. Run cd - again and you’re back
in ~/Desktop/shell-lesson-data/exercise-data/creatures

ABSOLUTE VS RELATIVE PATHS

Starting from /Users/amanda/data, which of the following commands could Amanda use to
navigate to her home directory, which is /Users/amanda?

1. cd .

2. cd /

3. cd /home/amanda

4. cd ../..

5. cd ~

6. cd home

7. cd ~/data/..

8. cd

9. cd ..

Show me the solution

1. No: . stands for the current directory.

2. No: / stands for the root directory.

3. No: Amanda’s home directory is /Users/amanda.

4. No: this command goes up two levels, i.e. ends in /Users.

5. Yes: ~ stands for the user’s home directory, in this case /Users/amanda.

6. No: this command would navigate into a directory home in the current directory if
it exists.

7. Yes: unnecessarily complicated, but correct.

8. Yes: shortcut to go back to the user’s home directory.

9. Yes: goes up one level.

RELATIVE PATH RESOLU TION

Using the filesystem diagram below, if pwd displays /Users/thing, what will ls -F
../backup display?

1. ../backup: No such file or directory

2. 2012-12-01 2013-01-08 2013-01-27

3. 2012-12-01/ 2013-01-08/ 2013-01-27/

4. original/ pnas_final/ pnas_sub/

Show me the solution

1. No: there is a directory backup in /Users.

2. No: this is the content of Users/thing/backup, but with .., we asked for one
level further up.

3. No: see previous explanation.

4. Yes: ../backup/ refers to /Users/backup/.

l s READING COMPREHENSIO N

Using the filesystem diagram below, if pwd displays /Users/backup, and -r tells ls to display
things in reverse order, what command(s) will result in the following output:

OUTPUT

pnas_sub/ pnas_final/ original/

1. ls pwd

2. ls -r -F

3. ls -r -F /Users/backup
Show me the solution
1. No: pwd is not the name of a directory.

2. Yes: ls without directory argument lists files and directories in the current
directory.

3. Yes: uses the absolute path explicitly.

General Syntax of a Shell Command

We have now encountered commands, options, and arguments, but it is perhaps useful to
formalise some terminology.

Consider the command below as a general example of a command, which we will dissect into its
component parts:

BASH

$ ls -F /

ls is the command, with an option -F and an argument /. We’ve already encountered options
which either start with a single dash (-), known as short options, or two dashes (--), known
as long options. [Options] change the behavior of a command and Arguments tell the command
what to operate on (e.g. files and directories). Sometimes options and arguments are referred to
as parameters. A command can be called with more than one option and more than one
argument, but a command doesn’t always require an argument or an option.

You might sometimes see options being referred to as switches or flags, especially for options
that take no argument. In this lesson we will stick with using the term option.
Each part is separated by spaces. If you omit the space between ls and -F the shell will look for
a command called ls-F, which doesn’t exist. Also, capitalization can be important. For
example, ls -s will display the size of files and directories alongside the names, while ls -
S will sort the files and directories by size, as shown below:

BASH

$ cd ~/Desktop/shell-lesson-data
$ ls -s exercise-data

OUTPUT

total 28
4 animal-counts 4 creatures 12 numbers.txt 4 alkanes 4 writing
Note that the sizes returned by ls -s are in blocks. As these are defined differently for different
operating systems, you may not obtain the same figures as in the example.

BASH

$ ls -S exercise-data

OUTPUT

animal-counts creatures alkanes writing numbers.txt

Putting all that together, our command ls -F / above gives us a listing of files and directories
in the root directory /. An example of the output you might get from the above command is
given below:

BASH
$ ls -F /

OUTPUT

Applications/ System/
Library/ Users/
Network/ Volumes/
WHEN TO USE SHORT OR LONG OPTIONS

When options exist as both short and long options:

 Use the short option when typing commands directly into the shell to minimize
keystrokes and get your task done faster.

 Use the long option in scripts to provide clarity. It will be read many times and
typed once.

Nelle’s Pipeline: Organizing Files

Knowing this much about files and directories, Nelle is ready to organize the files that the
protein assay machine will create.

She creates a directory called north-pacific-gyre (to remind herself where the data came
from), which will contain the data files from the assay machine and her data processing scripts.

Each of her physical samples is labelled according to her lab’s convention with a unique ten-
character ID, such as ‘NENE01729A’. This ID is what she used in her collection log to record
the location, time, depth, and other characteristics of the sample, so she decides to use it within
the filename of each data file. Since the output of the assay machine is plain text, she will call
her files NENE01729A.txt, NENE01812A.txt, and so on. All 1520 files will go into the same
directory.

Now in her current directory shell-lesson-data, Nelle can see what files she has using the
command:
BASH

$ ls north-pacific-gyre/
This command is a lot to type, but she can let the shell do most of the work through what is
called tab completion. If she types:

BASH

$ ls nor
and then presses Tab (the tab key on her keyboard), the shell automatically completes the
directory name for her:

BASH

$ ls north-pacific-gyre/
Pressing Tab again does nothing, since there are multiple possibilities; pressing Tab twice brings
up a list of all the files.

If Nelle then presses G and then presses Tab again, the shell will append ‘goo’ since all files that
start with ‘g’ share the first three characters ‘goo’.

BASH

$ ls north-pacific-gyre/goo
To see all of those files, she can press Tab twice more.

BASH

ls north-pacific-gyre/goo
goodiff.sh goostats.sh
This is called tab completion, and we will see it in many other tools as we go on.

KEYPOINTS

 The file system is responsible for managing information on the disk.

 Information is stored in files, which are stored in directories (folders).

 Directories can also store other directories, which then form a directory tree.

 pwd prints the user’s current working directory.

 ls [path] prints a listing of a specific file or directory; ls on its own lists the
current working directory.

 cd [path] changes the current working directory.

 Most commands take options that begin with a single -.

 Directory names in a path are separated with / on Unix, but \ on Windows.

 / on its own is the root directory of the whole file system.

 An absolute path specifies a location from the root of the file system.

 A relative path specifies a location starting from the current location.

 . on its own means ‘the current directory’; .. means ‘the directory above the
current one’.

Working With Files and

Directories
Last updated on 2023-06-18 | Edit this page

Collapse All Solutions

OVERVIEW
Questions

 How can I create, copy, and delete files and directories?

 How can I edit files?

Objectives

 Create a directory hierarchy that matches a given diagram.

 Create files in that hierarchy using an editor or by copying and renaming existing files.

 Delete, copy and move specified files and/or directories.

Creating directories
We now know how to explore files and directories, but how do we create them in the first place?
In this episode we will learn about creating and moving files and directories, using
the exercise-data/writing directory as an example.

Step one: see where we are and what we already have

We should still be in the shell-lesson-data directory on the Desktop, which we can check
using:

BASH

$ pwd

OUTPUT

/Users/nelle/Desktop/shell-lesson-data
Next we’ll move to the exercise-data/writing directory and see what it contains:

BASH

$ cd exercise-data/writing/
$ ls -F

OUTPUT

haiku.txt LittleWomen.txt

Create a directory

Let’s create a new directory called thesis using the command mkdir thesis (which has no
output):

BASH
$ mkdir thesis
As you might guess from its name, mkdir means ‘make directory’. Since thesis is a relative
path (i.e., does not have a leading slash, like /what/ever/thesis), the new directory is created
in the current working directory:

BASH

$ ls -F

OUTPUT

haiku.txt LittleWomen.txt thesis/

Since we’ve just created the thesis directory, there’s nothing in it yet:

BASH

$ ls -F thesis
Note that mkdir is not limited to creating single directories one at a time. The -p option
allows mkdir to create a directory with nested subdirectories in a single operation:

BASH

$ mkdir -p ../project/data ../project/results

The -R option to the ls command will list all nested subdirectories within a directory. Let’s
use ls -FR to recursively list the new directory hierarchy we just created in
the project directory:

BASH
$ ls -FR ../project

OUTPUT

../project/:
data/ results/

../project/data:

../project/results:
TWO WAYS OF DOING TH E SAME THING

Using the shell to create a directory is no different than using a file explorer. If you open the
current directory using your operating system’s graphical file explorer, the thesis directory will
appear there too. While the shell and the file explorer are two different ways of interacting with
the files, the files and directories themselves are the same.

GOOD NAMES FOR FILES AND DIRECTORIES

Complicated names of files and directories can make your life painful when working on the
command line. Here we provide a few useful tips for the names of your files and directories.

1. Don’t use spaces.

Spaces can make a name more meaningful, but since spaces are used to separate arguments on
the command line it is better to avoid them in names of files and directories. You can
use - or _ instead (e.g. north-pacific-gyre/ rather than north pacific gyre/). To test
this out, try typing mkdir north pacific gyreand see what directory (or directories!) are
made when you check with ls -F.

2. Don’t begin the name with - (dash).

Commands treat names starting with - as options.

3. Stick with letters, numbers, . (period or ‘full stop’), - (dash) and _ (underscore).
Many other characters have special meanings on the command line. We will learn about some of
these during this lesson. There are special characters that can cause your command to not work
as expected and can even result in data loss.

If you need to refer to names of files or directories that have spaces or other special characters,
you should surround the name in quotes ("").

Create a text file

Let’s change our working directory to thesis using cd, then run a text editor called Nano to
create a file called draft.txt:

BASH

$ cd thesis
$ nano draft.txt
WHICH EDITOR?

When we say, ‘nano is a text editor’ we really do mean ‘text’. It can only work with plain
character data, not tables, images, or any other human-friendly media. We use it in examples
because it is one of the least complex text editors. However, because of this trait, it may not be
powerful enough or flexible enough for the work you need to do after this workshop. On Unix
systems (such as Linux and macOS), many programmers use Emacs or Vim (both of which
require more time to learn), or a graphical editor such as Gedit or VScode. On Windows, you
may wish to use Notepad++. Windows also has a built-in editor called notepad that can be run
from the command line in the same way as nano for the purposes of this lesson.

No matter what editor you use, you will need to know where it searches for and saves files. If
you start it from the shell, it will (probably) use your current working directory as its default
location. If you use your computer’s start menu, it may want to save files in your Desktop or
Documents directory instead. You can change this by navigating to another directory the first
time you ‘Save As…’

Let’s type in a few lines of text.

Once we’re happy with our text, we can press Ctrl+O (press the Ctrl or Control key and, while
holding it down, press the O key) to write our data to disk. We will be asked to provide a name
for the file that will contain our text. Press Return to accept the suggested default of draft.txt.

Once our file is saved, we can use Ctrl+X to quit the editor and return to the shell.

CONTROL, CTRL, OR ^ KEY

The Control key is also called the ‘Ctrl’ key. There are various ways in which using the Control
key may be described. For example, you may see an instruction to press the Control key and,
while holding it down, press the X key, described as any of:

 Control-X

 Control+X

 Ctrl-X

 Ctrl+X

 ^X

 C-x

In nano, along the bottom of the screen you’ll see ^G Get Help ^O WriteOut. This means that
you can use Control-G to get help and Control-O to save your file.
nano doesn’t leave any output on the screen after it exits, but ls now shows that we have created
a file called draft.txt:

BASH

$ ls

OUTPUT

draft.txt
CREATING FILES A DIF FERENT WAY

We have seen how to create text files using the nano editor. Now, try the following command:

BASH

$ touch my_file.txt
1. What did the touch command do? When you look at your current directory using
the GUI file explorer, does the file show up?
2. Use ls -l to inspect the files. How large is my_file.txt?
3. When might you want to create a file this way?

