2.2 Navigating Files and Directories

Teaching: 40 min || Exercises: 20 min

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?
  • How can I create, copy, and delete files and directories?
  • How can I edit files?
Learning 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.
  • 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.
Key Points:
  • 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 forms a directory tree.
  • cd path changes the current working directory.
  • ls path prints a listing of a specific file or directory; ls on its own lists the current working directory.
  • pwd prints the user’s current working directory.
  • / on its own is the root directory of the whole file system.
  • A relative path specifies a location starting from the current location.
  • An absolute path specifies a location from the root of the file system.
  • Directory names in a path are separated with / on Unix, but \\ on Windows.
  • .. means ‘the directory above the current one’; . on its own means ‘the current directory’.
  • 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.
  • 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.

2.2.1 The file system

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:

pwd
/home/ubuntu

Here, the computer’s response is /home/ubuntu, which is your home directory:

Home Directory Variation

The home directory path will look different on different operating systems. On Mac it may look like /Users/ubuntu, and on Windows it will be similar to C:\Documents and Settings\ubuntu or C:\Users\ubuntu.

(Note that it may look slightly different for different versions of Windows, and ubuntu may be replaced with your username.) In future examples, we’ve used Linux output as the default - Mac and Windows output may differ slightly, but should be generally similar.

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 a typical Linux 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 a typical Linux computer, the filesystem looks like this:

The File System

At the top is the root directory that holds everything else. We refer to it using a slash character, /, on its own; this is the leading slash in /home/ubuntu.

Inside that directory are several other directories:

  • bin (which is where some built-in programs are stored),
  • usr (for miscellaneous user files),
  • home (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 /home/ubuntu is stored inside /home because /home is the first part of its name. Similarly, we know that /home 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 name, it’s just a separator.

Underneath /home, we find one directory for each user with an account on the machine, in this example imhotep, larry, and ubuntu (you).

Home Directories

The user imhotep’s files are stored in /home/imhotep, user larry’s in /home/larry, and yours in /home/ubuntu. Because you are the current user in our examples here, this is why we get /home/ubuntu 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, which stands for “listing”:

ls
Documents    Downloads    Music        Public
Desktop      Movies       Pictures     Templates
...

(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 (also known as a switch or a flag) , 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 default options, the shell might also use colors to indicate whether each entry is a file or directory.

ls -F
Documents/    Downloads/    Music/        Public/
Desktop/      Movies/       Pictures/     Templates/
...

Here, we can see that our home directory contains mostly sub-directories. Any names in your output that don’t have a classification symbol, are plain old files.

Clearing your terminal

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.

General syntax of a shell command

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

ls -F /

General syntax of a shell command

ls is the command, with an option -F and an argument /. We’ve already encountered options (also called switches or flags) which either start with a single dash (-) or two dashes (--), and they change the behaviour 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.

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, capitalisation can be important: ls -r is different to ls -R. Also, ls -s is different to ls -S. Find out what each does.

Putting all that together, our command 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 /
bin/  boot/  cdrom/  core  dev/  etc/  home/  home2/  initrd.img@  
initrd.img.old@  lib/  lib32/  lib64/  lost+found/  media/  mnt/  
opt/  proc/  root/  run/  sbin/  snap/  srv/  sys/  tmp/  usr/  var/

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:

  1. We can pass a --help option to the command, such as:

    ls --help

  2. We can read its manual with man, such as:

    man ls

The --help option

Many bash commands, and programs that people have written that can be run from within bash, support a --help option to display 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 none of -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
      --file-type            likewise, except do not append '*'
      --format=WORD          across -x, commas -m, horizontal -x, long -l,
                               single-column -1, verbose -l, vertical -C
      --full-time            like -l --time-style=full-iso
  -g                         like -l, but do not list owner
      --group-directories-first
                             group directories before files;
                               can be augmented with a --sort option, but any
                               use of --sort=none (-U) disables grouping
  -G, --no-group             in a long listing, don't print group names
  -h, --human-readable       with -l and/or -s, print human readable sizes
                               (e.g., 1K 234M 2G)
      --si                   likewise, but use powers of 1000 not 1024
...   ...                    ...
Unsupported command-line options

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

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

The man command

The other way to learn about ls is to type

man ls

This will turn your terminal into a page with a description of the ls command and its options and, if you’re lucky, some examples of how to use it.

