Navigating Files and Directories

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.

Questions to be answered in this lesson

  • 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?

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 shell_data/untrimmed_fastq directory, if you’re not already there.

$ cd
$ cd Desktop
$ cd unix_lesson
$ cd shell_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 shell_data? Try it and see what happens.

Command:

$ cd shell_data

Output: Note: This is an example

$ cd cd: shell_data: No such file or directory

Your computer looked for a directory or file called shell_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 to, and ls to check that the contents of the directory are correct.

Command:

$ pwd

Command:

$ ls

Output:

sra_metadata  untrimmed_fastq

From this output, we can see that .. did indeed take us back one level in our file system.

Command:

$ ls ../../

Exercise

Finding hidden directories

First navigate to the shell_data directory. There is a hidden directory within this directory. Explore the options for ls to 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 --help command to look at the options for ls.

$ --help ls

The -a option is short for all and says that it causes ls to “not ignore entries starting with .” This is the option we want.

Command:

$ ls -a

Output:

.  ..  .hidden  sra_metadata  untrimmed_fastq

The name of the hidden directory is .hidden. We can navigate to that directory using cd.

$ cd .hidden

And then list the contents of the directory using ls.

Command:

$ ls

Output:

youfoundit.txt

The name of the text file is youfoundit.txt.

In most commands the flags can be combined together in no particular order to obtain the desired results/output.

$ ls -Fa
$ ls -laF

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 give ls the names of other directories to view Navigate to your home directory if you are not already there.

$ cd

Then enter the command:

$ ls shell_data

Output:

sra_metadata  untrimmed_fastq

This will list the contents of the shell_data directory without you needing to navigate there. The cd command works in a similar way.

Try entering:

$ cd
$ cd shell_data/untrimmed_fastq

This will take you to the untrimmed_fastq directory without having to go through the intermediate directory.

Exercice

Navigating practice

Navigate to your home directory. From there, list the contents of the untrimmed_fastq directory.

Command:

$ cd
$ ls shell_data/untrimmed_fastq/

Output:

SRR097977.fastq  SRR098026.fastq

Full vs. Relative Paths

The 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 pwd command.

Command:

$ cd ~
$ pwd

Output: Note: This is an example

$ /usr/home/⟨username⟩

This command will display the full name of your home directory. The very top of the hierarchy is a directory called / which is usually referred to as the root directory .

Now lets navigate directly to the .hidden folder using the full path.

$ cd /usr/home/⟨username⟩/Desktop/unix_lesson/shell_data/.hidden

This jumps forward multiple levels to the .hidden directory. Now go back to the home directory.

$ cd

You can also navigate to the .hidden directory using:

$ cd Desktop/unix_lesson/shell_data/.hidden

These two commands have the same effect, they both take us to the .hidden directory. 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 full path. If we are in the working 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.