Show me the solution

1. The touch command generates a new file called my_file.txt in your current
directory. You can observe this newly generated file by typing ls at the command
line prompt. my_file.txt can also be viewed in your GUI file explorer.
2. When you inspect the file with ls -l, note that the size of my_file.txt is 0
bytes. In other words, it contains no data. If you open my_file.txt using your
text editor it is blank.
3. Some programs do not generate output files themselves, but instead require that
empty files have already been generated. When the program is run, it searches for
 an existing file to populate with its output. The touch command allows you to
efficiently generate a blank text file to be used by such programs.

CREATING FILES A DIF FERENT WAY (CONTINUED)

To avoid confusion later on, we suggest removing the file you’ve just created before proceeding
with the rest of the episode, otherwise future outputs may vary from those given in the lesson. To
do this, use the following command:

BASH

$ rm my_file.txt

WHAT’S IN A NAME?

You may have noticed that all of Nelle’s files are named ‘something dot something’, and in this
part of the lesson, we always used the extension .txt. This is just a convention; we can call a
file mythesis or almost anything else we want. However, most people use two-part names most
of the time to help them (and their programs) tell different kinds of files apart. The second part of
such a name is called the filename extension and indicates what type of data the file
holds: .txt signals a plain text file, .pdf indicates a PDF document, .cfg is a configuration file
full of parameters for some program or other, .png is a PNG image, and so on.

This is just a convention, albeit an important one. Files merely contain bytes; it’s up to us and
our programs to interpret those bytes according to the rules for plain text files, PDF documents,
configuration files, images, and so on.

Naming a PNG image of a whale as whale.mp3 doesn’t somehow magically turn it into a
recording of whale song, though it might cause the operating system to associate the file with a
music player program. In this case, if someone double-clicked whale.mp3 in a file explorer
program,the music player will automatically (and erroneously) attempt to open
the whale.mp3 file.
Moving files and directories

Returning to the shell-lesson-data/exercise-data/writing directory,

BASH

$ cd ~/Desktop/shell-lesson-data/exercise-data/writing
In our thesis directory we have a file draft.txt which isn’t a particularly informative name,
so let’s change the file’s name using mv, which is short for ‘move’:

BASH

$ mv thesis/draft.txt thesis/quotes.txt
The first argument tells mv what we’re ‘moving’, while the second is where it’s to go. In this
case, we’re moving thesis/draft.txt to thesis/quotes.txt, which has the same effect as
renaming the file. Sure enough, ls shows us that thesis now contains one file
called quotes.txt:

BASH

$ ls thesis

OUTPUT

quotes.txt
One must be careful when specifying the target file name, since mv will silently overwrite any
existing file with the same name, which could lead to data loss. By default, mv will not ask for
confirmation before overwriting files. However, an additional option, mv -i (or mv --
interactive), will cause mv to request such confirmation.
Note that mv also works on directories.

Let’s move quotes.txt into the current working directory. We use mv once again, but this time
we’ll use just the name of a directory as the second argument to tell mv that we want to keep the
filename but put the file somewhere new. (This is why the command is called ‘move’.) In this
case, the directory name we use is the special directory name . that we mentioned earlier.

BASH

$ mv thesis/quotes.txt .
The effect is to move the file from the directory it was in to the current working
directory. ls now shows us that thesis is empty:

BASH

$ ls thesis

OUTPUT

$
Alternatively, we can confirm the file quotes.txt is no longer present in the thesis directory
by explicitly trying to list it:

BASH

$ ls thesis/quotes.txt

ERROR

ls: cannot access 'thesis/quotes.txt': No such file or directory

ls with a filename or directory as an argument only lists the requested file or directory. If the file
given as the argument doesn’t exist, the shell returns an error as we saw above. We can use this
to see that quotes.txt is now present in our current directory:

BASH

$ ls quotes.txt

OUTPUT

quotes.txt
MOVING FILES TO A NE W FOLDER

After running the following commands, Jamie realizes that she put the
files sucrose.dat and maltose.dat into the wrong folder. The files should have been placed
in the raw folder.

BASH

$ ls -F
analyzed/ raw/
$ ls -F analyzed
fructose.dat glucose.dat maltose.dat sucrose.dat
$ cd analyzed
Fill in the blanks to move these files to the raw/ folder (i.e. the one she forgot to put them in)

BASH

$ mv sucrose.dat maltose.dat ____/____

Show me the solution

BASH

$ mv sucrose.dat maltose.dat ../raw

Recall that .. refers to the parent directory (i.e. one above the current directory) and that . refers
to the current directory.

Copying files and directories

The cp command works very much like mv, except it copies a file instead of moving it. We can
check that it did the right thing using ls with two paths as arguments — like most Unix
commands, ls can be given multiple paths at once:

BASH

$ cp quotes.txt thesis/quotations.txt
$ ls quotes.txt thesis/quotations.txt

OUTPUT

quotes.txt thesis/quotations.txt
We can also copy a directory and all its contents by using the recursive option -r, e.g. to back up
a directory:

BASH

$ cp -r thesis thesis_backup
We can check the result by listing the contents of both
the thesis and thesis_backup directory:

BASH

$ ls thesis thesis_backup

OUTPUT

thesis:
quotations.txt

thesis_backup:
quotations.txt
It is important to include the -r flag. If you want to copy a directory and you omit this option
you will see a message that the directory has been omitted because -r not specified.

BASH

$ cp thesis thesis_backup
cp: -r not specified; omitting directory 'thesis'
RENAMING FILES

Suppose that you created a plain-text file in your current directory to contain a list of the
statistical tests you will need to do to analyze your data, and named it statstics.txt

After creating and saving this file you realize you misspelled the filename! You want to correct
the mistake, which of the following commands could you use to do so?

1. cp statstics.txt statistics.txt

2. mv statstics.txt statistics.txt
 3. mv statstics.txt .

4. cp statstics.txt .

Show me the solution

1. No. While this would create a file with the correct name, the incorrectly named file
still exists in the directory and would need to be deleted.

2. Yes, this would work to rename the file.

3. No, the period(.) indicates where to move the file, but does not provide a new file
name; identical file names cannot be created.

4. No, the period(.) indicates where to copy the file, but does not provide a new file
name; identical file names cannot be created.

MOVING AND COPYING

What is the output of the closing ls command in the sequence shown below?

BASH

$ pwd

OUTPUT

/Users/jamie/data

BASH

$ ls

OUTPUT
proteins.dat

BASH

$ mkdir recombined
$ mv proteins.dat recombined/
$ cp recombined/proteins.dat ../proteins-saved.dat
$ ls

1. proteins-saved.dat recombined

2. recombined

3. proteins.dat recombined

4. proteins-saved.dat

Show me the solution

We start in the /Users/jamie/data directory, and create a new folder called recombined. The
second line moves (mv) the file proteins.dat to the new folder (recombined). The third line
makes a copy of the file we just moved. The tricky part here is where the file was copied to.
Recall that .. means ‘go up a level’, so the copied file is now in /Users/jamie. Notice
that .. is interpreted with respect to the current working directory, not with respect to the
location of the file being copied. So, the only thing that will show using ls
(in /Users/jamie/data) is the recombined folder.

1. No, see explanation above. proteins-saved.dat is located at /Users/jamie

2. Yes

3. No, see explanation above. proteins.dat is located

at /Users/jamie/data/recombined

4. No, see explanation above. proteins-saved.dat is located at /Users/jamie

Removing files and directories

Returning to the shell-lesson-data/exercise-data/writing directory, let’s tidy up this

directory by removing the quotes.txt file we created. The Unix command we’ll use for this
is rm (short for ‘remove’):

BASH

$ rm quotes.txt
We can confirm the file has gone using ls:

BASH

$ ls quotes.txt

ERROR

ls: cannot access 'quotes.txt': No such file or directory

DELETING IS FOREVER

The Unix shell doesn’t have a trash bin that we can recover deleted files from (though most
graphical interfaces to Unix do). Instead, when we delete files, they are unlinked from the file
system so that their storage space on disk can be recycled. Tools for finding and recovering
deleted files do exist, but there’s no guarantee they’ll work in any particular situation, since the
computer may recycle the file’s disk space right away.

USING rm SAFELY

What happens when we execute rm -i thesis_backup/quotations.txt? Why would we

want this protection when using rm?
Show me the solution

OUTPUT

rm: remove regular file 'thesis_backup/quotations.txt'? y

The -i option will prompt before (every) removal (use Y to confirm deletion or N to keep the
file). The Unix shell doesn’t have a trash bin, so all the files removed will disappear forever. By
using the -i option, we have the chance to check that we are deleting only the files that we want
to remove.

If we try to remove the thesis directory using rm thesis, we get an error message:

BASH

$ rm thesis

ERROR

rm: cannot remove `thesis': Is a directory

This happens because rm by default only works on files, not directories.

rm can remove a directory and all its contents if we use the recursive option -r, and it will do
so without any confirmation prompts:

BASH

$ rm -r thesis
Given that there is no way to retrieve files deleted using the shell, rm -r should be used with
great caution (you might consider adding the interactive option rm -r -i).
Operations with multiple files and
directories

Oftentimes one needs to copy or move several files at once. This can be done by providing a list
of individual filenames, or specifying a naming pattern using wildcards. Wildcards are special
characters that can be used to represent unknown characters or sets of characters when
navigating the Unix file system.

COPY WITH MULTIPLE F ILENAMES

For this exercise, you can test the commands in the shell-lesson-data/exercise-
data directory.

In the example below, what does cp do when given several filenames and a directory name?

BASH

$ mkdir backup
$ cp creatures/minotaur.dat creatures/unicorn.dat backup/
In the example below, what does cp do when given three or more file names?

BASH

$ cd creatures
$ ls -F

OUTPUT

basilisk.dat minotaur.dat unicorn.dat

BASH

$ cp minotaur.dat unicorn.dat basilisk.dat

Show me the solution

If given more than one file name followed by a directory name (i.e. the destination directory
must be the last argument), cp copies the files to the named directory.

If given three file names, cp throws an error such as the one below, because it is expecting a
directory name as the last argument.

ERROR

cp: target 'basilisk.dat' is not a directory

Using wildcards for accessing multiple files at once

WILDCARDS

* is a wildcard, which represents zero or more other characters. Let’s consider the shell-
lesson-data/exercise-
data/alkanes directory: *.pdb represents ethane.pdb, propane.pdb, and every file that
ends with ‘.pdb’. On the other hand, p*.pdb only represents pentane.pdb and propane.pdb,
because the ‘p’ at the front can only represent filenames that begin with the letter ‘p’.

? is also a wildcard, but it represents exactly one character. So ?ethane.pdb could

represent methane.pdb whereas *ethane.pdb represents
both ethane.pdb and methane.pdb.

Wildcards can be used in combination with each other. For example, ???ane.pdb indicates
three characters followed by ane.pdb, giving cubane.pdb ethane.pdb octane.pdb.

When the shell sees a wildcard, it expands the wildcard to create a list of matching
filenames before running the preceding command. As an exception, if a wildcard expression
does not match any file, Bash will pass the expression as an argument to the command as it is.
For example, typing ls *.pdf in the alkanes directory (which contains only files with names
ending with .pdb) results in an error message that there is no file called *.pdf. However,
generally commands like wc and ls see the lists of file names matching these expressions, but
not the wildcards themselves. It is the shell, not the other programs, that expands the wildcards.