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.

Exercise 2.2.1.1: Exploring More ls Flags

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.

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.

Exercise 2.2.1.2: Listing in Reverse Chronological 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.

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

2.2.2 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:

ls -F Desktop
...
workshop_files_Bact_Genomics_2023/
...

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 workshop_files_Bact_Genomics_2023 directory. On many systems, the command line Desktop directory is the same as your GUI Desktop. Take a look at your Desktop to confirm that your output is accurate.

As you may now see, using a bash shell is strongly dependent on the idea that your files and directories are organized in a hierarchical file system. Organizing things hierarchically in this way helps us keep track of our work: 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, but it’s a self-defeating strategy.

Now that we know the workshop_files_Bact_Genomics_2023 directory is located in our Desktop directory, we can do two things.

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

ls -F Desktop/workshop_files_Bact_Genomics_2023
01_intro_WGS/    02_unix_intro/    03_file_formats/    04_QC/    05_mapping/
...

Second, we can also change our location to that 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 idea of what directory we are in.

Let’s say we want to move to the 02_unix_intro directory we saw above. We can use the following series of commands to get there:

cd Desktop
cd workshop_files_Bact_Genomics_2023
cd 02_unix_intro

These commands will move us from our home directory onto our Desktop, then into the workshop_files_Bact_Genomics_2023 directory, then into the 02_unix_intro 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 /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro. If we run ls without arguments now, it lists the contents of /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro, because that’s where we are now:

pwd
/home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro
ls -F
amino-acids.txt   elements/     pdb/            salmon.txt
animals.txt       morse.txt     planets.txt     sunspot.txt

We now know how to go down the directory tree, but how do we go up? We might try the following:

Error 
cd workshop_files_Bact_Genomics_2023
-bash: cd: workshop_files_Bact_Genomics_2023: 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 will start with the simplest.

There is a shortcut in the shell to move up one directory level that looks like this:

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 /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023:

pwd
/home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023

The special directory .. doesn’t usually show up when we run ls. If we want to display it, we can give ls the -a option:

ls -F -a
./    01_intro_WGS/    03_file_formats/    05_mapping/
../   02_unix_intro/   04_QC/

-a stands for “show all”; it forces ls to show us file and directory names that begin with ., such as .. (which, if we’re in /home/ubuntu, refers to the /home 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 will see some uses for it soon.

Note

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 .bashrc. 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?

cd

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

pwd
/Users/name_of_user

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 02_unix_intro directory from before. Last time, we used three commands, but we can actually string together the list of directories to move to 02_unix_intro in one step:

cd Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro

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 02_unix_intro 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 workshop_files_Bact_Genomics_2023 directory from anywhere on the filesystem (including from inside 02_unix_intro). To find the absolute path we are looking for, we can use pwd and then extract the piece we need to move to workshop_files_Bact_Genomics_2023.

pwd
/home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro
cd /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023

Run pwd and ls -F to ensure that we are in the directory we expect.

