Navigating Files and Directories
OverviewTeaching: 30 min
Exercises: 20 minQuestions
How can I perform operations on files outside of my working directory?
What are some navigational shortcuts I can use to make my work more efficient?Objectives
Use a single command to navigate multiple steps in your directory structure, including moving backwards (one level up).
Perform operations on files in directories outside your working directory.
Work with hidden directories and hidden files.
Interconvert between absolute and relative paths.
Employ navigational shortcuts to move around your file system.
Moving around the file system
We’ve learned how to use
pwd to find our current location within our file system.
We’ve also learned how to use
cd to change locations and
ls to list the contents
of a directory. Now we’re going to learn some additional commands for moving around
within our file system.
Use the commands we’ve learned so far to navigate to the
dc_sample_data/untrimmed_fastq directory, if
you’re not already there.
$ cd $ cd dc_sample_data $ cd untrimmed_fastq
What if we want to move back up and out of this directory and to our top level
directory? Can we type
cd dc_sample_data? Try it and see what happens.
$ cd dc_sample_data
-bash: cd: dc_sample_data: No such file or directory
Your computer looked for a directory or file called
dc_sample_data within the
directory you were already in. It didn’t know you wanted to look at a directory level
above the one you were located in.
We have a special command to tell the computer to move us back or up one directory level.
$ cd ..
Now we can use
pwd to make sure that we are in the directory we intended to navigate
ls to check that the contents of the directory are correct.
From this output, we can see that
.. did indeed take us back one level in our file system.
You can chain these together like so:
$ ls ../../
prints the contents of
/home, which is one level up from your root directory.
Finding hidden directories
First navigate to the
dc_sample_datadirectory. There is a hidden directory within this directory. Explore the options for
lsto find out how to see hidden directories. List the contents of the directory and identify the name of the text file in that directory.
Hint: hidden files and folders in Unix start with
., for example .my_hidden_directory
First use the
mancommand to look at the options for
$ man ls
-aoption is short for
alland says that it causes
lsto “not ignore entries starting with .” This is the option we want.
$ ls -a
. .. .hidden sra_metadata untrimmed_fastq
The name of the hidden directory is
.hidden. We can navigate to that directory using
$ cd .hidden
And then list the contents of the directory using
The name of the text file is
Examining the contents of other directories
By default, the
ls commands lists the contents of the working
directory (i.e. the directory you are in). You can always find the
directory you are in using the
pwd command. However, you can also
ls the names of other directories to view. Navigate to your
home directory if you are not already there.
Then enter the command:
$ ls dc_sample_data
This will list the contents of the
dc_sample_data directory without
you needing to navigate there.
cd command works in a similar way.
$ cd $ cd dc_sample_data/untrimmed_fastq
This will take you to the
untrimmed_fastq directory without having to go through
the intermediate directory.
Navigate to your home directory. From there, list the contents of the
$ cd $ ls dc_sample_data/untrimmed_fastq/
Full vs. Relative Paths
cd command takes an argument which is a directory
name. Directories can be specified using either a relative path or a
full absolute path. The directories on the computer are arranged into a
hierarchy. The full path tells you where a directory is in that
hierarchy. Navigate to the home directory, then enter the
$ cd $ pwd
You will see:
This is the full name of your home directory. This tells you that you
are in a directory called
dcuser, which sits inside a directory called
home which sits inside the very top directory in the hierarchy. The
very top of the hierarchy is a directory called
/ which is usually
referred to as the root directory. So, to summarize:
dcuser is a
home which is a directory in
Now enter the following command:
$ cd /home/dcuser/dc_sample_data/.hidden
This jumps forward multiple levels to the
Now go back to the home directory.
You can also navigate to the
.hidden directory using:
$ cd dc_sample_data/.hidden
These two commands have the same effect, they both take us to the
The first uses the absolute path, giving the full address from the home directory. The
second uses a relative path, giving only the address from the working directory. A full
path always starts with a
/. A relative path does not.
A relative path is like getting directions from someone on the street. They tell you to “go right at the stop sign, and then turn left on Main Street”. That works great if you’re standing there together, but not so well if you’re trying to tell someone how to get there from another country. A full path is like GPS coordinates. It tells you exactly where something is no matter where you are right now.
You can usually use either a full path or a relative path depending on what is most convenient. If we are in the home directory, it is more convenient to enter the relative path since it involves less typing.
Over time, it will become easier for you to keep a mental note of the structure of the directories that you are using and how to quickly navigate amongst them.
Relative path resolution
Using the filesystem diagram below, if
/Users/thing, what will
../backup: No such file or directory
2012-12-01 2013-01-08 2013-01-27
2012-12-01/ 2013-01-08/ 2013-01-27/
original pnas_final pnas_sub
- 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. Also, we did not specify
/at the end of the directory names.
There are some shortcuts which you should know about. Dealing with the
home directory is very common. The tilde character,
~, is a shortcut for your home directory. Navigate to the
$ cd $ cd dc_sample_data
Then enter the command:
$ ls ~
dc_sample_data FastQC Trimmomatic-0.32
This prints the contents of your home directory, without you needing to type the full path.
cd ~ are very useful for quickly navigating back to your home directory. We will be using the
~ character in later lessons to specify our home directory.
..characters represent important navigational shortcuts.
Hidden files and directories start with
.and can be viewed using
Relative paths specify a location starting from the current location, while absolute paths specify a location from the root of the file system.