LIST FILENAMES MATCH ING A PATTERN

When run in the alkanes directory, which ls command(s) will produce this output?

ethane.pdb methane.pdb

1. ls *t*ane.pdb

2. ls *t?ne.*

3. ls *t??ne.pdb

4. ls ethane.*

Show me the solution

The solution is 3.

1. shows all files whose names contain zero or more characters (*) followed by the letter t, then
zero or more characters (*) followed by ane.pdb. This gives ethane.pdb methane.pdb
octane.pdb pentane.pdb.

2. shows all files whose names start with zero or more characters (*) followed by the letter t,
then a single character (?), then ne. followed by zero or more characters (*). This will give
us octane.pdb and pentane.pdb but doesn’t match anything which ends in thane.pdb.

3. fixes the problems of option 2 by matching two characters (??) between t and ne. This is the
solution.

4. only shows files starting with ethane..

MORE ON WILDCARDS

Sam has a directory containing calibration data, datasets, and descriptions of the datasets:
BASH

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│ ├── calibration
│ └── datasets
└── send_to_bob
├── all_datasets_created_on_a_23rd
└── all_november_files
Before heading off to another field trip, she wants to back up her data and send some datasets to
her colleague Bob. Sam uses the following commands to get the job done:

BASH

$ cp *dataset* backup/datasets
$ cp ____calibration____ backup/calibration
$ cp 2015-____-____ send_to_bob/all_november_files/
$ cp ____ send_to_bob/all_datasets_created_on_a_23rd/
Help Sam by filling in the blanks.

The resulting directory structure should look like this

BASH

.
├── 2015-10-23-calibration.txt
├── 2015-10-23-dataset1.txt
├── 2015-10-23-dataset2.txt
├── 2015-10-23-dataset_overview.txt
├── 2015-10-26-calibration.txt
├── 2015-10-26-dataset1.txt
├── 2015-10-26-dataset2.txt
├── 2015-10-26-dataset_overview.txt
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
├── 2015-11-23-dataset_overview.txt
├── backup
│ ├── calibration
│ │ ├── 2015-10-23-calibration.txt
│ │ ├── 2015-10-26-calibration.txt
│ │ └── 2015-11-23-calibration.txt
│ └── datasets
│ ├── 2015-10-23-dataset1.txt
│ ├── 2015-10-23-dataset2.txt
│ ├── 2015-10-23-dataset_overview.txt
│ ├── 2015-10-26-dataset1.txt
│ ├── 2015-10-26-dataset2.txt
│ ├── 2015-10-26-dataset_overview.txt
│ ├── 2015-11-23-dataset1.txt
│ ├── 2015-11-23-dataset2.txt
│ └── 2015-11-23-dataset_overview.txt
└── send_to_bob
├── all_datasets_created_on_a_23rd
│ ├── 2015-10-23-dataset1.txt
│ ├── 2015-10-23-dataset2.txt
 │ ├── 2015-10-23-dataset_overview.txt
│ ├── 2015-11-23-dataset1.txt
│ ├── 2015-11-23-dataset2.txt
│ └── 2015-11-23-dataset_overview.txt
└── all_november_files
├── 2015-11-23-calibration.txt
├── 2015-11-23-dataset1.txt
├── 2015-11-23-dataset2.txt
└── 2015-11-23-dataset_overview.txt

Show me the solution

BASH

$ cp *calibration.txt backup/calibration
$ cp 2015-11-* send_to_bob/all_november_files/
$ cp *-23-dataset* send_to_bob/all_datasets_created_on_a_23rd/

ORGANIZING DIRECTORI ES AND FILES

Jamie is working on a project, and she sees that her files aren’t very well organized:

BASH

$ ls -F

OUTPUT

analyzed/ fructose.dat raw/ sucrose.dat

The fructose.dat and sucrose.dat files contain output from her data analysis. What
command(s) covered in this lesson does she need to run so that the commands below will
produce the output shown?

BASH

$ ls -F

OUTPUT

analyzed/ raw/

BASH

$ ls analyzed

OUTPUT

fructose.dat sucrose.dat

Show me the solution

BASH

mv *.dat analyzed
Jamie needs to move her files fructose.dat and sucrose.dat to the analyzed directory. The
shell will expand *.dat to match all .dat files in the current directory. The mv command then
moves the list of .dat files to the ‘analyzed’ directory.

REPRODUCE A FOLDER S TRUCTURE

You’re starting a new experiment and would like to duplicate the directory structure from your
previous experiment so you can add new data.

Assume that the previous experiment is in a folder called 2016-05-18, which contains
a data folder that in turn contains folders named raw and processed that contain data files. The
goal is to copy the folder structure of the 2016-05-18 folder into a folder called 2016-05-20 so
that your final directory structure looks like this:

OUTPUT

2016-05-20/
└── data
├── processed
└── raw
Which of the following set of commands would achieve this objective? What would the other
commands do?

BASH

$ mkdir 2016-05-20
$ mkdir 2016-05-20/data
$ mkdir 2016-05-20/data/processed
$ mkdir 2016-05-20/data/raw

BASH

$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ cd data
$ mkdir raw processed
BASH

$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20/data/processed

BASH

$ mkdir -p 2016-05-20/data/raw
$ mkdir -p 2016-05-20/data/processed

BASH

$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ mkdir raw processed

Show me the solution

The first two sets of commands achieve this objective. The first set uses relative paths to create
the top-level directory before the subdirectories.

The third set of commands will give an error because the default behavior of mkdir won’t create
a subdirectory of a non-existent directory: the intermediate level folders must be created first.

The fourth set of commands achieve this objective. Remember, the -p option, followed by a path
of one or more directories, will cause mkdir to create any intermediate subdirectories as
required.

The final set of commands generates the ‘raw’ and ‘processed’ directories at the same level as
the ‘data’ directory.

KEYPOINTS
  cp [old] [new] copies a file.

 mkdir [path] creates a new directory.

 mv [old] [new] moves (renames) a file or directory.

 rm [path] removes (deletes) a file.

 * matches zero or more characters in a filename, so *.txt matches all files ending
in .txt.

 ? matches any single character in a filename, so ?.txt matches a.txt but

not any.txt.

 Use of the Control key may be described in many ways, including Ctrl-
X, Control-X, and ^X.

 The shell does not have a trash bin: once something is deleted, it’s really gone.

 Most files’ names are something.extension. The extension isn’t required, and
doesn’t guarantee anything, but is normally used to indicate the type of data in the
file.

 Depending on the type of work you do, you may need a more powerful text editor
than Nano.

Pipes and Filters

Last updated on 2023-07-19 | Edit this page

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OVERVIEW
Questions

 How can I combine existing commands to do new things?

Objectives

 Redirect a command’s output to a file.

 Construct command pipelines with two or more stages.

 Explain what usually happens if a program or pipeline isn’t given any input to process.

 Explain the advantage of linking commands with pipes and filters.

Now that we know a few basic commands, we can finally look at the shell’s most powerful
feature: the ease with which it lets us combine existing programs in new ways. We’ll start with
the directory shell-lesson-data/exercise-data/alkanes that contains six files describing
some simple organic molecules. The .pdb extension indicates that these files are in Protein Data
Bank format, a simple text format that specifies the type and position of each atom in the
molecule.

BASH

$ ls

OUTPUT

cubane.pdb methane.pdb pentane.pdb

ethane.pdb octane.pdb propane.pdb
Let’s run an example command:

BASH

$ wc cubane.pdb

OUTPUT

20 156 1158 cubane.pdb

wc is the ‘word count’ command: it counts the number of lines, words, and characters in files
(returning the values in that order from left to right).

If we run the command wc *.pdb, the * in *.pdb matches zero or more characters, so the shell
turns *.pdb into a list of all .pdb files in the current directory:

BASH

$ wc *.pdb

OUTPUT

20 156 1158 cubane.pdb

12 84 622 ethane.pdb
9 57 422 methane.pdb
30 246 1828 octane.pdb
21 165 1226 pentane.pdb
15 111 825 propane.pdb
107 819 6081 total
Note that wc *.pdb also shows the total number of all lines in the last line of the output.

If we run wc -l instead of just wc, the output shows only the number of lines per file:
BASH

$ wc -l *.pdb

OUTPUT

20 cubane.pdb
12 ethane.pdb
9 methane.pdb
30 octane.pdb
21 pentane.pdb
15 propane.pdb
107 total
The -m and -w options can also be used with the wc command to show only the number of
characters or the number of words, respectively.

WHY ISN’T IT DOING A NYTHING?

What happens if a command is supposed to process a file, but we don’t give it a filename? For
example, what if we type:

BASH

$ wc -l
but don’t type *.pdb (or anything else) after the command? Since it doesn’t have any
filenames, wc assumes it is supposed to process input given at the command prompt, so it just
sits there and waits for us to give it some data interactively. From the outside, though, all we see
is it sitting there, and the command doesn’t appear to do anything.

If you make this kind of mistake, you can escape out of this state by holding down the control
key (Ctrl) and pressing the letter C once: Ctrl+C. Then release both keys.
Capturing output from commands

Which of these files contains the fewest lines? It’s an easy question to answer when there are
only six files, but what if there were 6000? Our first step toward a solution is to run the
command:

BASH

$ wc -l *.pdb > lengths.txt

The greater than symbol, >, tells the shell to redirect the command’s output to a file instead of
printing it to the screen. This command prints no screen output, because everything
that wc would have printed has gone into the file lengths.txt instead. If the file doesn’t exist
prior to issuing the command, the shell will create the file. If the file exists already, it will be
silently overwritten, which may lead to data loss. Thus, redirect commands require caution.

ls lengths.txt confirms that the file exists:

BASH

$ ls lengths.txt

OUTPUT

lengths.txt
We can now send the content of lengths.txt to the screen using cat lengths.txt.
The cat command gets its name from ‘concatenate’ i.e. join together, and it prints the contents
of files one after another. There’s only one file in this case, so cat just shows us what it
contains:

BASH
$ cat lengths.txt

OUTPUT

20 cubane.pdb
12 ethane.pdb
9 methane.pdb
30 octane.pdb
21 pentane.pdb
15 propane.pdb
107 total
OUTPUT PAGE BY PAGE

We’ll continue to use cat in this lesson, for convenience and consistency, but it has the
disadvantage that it always dumps the whole file onto your screen. More useful in practice is the
command less (e.g. less lengths.txt). This displays a screenful of the file, and then stops.
You can go forward one screenful by pressing the spacebar, or back one by pressing b. Press q to
quit.

Filtering output

Next we’ll use the sort command to sort the contents of the lengths.txt file. But first we’ll
do an exercise to learn a little about the sort command:

WHAT DOES s o r t - n DO?

The file shell-lesson-data/exercise-data/numbers.txt contains the following lines:

10
2
19
22
6
If we run sort on this file, the output is:

OUTPUT

10
19
2
22
6
If we run sort -n on the same file, we get this instead:

OUTPUT

2
6
10
19
22
Explain why -n has this effect.

Show me the solution

The -n option specifies a numerical rather than an alphanumerical sort.

