Navigating Files and Directories
Last updated on 2023-05-02 | Edit this page
- 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?
- 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
Here, the computer’s response is
/Users/nelle, which is
Nelle’s home directory:
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
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:
At the top 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
Inside that directory are several other directories:
(which is where some built-in programs are stored),
(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
is stored inside
/Users is the
first part of its name. Similarly, we know that
stored inside the root directory
/ because its name begins
/Users, we find one directory for each user
with an account on Nelle’s machine, her colleagues imhotep and
The user imhotep’s files are stored in
/Users/imhotep, user larry’s in
/Users/larry, and Nelle’s in
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
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
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
-F option which tells
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.
$ ls -F
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.
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:
- We can pass a
--helpoption to any command (available on Linux and Git Bash), for example:
$ ls --help
- We can read its manual with
man(available on Linux and macOS):
$ man ls
We’ll describe both ways next.
Some commands are built in to the Bash shell, rather than existing as
separate programs on the filesystem. One example is the
(change directory) command. If you get a message like
No manual entry for cd, try
help cd instead.
help command is how you get usage information for Bash
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.
$ ls --help
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 ... ... ...
The other way to learn about
ls is to type
$ man ls
This command will turn your terminal into a page with a description
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
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.
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
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.
-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
5.3K instead of
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
-r options? Hint: You may need to use the
option to see the last changed dates.
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.
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
ls that we want a listing of something other than our
current working directory:
$ ls -F Desktop
Note that if a directory named
Desktop does not exist in
your current working directory, this command will return an error.
Desktop directory exists in your home
directory, which we assume is the current working directory of your bash
Your output should be a list of all the files and sub-directories in
your Desktop directory, including the
directory you downloaded at the setup for this
lesson. (On most systems, the contents of the
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
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 -F Desktop/shell-lesson-data
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.
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
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
directory we saw above. We can use the following series of commands to
$ 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
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
If we run
ls -F without arguments now, it lists the
because that’s where we now are:
$ ls -F
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:
$ cd shell-lesson-data
-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
There is a shortcut in the shell to move up one directory level. It works as follows:
$ 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
cd .., we’re back in
The special directory
.. doesn’t usually show up when we
ls. If we want to display it, we can add the
-a option to
$ ls -F -a
./ ../ exercise-data/ north-pacific-gyre/
-a stands for ‘show all’ (including hidden files); it
ls to show us file and directory names that begin
., such as
.. (which, if we’re in
/Users/nelle, refers to the
As you can see, it also displays another special directory that’s just
., which means ‘the current working directory’. It
may seem redundant to have a name for it, but we’ll see some uses for it
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
These three commands are the basic commands for navigating the
filesystem on your computer:
cd. Let’s explore some variations on those commands. What
happens if you type
cd on its own, without giving a
How can you check what happened?
pwd gives us the
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
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
in one step:
$ cd Desktop/shell-lesson-data/exercise-data
Check that we’ve moved to the right place by running
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
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
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
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
$ cd /Users/nelle/Desktop/shell-lesson-data
ls -F to ensure that we’re in
the directory we expect.
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
~/data is equivalent to
This only works if it is the first character in the path;
here/there/~/elsewhere is not
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
Try it! First navigate to
(you should already be there).
$ cd ~/Desktop/shell-lesson-data
cd into the
$ cd exercise-data/creatures
Now if you run
$ cd -
you’ll see you’re back in
cd - again and you’re back in
.stands for the current directory.
/stands for the root directory.
- No: Amanda’s home directory is
- No: this command goes up two levels, i.e. ends in
~stands for the user’s home directory, in this case
- No: this command would navigate into a directory
homein the current directory if it exists.
- Yes: unnecessarily complicated, but correct.
- Yes: shortcut to go back to the user’s home directory.
- Yes: goes up one level.
- No: there is a directory
- No: this is the content of
Users/thing/backup, but with
.., we asked for one level further up.
- No: see previous explanation.
pwdis not the name of a directory.
lswithout directory argument lists files and directories in the current directory.
- Yes: uses the absolute path explicitly.
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:
$ ls -F /
ls is the command, with an
-F and an argument
/. We’ve already encountered options which either start
with a single dash (
-) or two dashes (
they change the behavior of a command. 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
-F the shell will look for a command
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:
$ cd ~/Desktop/shell-lesson-data $ ls -s exercise-data
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
$ ls -S exercise-data
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:
$ ls -F /
Applications/ System/ Library/ Users/ Network/ Volumes/
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
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
NENE01812A.txt, and so on. All
1520 files will go into the same directory.
Now in her current directory
can see what files she has using the command:
$ 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:
$ ls nor
and then presses Tab (the tab key on her keyboard), the shell automatically completes the directory name for her:
$ 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’.
$ ls north-pacific-gyre/goo
To see all of those files, she can press Tab twice more.
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.
- 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.
pwdprints the user’s current working directory.
ls [path]prints a listing of a specific file or directory;
lson 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 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’.