Navigating Files and Directories

Overview

Questions

• 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_workshop/data/untrimmed_fastq directory, if you’re not already there.

BASH

$ cd
$ cd dc_workshop
$ cd 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_workshop? Try it and see what happens.

BASH

$ cd dc_workshop

OUTPUT

-bash: cd: dc_workshop: No such file or directory

Your computer looked for a directory or file called dc_workshop 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.

BASH

$ 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.

BASH

$ pwd

OUTPUT

/home/dcuser/dc_workshop/data

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

You can chain these together to move several levels:

BASH

$ cd ../../..

Excercise 1: Finding hidden directories

First navigate to the dc_workshop 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

Show me the solution

First use the man command to look at the options for ls.

BASH

$ man 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.

BASH

$ ls -a

OUTPUT

.  ..  data  .hidden  mags  taxonomy

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

BASH

$ cd .hidden

And then list the contents of the directory using ls.

BASH

$ ls

OUTPUT

youfoundit.txt

The name of the text file is youfoundit.txt.

File permissions

Another option that the ls command has is to check the permissions on a file. If we are organized and we have a folder with the backup of all our files, we can rescue files that we have accidentally deleted, for example, but just because we have two copies doesn’t make us safe. We can still accidentally delete or overwrite both copies. To make sure we can’t accidentally mess up a file, we’re going to change the permissions on the file so that we’re only allowed to read (i.e. view) the file, not write to it (i.e. make new changes).

View the current permissions on a file using the -l (long) flag for the ls command.

BASH

$ ls -l

OUTPUT

total 0
-rw-rw-r-- 1 dcuser dcuser 0 May 27 23:16 youfoundit.txt

The first part of the output for the -l flag gives you information about the file’s current permissions. There are ten slots in the permissions list. The first character in this list is related to file type, not permissions, so we’ll ignore it for now. The next three characters relate to the permissions that the file owner has, the next three relate to the permissions for group members, and the final three characters specify what other users outside of your group can do with the file. We’re going to concentrate on the three positions that deal with your permissions (as the file owner).

Here the three positions that relate to the file owner are rw-. The r means that you have permission to read the file, the w indicates that you have permission to write to (i.e. make changes to) the file, and the third position is a -, indicating that you don’t have permission to carry out the ability encoded by that space (this is the space where x or executable ability is stored, we’ll talk more about this in a later lesson).

Our goal for now is to change permissions on this file so that you no longer have w or write permissions. We can do this using the chmod (change mode) command and subtracting (-) the write permission -w.

BASH

$ chmod -w youfoundit.txt 
$ ls -l 

OUTPUT

total 0
-r--r--r-- 1 dcuser dcuser 0 May 27 23:16 youfoundit.txt

Absolute 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.

BASH

$ cd  
$ pwd  

You will see:

OUTPUT

/home/dcuser

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 directory in home which is a directory in /.

Now enter the following command:

BASH

$ cd /home/dcuser/dc_workshop/.hidden

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

BASH

$ cd 

And then

BASH

$ cd dc_workshop/.hidden

These two commands have the same effect, they both take us to the .hidden directory. The first one 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.

Excercise 2: Relative path resolution

Using the filesystem diagram below, if pwd displays /Users/thing, what will ls ../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. Also, we did not specify -F to display / at the end of the directory names.
4. Yes: ../backup refers to /Users/backup.

The commands cd, and 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.

Key Points

• The /, ~, and .. characters represent important navigational shortcuts.
• Hidden files and directories start with . and can be viewed using ls -a.
• Relative paths specify a location starting from the current location, while absolute paths specify a location from the root of the file system.