We will also use the -n option to specify that the sort is numerical instead of alphanumerical.
This does not change the file; instead, it sends the sorted result to the screen:

BASH
$ sort -n lengths.txt

OUTPUT

9 methane.pdb
12 ethane.pdb
15 propane.pdb
20 cubane.pdb
21 pentane.pdb
30 octane.pdb
107 total
We can put the sorted list of lines in another temporary file called sorted-lengths.txt by
putting > sorted-lengths.txt after the command, just as we used > lengths.txt to put the
output of wc into lengths.txt. Once we’ve done that, we can run another command
called head to get the first few lines in sorted-lengths.txt:

BASH

$ sort -n lengths.txt > sorted-lengths.txt

$ head -n 1 sorted-lengths.txt

OUTPUT

9 methane.pdb
Using -n 1 with head tells it that we only want the first line of the file; -n 20 would get the
first 20, and so on. Since sorted-lengths.txt contains the lengths of our files ordered from
least to greatest, the output of head must be the file with the fewest lines.

REDIRECTING TO THE S AME FILE

It’s a very bad idea to try redirecting the output of a command that operates on a file to the same
file. For example:

BASH

$ sort -n lengths.txt > lengths.txt

Doing something like this may give you incorrect results and/or delete the contents
of lengths.txt.

WHAT DOES > > MEAN?

We have seen the use of >, but there is a similar operator >> which works slightly differently.
We’ll learn about the differences between these two operators by printing some strings. We can
use the echo command to print strings e.g.

BASH

$ echo The echo command prints text

OUTPUT

The echo command prints text

Now test the commands below to reveal the difference between the two operators:

BASH

$ echo hello > testfile01.txt

and:

BASH
$ echo hello >> testfile02.txt
Hint: Try executing each command twice in a row and then examining the output files.

Show me the solution

In the first example with >, the string ‘hello’ is written to testfile01.txt, but the file gets
overwritten each time we run the command.

We see from the second example that the >> operator also writes ‘hello’ to a file (in this
case testfile02.txt), but appends the string to the file if it already exists (i.e. when we run it
for the second time).

APPENDING DATA

We have already met the head command, which prints lines from the start of a file. tail is
similar, but prints lines from the end of a file instead.

Consider the file shell-lesson-data/exercise-data/animal-counts/animals.csv.

After these commands, select the answer that corresponds to the file animals-subset.csv:

BASH

$ head -n 3 animals.csv > animals-subset.csv

$ tail -n 2 animals.csv >> animals-subset.csv

1. The first three lines of animals.csv

2. The last two lines of animals.csv

3. The first three lines and the last two lines of animals.csv

4. The second and third lines of animals.csv

Show me the solution

Option 3 is correct. For option 1 to be correct we would only run the head command. For option
2 to be correct we would only run the tail command. For option 4 to be correct we would have
to pipe the output of head into tail -n 2 by doing head -n 3 animals.csv | tail -n 2
> animals-subset.csv

Passing output to another command

In our example of finding the file with the fewest lines, we are using two intermediate
files lengths.txt and sorted-lengths.txt to store output. This is a confusing way to work
because even once you understand what wc, sort, and head do, those intermediate files make it
hard to follow what’s going on. We can make it easier to understand by
running sort and head together:

BASH

$ sort -n lengths.txt | head -n 1

OUTPUT

9 methane.pdb
The vertical bar, |, between the two commands is called a pipe. It tells the shell that we want to
use the output of the command on the left as the input to the command on the right.

This has removed the need for the sorted-lengths.txt file.

Combining multiple commands

Nothing prevents us from chaining pipes consecutively. We can for example send the output
of wc directly to sort, and then send the resulting output to head. This removes the need for any
intermediate files.

We’ll start by using a pipe to send the output of wc to sort:

BASH

$ wc -l *.pdb | sort -n

OUTPUT

9 methane.pdb
12 ethane.pdb
15 propane.pdb
20 cubane.pdb
21 pentane.pdb
30 octane.pdb
107 total
We can then send that output through another pipe, to head, so that the full pipeline becomes:

BASH

$ wc -l *.pdb | sort -n | head -n 1

OUTPUT

9 methane.pdb
This is exactly like a mathematician nesting functions like log(3x) and saying ‘the log of three
times x’. In our case, the algorithm is ‘head of sort of line count of *.pdb’.
The redirection and pipes used in the last few commands are illustrated below:

PIPING COMMANDS TOGE THER

In our current directory, we want to find the 3 files which have the least number of lines. Which
command listed below would work?

1. wc -l * > sort -n > head -n 3

2. wc -l * | sort -n | head -n 1-3

3. wc -l * | head -n 3 | sort -n

4. wc -l * | sort -n | head -n 3

Show me the solution

Option 4 is the solution. The pipe character | is used to connect the output from one command to
the input of another. > is used to redirect standard output to a file. Try it in the shell-lesson-
data/exercise-data/alkanes directory!

Tools designed to work together

This idea of linking programs together is why Unix has been so successful. Instead of creating
enormous programs that try to do many different things, Unix programmers focus on creating
lots of simple tools that each do one job well, and that work well with each other. This
programming model is called ‘pipes and filters’. We’ve already seen pipes; a filter is a program
like wc or sort that transforms a stream of input into a stream of output. Almost all of the
standard Unix tools can work this way. Unless told to do otherwise, they read from standard
input, do something with what they’ve read, and write to standard output.

The key is that any program that reads lines of text from standard input and writes lines of text to
standard output can be combined with every other program that behaves this way as well. You
can and should write your programs this way so that you and other people can put those
programs into pipes to multiply their power.

PIPE READING COMPREH ENSION

A file called animals.csv (in the shell-lesson-data/exercise-data/animal-

counts folder) contains the following data:

2012-11-05,deer,5
2012-11-05,rabbit,22
2012-11-05,raccoon,7
2012-11-06,rabbit,19
2012-11-06,deer,2
2012-11-06,fox,4
2012-11-07,rabbit,16
2012-11-07,bear,1
What text passes through each of the pipes and the final redirect in the pipeline below? Note,
the sort -r command sorts in reverse order.

BASH

$ cat animals.csv | head -n 5 | tail -n 3 | sort -r > final.txt

Hint: build the pipeline up one command at a time to test your understanding

Show me the solution

The head command extracts the first 5 lines from animals.csv. Then, the last 3 lines are
extracted from the previous 5 by using the tail command. With the sort -r command those 3
lines are sorted in reverse order. Finally, the output is redirected to a file: final.txt. The
content of this file can be checked by executing cat final.txt. The file should contain the
following lines:

2012-11-06,rabbit,19
2012-11-06,deer,2
2012-11-05,raccoon,7
PIPE CONSTRUCTION

For the file animals.csv from the previous exercise, consider the following command:

BASH

$ cut -d , -f 2 animals.csv
The cut command is used to remove or ‘cut out’ certain sections of each line in the file,
and cut expects the lines to be separated into columns by a Tab character. A character used in
this way is a called a delimiter. In the example above we use the -d option to specify the comma
as our delimiter character. We have also used the -f option to specify that we want to extract the
second field (column). This gives the following output:

OUTPUT

deer
rabbit
raccoon
rabbit
deer
fox
rabbit
bear
The uniq command filters out adjacent matching lines in a file. How could you extend this
pipeline (using uniq and another command) to find out what animals the file contains (without
any duplicates in their names)?

Show me the solution

BASH

$ cut -d , -f 2 animals.csv | sort | uniq

WHICH PIPE?

The file animals.csv contains 8 lines of data formatted as follows:

OUTPUT

2012-11-05,deer,5
2012-11-05,rabbit,22
2012-11-05,raccoon,7
2012-11-06,rabbit,19
...
The uniq command has a -c option which gives a count of the number of times a line occurs in
its input. Assuming your current directory is shell-lesson-data/exercise-data/animal-
counts, what command would you use to produce a table that shows the total count of each type
of animal in the file?

1. sort animals.csv | uniq -c

2. sort -t, -k2,2 animals.csv | uniq -c

3. cut -d, -f 2 animals.csv | uniq -c

4. cut -d, -f 2 animals.csv | sort | uniq -c

5. cut -d, -f 2 animals.csv | sort | uniq -c | wc -l

Show me the solution

Option 4. is the correct answer. If you have difficulty understanding why, try running the
commands, or sub-sections of the pipelines (make sure you are in the shell-lesson-
data/exercise-data/animal-counts directory).

Nelle’s Pipeline: Checking Files

Nelle has run her samples through the assay machines and created 17 files in the north-
pacific-gyre directory described earlier. As a quick check, starting from the shell-lesson-
data directory, Nelle types:

BASH

$ cd north-pacific-gyre
$ wc -l *.txt
The output is 18 lines that look like this:

OUTPUT

300 NENE01729A.txt
300 NENE01729B.txt
300 NENE01736A.txt
300 NENE01751A.txt
300 NENE01751B.txt
300 NENE01812A.txt
... ...
Now she types this:

BASH

$ wc -l *.txt | sort -n | head -n 5

OUTPUT

240 NENE02018B.txt
300 NENE01729A.txt
300 NENE01729B.txt
 300 NENE01736A.txt
300 NENE01751A.txt
Whoops: one of the files is 60 lines shorter than the others. When she goes back and checks it,
she sees that she did that assay at 8:00 on a Monday morning — someone was probably in using
the machine on the weekend, and she forgot to reset it. Before re-running that sample, she checks
to see if any files have too much data:

BASH

$ wc -l *.txt | sort -n | tail -n 5

OUTPUT

300 NENE02040B.txt
300 NENE02040Z.txt
300 NENE02043A.txt
300 NENE02043B.txt
5040 total
Those numbers look good — but what’s that ‘Z’ doing there in the third-to-last line? All of her
samples should be marked ‘A’ or ‘B’; by convention, her lab uses ‘Z’ to indicate samples with
missing information. To find others like it, she does this:

BASH

$ ls *Z.txt

OUTPUT

NENE01971Z.txt NENE02040Z.txt
Sure enough, when she checks the log on her laptop, there’s no depth recorded for either of those
samples. Since it’s too late to get the information any other way, she must exclude those two
files from her analysis. She could delete them using rm, but there are actually some analyses she
might do later where depth doesn’t matter, so instead, she’ll have to be careful later on to select
files using the wildcard expressions NENE*A.txt NENE*B.txt.

REMOVING UNNEEDED FI LES

Suppose you want to delete your processed data files, and only keep your raw files and
processing script to save storage. The raw files end in .dat and the processed files end in .txt.
Which of the following would remove all the processed data files, and only the processed data
files?

1. rm ?.txt

2. rm *.txt

3. rm * .txt

4. rm *.*

Show me the solution

1. This would remove .txt files with one-character names

2. This is the correct answer

3. The shell would expand * to match everything in the current directory, so the
command would try to remove all matched files and an additional file called .txt

4. The shell expands *.* to match all filenames containing at least one ., including
the processed files (.txt) and raw files (.dat)

KEYPOINTS

 wc counts lines, words, and characters in its inputs.

 cat displays the contents of its inputs.

 sort sorts its inputs.

 head displays the first 10 lines of its input.

  tail displays the last 10 lines of its input.

 command > [file] redirects a command’s output to a file (overwriting any

existing content).

 command >> [file] appends a command’s output to a file.

 [first] | [second] is a pipeline: the output of the first command is used as the
input to the second.

 The best way to use the shell is to use pipes to combine simple single-purpose
programs (filters).

Loops
Last updated on 2023-05-16 | Edit this page

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OVERVIEW
Questions

 How can I perform the same actions on many different files?

Objectives

 Write a loop that applies one or more commands separately to each file in a set of files.

 Trace the values taken on by a loop variable during execution of the loop.

 Explain the difference between a variable’s name and its value.

 Explain why spaces and some punctuation characters shouldn’t be used in file names.

 Demonstrate how to see what commands have recently been executed.

 Re-run recently executed commands without retyping them.

Loops are a programming construct which allow us to repeat a command or set of commands for
each item in a list. As such they are key to productivity improvements through automation.
Similar to wildcards and tab completion, using loops also reduces the amount of typing required
(and hence reduces the number of typing mistakes).

Suppose we have several hundred genome data files named basilisk.dat, minotaur.dat,
and unicorn.dat. For this example, we’ll use the exercise-data/creatures directory
which only has three example files, but the principles can be applied to many many more files at
once.

The structure of these files is the same: the common name, classification, and updated date are
presented on the first three lines, with DNA sequences on the following lines. Let’s look at the
files:

BASH

$ head -n 5 basilisk.dat minotaur.dat unicorn.dat

We would like to print out the classification for each species, which is given on the second line
of each file. For each file, we would need to execute the command head -n 2 and pipe this
to tail -n 1. We’ll use a loop to solve this problem, but first let’s look at the general form of a
loop, using the pseudo-code below:

BASH

# The word "for" indicated the start of a "For-loop" command

for thing in list_of_things
#The word "do" indicates the start of job execution list
do
# Indentation within the loop is not required, but aids legibility
operation_using/command $thing
# The word "done" indicates the end of a loop
done
and we can apply this to our example like this:

BASH

$ for filename in basilisk.dat minotaur.dat unicorn.dat

> do
> echo $filename
> head -n 2 $filename | tail -n 1
> done

OUTPUT

basilisk.dat
CLASSIFICATION: basiliscus vulgaris
minotaur.dat
CLASSIFICATION: bos hominus
unicorn.dat
CLASSIFICATION: equus monoceros
FOLLOW THE PROMPT
The shell prompt changes from $ to > and back again as we were typing in our loop. The second
prompt, >, is different to remind us that we haven’t finished typing a complete command yet. A
semicolon, ;, can be used to separate two commands written on a single line.

When the shell sees the keyword for, it knows to repeat a command (or group of commands)
once for each item in a list. Each time the loop runs (called an iteration), an item in the list is
assigned in sequence to the variable, and the commands inside the loop are executed, before
moving on to the next item in the list. Inside the loop, we call for the variable’s value by
putting $ in front of it. The $ tells the shell interpreter to treat the variable as a variable name and
substitute its value in its place, rather than treat it as text or an external command.

In this example, the list is three filenames: basilisk.dat, minotaur.dat, and unicorn.dat.
Each time the loop iterates, we first use echo to print the value that the
variable $filename currently holds. This is not necessary for the result, but beneficial for us
here to have an easier time to follow along. Next, we will assign a file name to the
variable filename and run the head command. The first time through the
loop, $filename is basilisk.dat. The interpreter runs the
command head on basilisk.dat and pipes the first two lines to the tail command, which
then prints the second line of basilisk.dat. For the second
iteration, $filename becomes minotaur.dat. This time, the shell
runs head on minotaur.dat and pipes the first two lines to the tail command, which then
prints the second line of minotaur.dat. For the third
iteration, $filename becomes unicorn.dat, so the shell runs the head command on that file,
and tail on the output of that. Since the list was only three items, the shell exits the for loop.

SAME SYMBOLS, DIFFER ENT MEANINGS

Here we see > being used as a shell prompt, whereas > is also used to redirect output.
Similarly, $ is used as a shell prompt, but, as we saw earlier, it is also used to ask the shell to get
the value of a variable.

If the shell prints > or $ then it expects you to type something, and the symbol is a prompt.

If you type > or $ yourself, it is an instruction from you that the shell should redirect output or
get the value of a variable.
When using variables it is also possible to put the names into curly braces to clearly delimit the
variable name: $filename is equivalent to ${filename}, but is different from ${file}name.
You may find this notation in other people’s programs.

We have called the variable in this loop filename in order to make its purpose clearer to human
readers. The shell itself doesn’t care what the variable is called; if we wrote this loop as:

BASH

$ for x in basilisk.dat minotaur.dat unicorn.dat

> do
> head -n 2 $x | tail -n 1
> done
or:

BASH

$ for temperature in basilisk.dat minotaur.dat unicorn.dat

> do
> head -n 2 $temperature | tail -n 1
> done
it would work exactly the same way. Don’t do this. Programs are only useful if people can
understand them, so meaningless names (like x) or misleading names (like temperature)
increase the odds that the program won’t do what its readers think it does.

In the above examples, the variables (thing, filename, x and temperature) could have been
given any other name, as long as it is meaningful to both the person writing the code and the
person reading it.

Note also that loops can be used for other things than filenames, like a list of numbers or a subset
of data.

WRITE YOUR OWN LOOP

How would you write a loop that echoes all 10 numbers from 0 to 9?

Show me the solution

BASH

$ for loop_variable in 0 1 2 3 4 5 6 7 8 9
> do
> echo $loop_variable
> done

OUTPUT

0
1
2
3
4
5
6
7
8
9

VARIABLES IN LOOPS

This exercise refers to the shell-lesson-data/exercise-data/alkanes directory. ls

*.pdb gives the following output:

OUTPUT

cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb

What is the output of the following code?

BASH

$ for datafile in *.pdb

> do
> ls *.pdb
> done
Now, what is the output of the following code?

BASH

$ for datafile in *.pdb

> do
> ls $datafile
> done
Why do these two loops give different outputs?

Show me the solution

The first code block gives the same output on each iteration through the loop. Bash expands the
wildcard *.pdb within the loop body (as well as before the loop starts) to match all files ending
in .pdb and then lists them using ls. The expanded loop would look like this:

BASH

$ for datafile in cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb

> do
> ls cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
> done

OUTPUT
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb
The second code block lists a different file on each loop iteration. The value of
the datafile variable is evaluated using $datafile, and then listed using ls.

OUTPUT

cubane.pdb
ethane.pdb
methane.pdb
octane.pdb
pentane.pdb
propane.pdb

LIMITING SETS OF FIL ES

What would be the output of running the following loop in the shell-lesson-
data/exercise-data/alkanes directory?

BASH

$ for filename in c*
> do
> ls $filename
> done

1. No files are listed.

2. All files are listed.

 3. Only cubane.pdb, octane.pdb and pentane.pdb are listed.

4. Only cubane.pdb is listed.

Show me the solution

4 is the correct answer. * matches zero or more characters, so any file name starting with the
letter c, followed by zero or more other characters will be matched.

LIMITING SETS OF FIL ES (CONTINUED)

How would the output differ from using this command instead?

BASH

$ for filename in *c*

> do
> ls $filename
> done

1. The same files would be listed.

2. All the files are listed this time.

3. No files are listed this time.

4. The files cubane.pdb and octane.pdb will be listed.

5. Only the file octane.pdb will be listed.

Show me the solution

4 is the correct answer. * matches zero or more characters, so a file name with zero or more
characters before a letter c and zero or more characters after the letter c will be matched.

SAVING TO A FILE IN A LOOP - PART ONE

In the shell-lesson-data/exercise-data/alkanes directory, what is the effect of this

loop?
BASH

for alkanes in *.pdb

do
echo $alkanes
cat $alkanes > alkanes.pdb
done

1. Prints cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb an

d propane.pdb, and the text from propane.pdb will be saved to a file
called alkanes.pdb.

2. Prints cubane.pdb, ethane.pdb, and methane.pdb, and the text from all three
files would be concatenated and saved to a file called alkanes.pdb.

3. Prints cubane.pdb, ethane.pdb, methane.pdb, octane.pdb,

and pentane.pdb, and the text from propane.pdb will be saved to a file
called alkanes.pdb.

4. None of the above.

Show me the solution

1. The text from each file in turn gets written to the alkanes.pdb file. However, the
file gets overwritten on each loop iteration, so the final content of alkanes.pdb is
the text from the propane.pdb file.

SAVING TO A FILE IN A LOOP - PART TWO

Also in the shell-lesson-data/exercise-data/alkanes directory, what would be the

output of the following loop?

BASH

for datafile in *.pdb

do
cat $datafile >> all.pdb
done
 1. All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb,
and pentane.pdb would be concatenated and saved to a file called all.pdb.

2. The text from ethane.pdb will be saved to a file called all.pdb.

3. All of the text

from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and
propane.pdb would be concatenated and saved to a file called all.pdb.

4. All of the text

from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and
propane.pdb would be printed to the screen and saved to a file called all.pdb.

Show me the solution

3 is the correct answer. >> appends to a file, rather than overwriting it with the redirected output
from a command. Given the output from the cat command has been redirected, nothing is
printed to the screen.

Let’s continue with our example in the shell-lesson-data/exercise-

data/creatures directory. Here’s a slightly more complicated loop:

BASH

$ for filename in *.dat

> do
> echo $filename
> head -n 100 $filename | tail -n 20
> done
The shell starts by expanding *.dat to create the list of files it will process. The loop body then
executes two commands for each of those files. The first command, echo, prints its command-
line arguments to standard output. For example:

BASH

$ echo hello there

prints:
OUTPUT

hello there
In this case, since the shell expands $filename to be the name of a file, echo
$filename prints the name of the file. Note that we can’t write this as:

BASH

$ for filename in *.dat

> do
> $filename
> head -n 100 $filename | tail -n 20
> done
because then the first time through the loop, when $filename expanded to basilisk.dat, the
shell would try to run basilisk.dat as a program. Finally, the head and tail combination
selects lines 81-100 from whatever file is being processed (assuming the file has at least 100
lines).

SPACES IN NAMES

Spaces are used to separate the elements of the list that we are going to loop over. If one of those
elements contains a space character, we need to surround it with quotes, and do the same thing to
our loop variable. Suppose our data files are named:

red dragon.dat
purple unicorn.dat
To loop over these files, we would need to add double quotes like so:

BASH

$ for filename in "red dragon.dat" "purple unicorn.dat"

> do
> head -n 100 "$filename" | tail -n 20
> done
It is simpler to avoid using spaces (or other special characters) in filenames.

The files above don’t exist, so if we run the above code, the head command will be unable to
find them; however, the error message returned will show the name of the files it is expecting:

ERROR

head: cannot open ‘red dragon.dat' for reading: No such file or directory
head: cannot open ‘purple unicorn.dat' for reading: No such file or
directory
Try removing the quotes around $filename in the loop above to see the effect of the quote
marks on spaces. Note that we get a result from the loop command for unicorn.dat when we run
this code in the creatures directory:

OUTPUT

head: cannot open ‘red' for reading: No such file or directory

head: cannot open ‘dragon.dat' for reading: No such file or directory
head: cannot open ‘purple' for reading: No such file or directory
CGGTACCGAA
AAGGGTCGCG
CAAGTGTTCC
...

We would like to modify each of the files in shell-lesson-data/exercise-

data/creatures, but also save a version of the original files. We want to copy the original files
to new files named original-basilisk.dat and original-unicorn.dat, for example. We
can’t use:

BASH
$ cp *.dat original-*.dat
because that would expand to:

BASH

$ cp basilisk.dat minotaur.dat unicorn.dat original-*.dat

This wouldn’t back up our files, instead we get an error:

ERROR

cp: target `original-*.dat' is not a directory

This problem arises when cp receives more than two inputs. When this happens, it expects the
last input to be a directory where it can copy all the files it was passed. Since there is no
directory named original-*.dat in the creatures directory, we get an error.

Instead, we can use a loop:

BASH

$ for filename in *.dat

> do
> cp $filename original-$filename
> done
This loop runs the cp command once for each filename. The first time,
when $filename expands to basilisk.dat, the shell executes:

BASH

cp basilisk.dat original-basilisk.dat
The second time, the command is:

BASH

cp minotaur.dat original-minotaur.dat
The third and last time, the command is:

BASH

cp unicorn.dat original-unicorn.dat
Since the cp command does not normally produce any output, it’s hard to check that the loop is
working correctly. However, we learned earlier how to print strings using echo, and we can
modify the loop to use echo to print our commands without actually executing them. As such we
can check what commands would be run in the unmodified loop.

The following diagram shows what happens when the modified loop is executed and
demonstrates how the judicious use of echo is a good debugging technique.

Nelle’s Pipeline: Processing Files

Nelle is now ready to process her data files using goostats.sh — a shell script written by her
supervisor. This calculates some statistics from a protein sample file and takes two arguments:

1. an input file (containing the raw data)

2. an output file (to store the calculated statistics)

Since she’s still learning how to use the shell, she decides to build up the required commands in
stages. Her first step is to make sure that she can select the right input files — remember, these
are ones whose names end in ‘A’ or ‘B’, rather than ‘Z’. Starting from her home directory, Nelle
types:

BASH

$ cd north-pacific-gyre
$ for datafile in NENE*A.txt NENE*B.txt
> do
> echo $datafile
> done

OUTPUT

NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
...
NENE02043A.txt
NENE02043B.txt
Her next step is to decide what to call the files that the goostats.sh analysis program will
create. Prefixing each input file’s name with ‘stats’ seems simple, so she modifies her loop to do
that:

BASH

$ for datafile in NENE*A.txt NENE*B.txt

> do
> echo $datafile stats-$datafile
> done

OUTPUT
NENE01729A.txt stats-NENE01729A.txt
NENE01729B.txt stats-NENE01729B.txt
NENE01736A.txt stats-NENE01736A.txt
...
NENE02043A.txt stats-NENE02043A.txt
NENE02043B.txt stats-NENE02043B.txt
She hasn’t actually run goostats.sh yet, but now she’s sure she can select the right files and
generate the right output filenames.

Typing in commands over and over again is becoming tedious, though, and Nelle is worried
about making mistakes, so instead of re-entering her loop, she presses ↑. In response, the shell
redisplays the whole loop on one line (using semi-colons to separate the pieces):

BASH

$ for datafile in NENE*A.txt NENE*B.txt; do echo $datafile stats-$datafile; done

Using the ←, Nelle navigates to the echo command and changes it to bash goostats.sh:

BASH

$ for datafile in NENE*A.txt NENE*B.txt; do bash goostats.sh $datafile stats-$datafile; done

When she presses Enter, the shell runs the modified command. However, nothing appears to
happen — there is no output. After a moment, Nelle realizes that since her script doesn’t print
anything to the screen any longer, she has no idea whether it is running, much less how quickly.
She kills the running command by typing Ctrl+C, uses ↑ to repeat the command, and edits it to
read:

BASH

$ for datafile in NENE*A.txt NENE*B.txt; do echo $datafile;

bash goostats.sh $datafile stats-$datafile; done
BEGINNING AND END

We can move to the beginning of a line in the shell by typing Ctrl+A and to the end using Ctrl+E.

When she runs her program now, it produces one line of output every five seconds or so:

OUTPUT

NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
...
1518 times 5 seconds, divided by 60, tells her that her script will take about two hours to run. As
a final check, she opens another terminal window, goes into north-pacific-gyre, and
uses cat stats-NENE01729B.txt to examine one of the output files. It looks good, so she
decides to get some coffee and catch up on her reading.

THOSE WHO KNOW HISTO RY CAN CHOOSE TO REP EAT IT

Another way to repeat previous work is to use the history command to get a list of the last few
hundred commands that have been executed, and then to use !123 (where ‘123’ is replaced by
the command number) to repeat one of those commands. For example, if Nelle types this:

BASH

$ history | tail -n 5

OUTPUT

456 for datafile in NENE*A.txt NENE*B.txt; do echo $datafile stats-

$datafile; done
457 for datafile in NENE*A.txt NENE*B.txt; do echo $datafile stats-
$datafile; done
458 for datafile in NENE*A.txt NENE*B.txt; do bash goostats.sh $datafile
stats-$datafile; done
459 for datafile in NENE*A.txt NENE*B.txt; do echo $datafile; bash
goostats.sh $datafile
stats-$datafile; done
460 history | tail -n 5
then she can re-run goostats.sh on the files simply by typing !459.

OTHER HISTORY COMMAN DS

There are a number of other shortcut commands for getting at the history.

 Ctrl+R enters a history search mode ‘reverse-i-search’ and finds the most recent
command in your history that matches the text you enter next. Press Ctrl+R one or
more additional times to search for earlier matches. You can then use the left and
right arrow keys to choose that line and edit it then hit Return to run the command.

 !! retrieves the immediately preceding command (you may or may not find this
more convenient than using ↑)

 !$ retrieves the last word of the last command. That’s useful more often than you
might expect: after bash goostats.sh NENE01729B.txt stats-
NENE01729B.txt, you can type less !$ to look at the file stats-
NENE01729B.txt, which is quicker than doing ↑ and editing the command-line.

DOING A DRY RUN

A loop is a way to do many things at once — or to make many mistakes at once if it does the
wrong thing. One way to check what a loop would do is to echo the commands it would run
instead of actually running them.

Suppose we want to preview the commands the following loop will execute without actually
running those commands:

BASH
$ for datafile in *.pdb
> do
> cat $datafile >> all.pdb
> done
What is the difference between the two loops below, and which one would we want to run?

BASH

# Version 1
$ for datafile in *.pdb
> do
> echo cat $datafile >> all.pdb
> done

BASH

# Version 2
$ for datafile in *.pdb
> do
> echo "cat $datafile >> all.pdb"
> done

Show me the solution

The second version is the one we want to run. This prints to screen everything enclosed in the
quote marks, expanding the loop variable name because we have prefixed it with a dollar sign. It
also does not modify nor create the file all.pdb, as the >> is treated literally as part of a string
rather than as a redirection instruction.

The first version appends the output from the command echo cat $datafile to the
file, all.pdb. This file will just contain the list; cat cubane.pdb, cat ethane.pdb, cat
methane.pdb etc.
Try both versions for yourself to see the output! Be sure to open the all.pdb file to view its
contents.

NESTED LOOPS

Suppose we want to set up a directory structure to organize some experiments measuring

reaction rate constants with different compounds and different temperatures. What would be the
result of the following code:

BASH

$ for species in cubane ethane methane

> do
> for temperature in 25 30 37 40
> do
> mkdir $species-$temperature
> done
> done

Show me the solution

We have a nested loop, i.e. contained within another loop, so for each species in the outer loop,
the inner loop (the nested loop) iterates over the list of temperatures, and creates a new directory
for each combination.

Try running the code for yourself to see which directories are created!

KEYPOINTS

 A for loop repeats commands once for every thing in a list.

 Every for loop needs a variable to refer to the thing it is currently operating on.

 Use $name to expand a variable (i.e., get its value). ${name} can also be used.

 Do not use spaces, quotes, or wildcard characters such as ‘*’ or ‘?’ in filenames, as
it complicates variable expansion.
  Give files consistent names that are easy to match with wildcard patterns to make
it easy to select them for looping.

 Use the up-arrow key to scroll up through previous commands to edit and repeat
them.

 Use Ctrl+R to search through the previously entered commands.

 Use history to display recent commands, and ![number] to repeat a command

by number.

Shell Scripts
Last updated on 2023-06-05 | Edit this page

Collapse All Solutions

OVERVIEW
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.

Not only will writing shell scripts make your work faster, but also you won’t have to retype the
same commands over and over again. It will also make it more accurate (fewer chances for
typos) and more reproducible. If you come back to your work later (or if someone else finds your
work and wants to build on it), you will be able to reproduce the same results simply by running
your script, rather than having to remember or retype a long list of commands.

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

BASH

$ cd alkanes
$ 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:

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

This is a variation on the pipe we constructed earlier, which selects lines 11-15 of the
file octane.pdb. Remember, we are not running it as a command just yet; we are only
incorporating 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 alkanes now contains a file called middle.sh.
Once we have saved the file, we can ask the shell to execute the commands it contains. Our shell
is called bash, so we run the following command:

BASH

$ bash middle.sh

OUTPUT

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, which expects 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.

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:

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

head -n 15 "$1" | tail -n 5

Inside a shell script, $1 means ‘the first filename (or other argument) on the command line’. We
can now run our script like this:

BASH

$ bash middle.sh octane.pdb

OUTPUT

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:

BASH

$ bash middle.sh pentane.pdb

OUTPUT

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.

Currently, we need to edit middle.sh each time we want to adjust the range of lines that is
returned. Let’s fix that by configuring our script to instead use three command-line arguments.
After the first command-line argument ($1), each additional argument that we provide will be
accessible via the special variables $1, $2, $3, which refer to the first, second, third command-
line arguments, respectively.

Knowing this, we can use additional arguments to define the range of lines to be passed
to head and tail respectively:

BASH

$ nano middle.sh
head -n "$2" "$1" | tail -n "$3"
We can now run:

BASH

$ bash middle.sh pentane.pdb 15 5

OUTPUT

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

$ bash middle.sh pentane.pdb 20 5

OUTPUT

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:

BASH

$ nano 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:

BASH

$ 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 special syntax and is equivalent to "$1" "$2" …).

Here’s an example:

BASH

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

BASH

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

OUTPUT

9 methane.pdb
12 ethane.pdb
15 propane.pdb
20 cubane.pdb
21 pentane.pdb
30 octane.pdb
163 ../creatures/basilisk.dat
163 ../creatures/minotaur.dat
163 ../creatures/unicorn.dat
596 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 shell-lesson-data/exercise-data/animal-
counts/animals.csv.

We can use the command cut -d , -f 2 animals.csv | sort | uniq to produce the
unique species in animals.csv. 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.

Show me the solution

BASH
# 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

Suppose we have just run a series of commands that did something useful — for example,
creating a graph we’d like to use in a paper. We’d like to be able to re-create the graph later if we
need to, so we want to save the commands in a file. Instead of typing them in again (and
potentially getting them wrong) we can do this:

BASH

$ history | tail -n 5 > redo-figure-3.sh

The file redo-figure-3.sh now contains:

297 bash goostats.sh NENE01729B.txt stats-NENE01729B.txt

298 bash goodiff.sh stats-NENE01729B.txt /data/validated/01729.txt > 01729-
differences.txt
299 cut -d ',' -f 2-3 01729-differences.txt > 01729-time-series.txt
300 ygraph --format scatter --color bw --borders none 01729-time-series.txt
figure-3.png
301 history | tail -n 5 > redo-figure-3.sh
After a moment’s work in an editor to remove the serial numbers on the commands, and to
remove the final line where we called the history command, we have a completely accurate
record of how we created that figure.

WHY RECORD COMMANDS IN THE HISTORY BEFOR E RUNNING

THEM?
If you run the command:

BASH

$ history | tail -n 5 > recent.sh

the last command in the file is the history command itself, i.e., the shell has added history to
the command log before actually running it. In fact, the shell always adds commands to the log
before running them. Why do you think it does this?

Show me the solution

If a command causes something to crash or hang, it might be useful to know what that command
was, in order to investigate the problem. Were the command only be recorded after running it,
we would not have a record of the last command run in the event of a crash.

In practice, most people develop shell scripts by running commands at the shell prompt a few
times to make sure they’re doing the right thing, then saving them in a file for re-use. This style
of work allows people to recycle what they discover about their data and their workflow with one
call to history and a bit of editing to clean up the output and save it as a shell script.

Nelle’s Pipeline: Creating a Script

Nelle’s supervisor insisted that all her analytics must be reproducible. The easiest way to capture
all the steps is in a script.

First we return to Nelle’s project directory:

BASH

$ cd ../../north-pacific-gyre/
She creates a file using nano …

BASH

$ nano do-stats.sh
…which contains the following:

BASH

# Calculate stats for data files.

for datafile in "$@"
do
echo $datafile
bash goostats.sh $datafile stats-$datafile
done
She saves this in a file called do-stats.sh so that she can now re-do the first stage of her
analysis by typing:

BASH

$ bash do-stats.sh NENE*A.txt NENE*B.txt

She can also do this:

BASH

$ bash do-stats.sh NENE*A.txt NENE*B.txt | wc -l

so that the output is just the number of files processed rather than the names of the files that were
processed.

One thing to note about Nelle’s script is that it lets the person running it decide what files to
process. She could have written it as:
BASH

# Calculate stats for Site A and Site B data files.

for datafile in NENE*A.txt NENE*B.txt
do
echo $datafile
bash goostats.sh $datafile stats-$datafile
done
The advantage is that this always selects the right files: she doesn’t have to remember to exclude
the ‘Z’ files. The disadvantage is that it always selects just those files — she can’t run it on all
files (including the ‘Z’ files), or on the ‘G’ or ‘H’ files her colleagues in Antarctica are
producing, without editing the script. If she wanted to be more adventurous, she could modify
her script to check for command-line arguments, and use NENE*A.txt NENE*B.txt if none
were provided. Of course, this introduces another tradeoff between flexibility and complexity.

VARIABLES IN SHELL S CRIPTS

In the alkanes directory, imagine you have a shell script called script.sh containing the
following commands:

BASH

head -n $2 $1
tail -n $3 $1
While you are in the alkanes directory, you type the following command:

BASH

$ bash script.sh '*.pdb' 1 1

Which of the following outputs would you expect to see?

1. All of the lines between the first and the last lines of each file ending in .pdb in
the alkanes directory
 2. The first and the last line of each file ending in .pdb in the alkanes directory

3. The first and the last line of each file in the alkanes directory

4. An error because of the quotes around *.pdb

Show me the 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:

BASH

$ 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 FIL E WITH A GIVEN EXTEN SION

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

$ bash longest.sh shell-lesson-data/exercise-data/alkanes pdb

would print the name of the .pdb file in shell-lesson-data/exercise-data/alkanes that
has the most lines.

Feel free to test your script on another directory e.g.

BASH
$ bash longest.sh shell-lesson-data/exercise-data/writing txt

Show me the solution

BASH

# 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

The first part of the pipeline, wc -l $1/*.$2 | sort -n, counts the lines in each file and
sorts them numerically (largest last). When there’s more than one file, wc also outputs a final
summary line, giving the total number of lines across all files. We use tail -n 2 | head -n
1 to throw away this last line.

With wc -l $1/*.$2 | sort -n | tail -n 1 we’ll see the final summary line: we can
build our pipeline up in pieces to be sure we understand the output.

SCRIPT READING COMPR EHENSION

For this question, consider the shell-lesson-data/exercise-data/alkanes directory once

again. This contains a number of .pdb files in addition to any other files you may have created.
Explain what each of the following three scripts would do when run as bash script1.sh
*.pdb, bash script2.sh *.pdb, and bash script3.sh *.pdb respectively.

BASH

# Script 1
echo *.*
BASH

# Script 2
for filename in $1 $2 $3
do
cat $filename
done

BASH

# Script 3
echo $@.pdb

Solutions
In each case, the shell expands the wildcard in *.pdb before passing the resulting list of file
names as arguments to the script.

Script 1 would print out a list of all files containing a dot in their name. The arguments passed to
the script are not actually used anywhere in the script.

Script 2 would print the contents of the first 3 files with a .pdb file extension. $1, $2,
and $3 refer to the first, second, and third argument respectively.

Script 3 would print all the arguments to the script (i.e. all the .pdb files), followed
by .pdb. $@ refers to all the arguments given to a shell script.

OUTPUT

cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb.pdb

DEBUGGING SCRIPTS
Suppose you have saved the following script in a file called do-errors.sh in Nelle’s north-
pacific-gyre directory:

BASH

# Calculate stats for data files.

for datafile in "$@"
do
echo $datfile
bash goostats.sh $datafile stats-$datafile
done
When you run it from the north-pacific-gyre directory:

BASH

$ bash do-errors.sh NENE*A.txt NENE*B.txt

the output is blank. To figure out why, re-run the script using the -x option:

BASH

$ bash -x do-errors.sh NENE*A.txt NENE*B.txt

What is the output showing you? Which line is responsible for the error?

Show me the solution

The -x option causes bash to run in debug mode. This prints out each command as it is run,
which will help you to locate errors. In this example, we can see that echo isn’t printing
anything. We have made a typo in the loop variable name, and the variable datfile doesn’t
exist, hence returning an empty string.

KEYPOINTS

 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.

Finding Things
Last updated on 2023-05-02 | Edit this page

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OVERVIEW
Questions
  How can I find files?

 How can I find things in files?

Objectives

 Use grep to select lines from text files that match simple patterns.

 Use find to find files and directories whose names match simple patterns.
  Use the output of one command as the command-line argument(s) to another command.

 Explain what is meant by ‘text’ and ‘binary’ files, and why many common tools don’t
handle the latter well.

In the same way that many of us now use ‘Google’ as a verb meaning ‘to find’, Unix
programmers often use the word ‘grep’. ‘grep’ is a contraction of ‘global/regular
expression/print’, a common sequence of operations in early Unix text editors. It is also the name
of a very useful command-line program.

grep finds and prints lines in files that match a pattern. For our examples, we will use a file that
contains three haiku taken from a 1998 competition in Salon magazine (Credit to authors Bill
Torcaso, Howard Korder, and Margaret Segall, respectively. See Haiku Error Messsages
archived Page 1 and Page 2 .). For this set of examples, we’re going to be working in the writing
subdirectory:

BASH

$ cd
$ cd Desktop/shell-lesson-data/exercise-data/writing
$ cat haiku.txt

OUTPUT

The Tao that is seen

Is not the true Tao, until
You bring fresh toner.

With searching comes loss

and the presence of absence:
"My Thesis" not found.

Yesterday it worked
Today it is not working
Software is like that.
Let’s find lines that contain the word ‘not’:

BASH

$ grep not haiku.txt

OUTPUT

Is not the true Tao, until

"My Thesis" not found
Today it is not working
Here, not is the pattern we’re searching for. The grep command searches through the file,
looking for matches to the pattern specified. To use it type grep, then the pattern we’re
searching for and finally the name of the file (or files) we’re searching in.

The output is the three lines in the file that contain the letters ‘not’.

By default, grep searches for a pattern in a case-sensitive way. In addition, the search pattern we
have selected does not have to form a complete word, as we will see in the next example.

Let’s search for the pattern: ‘The’.

BASH

$ grep The haiku.txt

OUTPUT

The Tao that is seen

"My Thesis" not found.
This time, two lines that include the letters ‘The’ are outputted, one of which contained our
search pattern within a larger word, ‘Thesis’.

To restrict matches to lines containing the word ‘The’ on its own, we can give grep the -
w option. This will limit matches to word boundaries.

Later in this lesson, we will also see how we can change the search behavior of grep with respect
to its case sensitivity.

BASH

$ grep -w The haiku.txt

OUTPUT

The Tao that is seen

Note that a ‘word boundary’ includes the start and end of a line, so not just letters surrounded by
spaces. Sometimes we don’t want to search for a single word, but a phrase. This is also easy to
do with grep by putting the phrase in quotes.

BASH

$ grep -w "is not" haiku.txt

OUTPUT

Today it is not working

We’ve now seen that you don’t have to have quotes around single words, but it is useful to use
quotes when searching for multiple words. It also helps to make it easier to distinguish between
the search term or phrase and the file being searched. We will use quotes in the remaining
examples.
Another useful option is -n, which numbers the lines that match:

BASH

$ grep -n "it" haiku.txt

OUTPUT

5:With searching comes loss

9:Yesterday it worked
10:Today it is not working
Here, we can see that lines 5, 9, and 10 contain the letters ‘it’.

We can combine options (i.e. flags) as we do with other Unix commands. For example, let’s find
the lines that contain the word ‘the’. We can combine the option -w to find the lines that contain
the word ‘the’ and -n to number the lines that match:

BASH

$ grep -n -w "the" haiku.txt

OUTPUT

2:Is not the true Tao, until

6:and the presence of absence:
Now we want to use the option -i to make our search case-insensitive:

BASH

$ grep -n -w -i "the" haiku.txt

OUTPUT

1:The Tao that is seen

2:Is not the true Tao, until
6:and the presence of absence:
Now, we want to use the option -v to invert our search, i.e., we want to output the lines that do
not contain the word ‘the’.

BASH

$ grep -n -w -v "the" haiku.txt

OUTPUT

1:The Tao that is seen

3:You bring fresh toner.
4:
5:With searching comes loss
7:"My Thesis" not found.
8:
9:Yesterday it worked
10:Today it is not working
11:Software is like that.
If we use the -r (recursive) option, grep can search for a pattern recursively through a set of
files in subdirectories.

Let’s search recursively for Yesterday in the shell-lesson-data/exercise-

data/writing directory:

BASH
$ grep -r Yesterday .

OUTPUT

./LittleWomen.txt:"Yesterday, when Aunt was asleep and I was trying to be as

still as a
./LittleWomen.txt:Yesterday at dinner, when an Austrian officer stared at us
and then
./LittleWomen.txt:Yesterday was a quiet day spent in teaching, sewing, and
writing in my
./haiku.txt:Yesterday it worked
grep has lots of other options. To find out what they are, we can type:

BASH

$ grep --help

OUTPUT

Usage: grep [OPTION]... PATTERN [FILE]...

Search for PATTERN in each FILE or standard input.
PATTERN is, by default, a basic regular expression (BRE).
Example: grep -i 'hello world' menu.h main.c

Regexp selection and interpretation:

-E, --extended-regexp PATTERN is an extended regular expression (ERE)
-F, --fixed-strings PATTERN is a set of newline-separated fixed
strings
-G, --basic-regexp PATTERN is a basic regular expression (BRE)
-P, --perl-regexp PATTERN is a Perl regular expression
 -e, --regexp=PATTERN use PATTERN for matching
-f, --file=FILE obtain PATTERN from FILE
-i, --ignore-case ignore case distinctions
-w, --word-regexp force PATTERN to match only whole words
-x, --line-regexp force PATTERN to match only whole lines
-z, --null-data a data line ends in 0 byte, not newline

Miscellaneous:
... ... ...
USING gr e p

Which command would result in the following output:

OUTPUT

and the presence of absence:

1. grep "of" haiku.txt

2. grep -E "of" haiku.txt

3. grep -w "of" haiku.txt

4. grep -i "of" haiku.txt

Show me the solution

The correct answer is 3, because the -w option looks only for whole-word matches. The other
options will also match ‘of’ when part of another word.

WILDCARDS

grep‘s real power doesn’t come from its options, though; it comes from the fact that patterns can
include wildcards. (The technical name for these is regular expressions, which is what the ’re’
in ‘grep’ stands for.) Regular expressions are both complex and powerful; if you want to do
complex searches, please look at the lesson on our website. As a taster, we can find lines that
have an ‘o’ in the second position like this:

BASH

$ grep -E "^.o" haiku.txt

OUTPUT

You bring fresh toner.

Today it is not working
Software is like that.
We use the -E option and put the pattern in quotes to prevent the shell from trying to interpret it.
(If the pattern contained a *, for example, the shell would try to expand it before running grep.)
The ^ in the pattern anchors the match to the start of the line. The . matches a single character
(just like ? in the shell), while the o matches an actual ‘o’.

TRACKING A SPECIES

Leah has several hundred data files saved in one directory, each of which is formatted like this:

2012-11-05,deer,5
2012-11-05,rabbit,22
2012-11-05,raccoon,7
2012-11-06,rabbit,19
2012-11-06,deer,2
2012-11-06,fox,4
2012-11-07,rabbit,16
2012-11-07,bear,1
She wants to write a shell script that takes a species as the first command-line argument and a
directory as the second argument. The script should return one file
called <species>.txt containing a list of dates and the number of that species seen on each
date. For example using the data shown above, rabbit.txt would contain:
2012-11-05,22
2012-11-06,19
2012-11-07,16
Below, each line contains an individual command, or pipe. Arrange their sequence in one
command in order to achieve Leah’s goal:

BASH

cut -d : -f 2
>
|
grep -w $1 -r $2
|
$1.txt
cut -d , -f 1,3
Hint: use man grep to look for how to grep text recursively in a directory and man cut to select
more than one field in a line.

An example of such a file is provided in shell-lesson-data/exercise-data/animal-

counts/animals.csv

Show me the solution

grep -w $1 -r $2 | cut -d : -f 2 | cut -d , -f 1,3 > $1.txt
Actually, you can swap the order of the two cut commands and it still works. At the command
line, try changing the order of the cut commands, and have a look at the output from each step to
see why this is the case.

You would call the script above like this:

BASH

$ bash count-species.sh bear .

LITTLE WOMEN
You and your friend, having just finished reading Little Women by Louisa May Alcott, are in an
argument. Of the four sisters in the book, Jo, Meg, Beth, and Amy, your friend thinks that Jo was
the most mentioned. You, however, are certain it was Amy. Luckily, you have a
file LittleWomen.txt containing the full text of the novel (shell-lesson-data/exercise-
data/writing/LittleWomen.txt). Using a for loop, how would you tabulate the number of
times each of the four sisters is mentioned?

Hint: one solution might employ the commands grep and wc and a |, while another might
utilize grep options. There is often more than one way to solve a programming task, so a
particular solution is usually chosen based on a combination of yielding the correct result,
elegance, readability, and speed.

Solutions
for sis in Jo Meg Beth Amy
do
echo $sis:
grep -ow $sis LittleWomen.txt | wc -l
done
Alternative, slightly inferior solution:

for sis in Jo Meg Beth Amy

do
echo $sis:
grep -ocw $sis LittleWomen.txt
done
This solution is inferior because grep -c only reports the number of lines matched. The total
number of matches reported by this method will be lower if there is more than one match per
line.

Perceptive observers may have noticed that character names sometimes appear in all-uppercase
in chapter titles (e.g. ‘MEG GOES TO VANITY FAIR’). If you wanted to count these as well,
you could add the -i option for case-insensitivity (though in this case, it doesn’t affect the
answer to which sister is mentioned most frequently).
While grep finds lines in files, the find command finds files themselves. Again, it has a lot of
options; to show how the simplest ones work, we’ll use the shell-lesson-data/exercise-
data directory tree shown below.

OUTPUT

.
├── animal-counts/
│ └── animals.csv
├── creatures/
│ ├── basilisk.dat
│ ├── minotaur.dat
│ └── unicorn.dat
├── numbers.txt
├── alkanes/
│ ├── cubane.pdb
│ ├── ethane.pdb
│ ├── methane.pdb
│ ├── octane.pdb
│ ├── pentane.pdb
│ └── propane.pdb
└── writing/
├── haiku.txt
└── LittleWomen.txt
The exercise-data directory contains one file, numbers.txt and four directories: animal-
counts, creatures, alkanes and writing containing various files.

For our first command, let’s run find . (remember to run this command from the shell-
lesson-data/exercise-data folder).

BASH

$ find .
OUTPUT

.
./writing
./writing/LittleWomen.txt
./writing/haiku.txt
./creatures
./creatures/basilisk.dat
./creatures/unicorn.dat
./creatures/minotaur.dat
./animal-counts
./animal-counts/animals.csv
./numbers.txt
./alkanes
./alkanes/ethane.pdb
./alkanes/propane.pdb
./alkanes/octane.pdb
./alkanes/pentane.pdb
./alkanes/methane.pdb
./alkanes/cubane.pdb
As always, the . on its own means the current working directory, which is where we want our
search to start. find’s output is the names of every file and directory under the current working
directory. This can seem useless at first but find has many options to filter the output and in this
lesson we will discover some of them.

The first option in our list is -type d that means ‘things that are directories’. Sure
enough, find’s output is the names of the five directories (including .):

BASH

$ find . -type d

OUTPUT
.
./writing
./creatures
./animal-counts
./alkanes
Notice that the objects find finds are not listed in any particular order. If we change -type
d to -type f, we get a listing of all the files instead:

BASH

$ find . -type f

OUTPUT

./writing/LittleWomen.txt
./writing/haiku.txt
./creatures/basilisk.dat
./creatures/unicorn.dat
./creatures/minotaur.dat
./animal-counts/animals.csv
./numbers.txt
./alkanes/ethane.pdb
./alkanes/propane.pdb
./alkanes/octane.pdb
./alkanes/pentane.pdb
./alkanes/methane.pdb
./alkanes/cubane.pdb
Now let’s try matching by name:

BASH
$ find . -name *.txt

OUTPUT

./numbers.txt
We expected it to find all the text files, but it only prints out ./numbers.txt. The problem is
that the shell expands wildcard characters like * before commands run. Since *.txt in the
current directory expands to ./numbers.txt, the command we actually ran was:

BASH

$ find . -name numbers.txt

find did what we asked; we just asked for the wrong thing.

To get what we want, let’s do what we did with grep: put *.txt in quotes to prevent the shell
from expanding the * wildcard. This way, find actually gets the pattern *.txt, not the
expanded filename numbers.txt:

BASH

$ find . -name "*.txt"

OUTPUT

./writing/LittleWomen.txt
./writing/haiku.txt
./numbers.txt
LISTING VS. FINDING
ls and find can be made to do similar things given the right options, but under normal
circumstances, ls lists everything it can, while find searches for things with certain properties
and shows them.

As we said earlier, the command line’s power lies in combining tools. We’ve seen how to do that
with pipes; let’s look at another technique. As we just saw, find . -name "*.txt" gives us a
list of all text files in or below the current directory. How can we combine that with wc -l to
count the lines in all those files?

The simplest way is to put the find command inside $():

BASH

$ wc -l $(find . -name "*.txt")

OUTPUT

21022 ./writing/LittleWomen.txt
11 ./writing/haiku.txt
5 ./numbers.txt
21038 total
When the shell executes this command, the first thing it does is run whatever is inside the $(). It
then replaces the $() expression with that command’s output. Since the output of find is the
three filenames ./writing/LittleWomen.txt, ./writing/haiku.txt,
and ./numbers.txt, the shell constructs the command:

BASH

$ wc -l ./writing/LittleWomen.txt ./writing/haiku.txt ./numbers.txt

which is what we wanted. This expansion is exactly what the shell does when it expands
wildcards like * and ?, but lets us use any command we want as our own ‘wildcard’.
It’s very common to use find and grep together. The first finds files that match a pattern; the
second looks for lines inside those files that match another pattern. Here, for example, we can
find txt files that contain the word “searching” by looking for the string ‘searching’ in all
the .txt files in the current directory:

BASH

$ grep "searching" $(find . -name "*.txt")

OUTPUT

./writing/LittleWomen.txt:sitting on the top step, affected to be searching

for her book, but was
./writing/haiku.txt:With searching comes loss
MATCHING AND SUBTRAC TING

The -v option to grep inverts pattern matching, so that only lines which do not match the pattern
are printed. Given that, which of the following commands will find all .dat files
in creatures except unicorn.dat? Once you have thought about your answer, you can test
the commands in the shell-lesson-data/exercise-data directory.

1. find creatures -name "*.dat" | grep -v unicorn

2. find creatures -name *.dat | grep -v unicorn

3. grep -v "unicorn" $(find creatures -name "*.dat")

4. None of the above.

Show me the solution

Option 1. is correct. Putting the match expression in quotes prevents the shell expanding it, so it
gets passed to the find command.
Option 2 is also works in this instance because the shell tries to expand *.dat but there are
no *.dat files in the current directory, so the wildcard expression gets passed to find. We first
encountered this in episode 3.

Option 3 is incorrect because it searches the contents of the files for lines which do not match
‘unicorn’, rather than searching the file names.

BINARY FILES

We have focused exclusively on finding patterns in text files. What if your data is stored as
images, in databases, or in some other format?

A handful of tools extend grep to handle a few non text formats. But a more generalizable
approach is to convert the data to text, or extract the text-like elements from the data. On the one
hand, it makes simple things easy to do. On the other hand, complex things are usually
impossible. For example, it’s easy enough to write a program that will extract X and Y
dimensions from image files for grep to play with, but how would you write something to find
values in a spreadsheet whose cells contained formulas?

A last option is to recognize that the shell and text processing have their limits, and to use
another programming language. When the time comes to do this, don’t be too hard on the shell.
Many modern programming languages have borrowed a lot of ideas from it, and imitation is also
the sincerest form of praise.

The Unix shell is older than most of the people who use it. It has survived so long because it is
one of the most productive programming environments ever created — maybe even the most
productive. Its syntax may be cryptic, but people who have mastered it can experiment with
different commands interactively, then use what they have learned to automate their work.
Graphical user interfaces may be easier to use at first, but once learned, the productivity in the
shell is unbeatable. And as Alfred North Whitehead wrote in 1911, ‘Civilization advances by
extending the number of important operations which we can perform without thinking about
them.’

f i n d PIPELINE READING COMPREHENS ION

Write a short explanatory comment for the following shell script:

BASH

wc -l $(find . -name "*.dat") | sort -n

Show me the solution

1. Find all files with a .dat extension recursively from the current directory

2. Count the number of lines each of these files contains

3. Sort the output from step 2. numerically

KEYPOINTS

 find finds files with specific properties that match patterns.

 grep selects lines in files that match patterns.

 --help is an option supported by many bash commands, and programs that can be
run from within Bash, to display more information on how to use these commands
or programs.

 man [command] displays the manual page for a given command.

 $([command]) inserts a command’s output in place.