Two More Shortcuts

The shell interprets the tilde (~) character at the start of a path to mean “the current user’s home directory”. For example, for your home directory,/home/ubuntu, then ~/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro is equivalent to /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro. This only works if it is the first character in the path: here/there/~/elsewhere is not here/there/home/ubuntu/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/workshop_files_Bact_Genomics_2023 (you should already be there).

cd ~/Desktop/workshop_files_Bact_Genomics_2023

Then cd into the exercise-data/creatures directory

cd 02_unix_intro/bacteria_rpob

Now if you run

cd -

you’ll see you’re back in ~/Desktop/workshop_files_Bact_Genomics_2023. Run cd - again and you’re back in ~/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro/bacteria_rpob

Tab completion

Sometimes file and directory names get too long and it’s tedious to have to type the full name for example when moving with cd. We can let the shell do most of the work > through what is called tab completion. Let’s say we are in the /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro/ and we type:

ls nor

and then press Tab or ↹(the tab key on the keyboard), the shell automatically completes the directory name:

ls north-pacific-gyre/

If we press Tab or ↹ again, Bash will add 2012-07-03/ to the command, since it’s the only possible completion (NB. this may not be the case if there is another directory in there). Pressing Tab or ↹ again does nothing, since there are 19 possibilities; pressing Tab or ↹ twice brings up a list of all the files, and so on. This is very useful in practise and we will see more of it later.

Exercise 2.2.2.1: Absolute vs Relative Paths

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

  1. cd .
  2. cd /
  3. cd /home/amanda
  4. cd ../..
  5. cd ~
  6. cd home
  7. cd ~/data/..
  8. cd
  9. cd ..
  1. No: . stands for the current directory.
  2. No: / stands for the root directory.
  3. Yes: This is an example of using the full absolute path.
  4. No: this goes up two levels, i.e. ends in /home.
  5. Yes: ~ stands for the user’s home directory, in this case /home/amanda.
  6. No: this 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.
Exercise 2.2.2.2: Relative Path Resolution

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/

File System for Challenge Questions

  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/.
Exercise 2.2.2.3: ls Reading Comprehension

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:

pnas_sub/ pnas_final/ original/

File System for Challenge Questions

  1. ls pwd
  2. ls -r -F
  3. ls -r -F /Users/backup
  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.

2.2.3 Creating directories

We now know how to explore files and directories, but how do we create them in the first place?

Step 1: see where we are and what we already have

Let’s go back to our workshop_files_Bact_Genomics_2023 directory on the Desktop and use ls -F to see what it contains:

pwd
/home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023
ls -F
01_intro_WGS/    02_unix_intro/    03_file_formats/    04_QC/    05_mapping/
...

Step 2: Create a directory

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

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:

ls -F
01_intro_WGS/    02_unix_intro/    03_file_formats/    04_QC/    05_mapping/
thesis/
...

Two ways of doing the 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.

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/).

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 ("").

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

ls -F thesis

Step 3: 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 firstdraft.txt:

cd thesis
nano firstdraft.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 may need to do after this workshop.

On Unix systems (such as Linux and Mac OS X), many programmers use Emacs or Vim (both of which require more time to learn), or a graphical editor such as Gedit. 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’ll be asked what file we want to save this to: press Return or Enter to accept the suggested default of firstdraft.txt).

Nano in Action

Once our file is saved, we can use Ctrl-X to quit the editor and return to the shell. Note that pressing Ctrl-X without previously saving the file can achieve both aim of saving and exiting. You can try this out.

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 firstdraft.txt:

ls
firstdraft.txt
Exercise 2.2.3.1: Creating Files a Different Way

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

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?

  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.

What’s In A Name?

You may have noticed that all of the files in our data directory 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 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.

NB. Naming a PNG image of a whale as whale.mp3 doesn’t somehow magically turn it into a recording of whalesong, though it might cause the operating system to try to open it with a music player when someone double-clicks it.

2.2.4 Moving files and directories

Returning to the workshop_files_Bact_Genomics_2023 directory,

cd ~/Desktop/workshop_files_Bact_Genomics_2023/

In our thesis directory we have a file firstdraft.txt which isn’t a particularly informative name, so let’s change the file’s name using mv, which is short for “move”:

mv thesis/firstdraft.txt thesis/second_draft.txt

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

ls thesis
second_draft.txt
Warning

One has to 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.

An additional option, mv -i (or mv --interactive), can be used to make mv ask you for confirmation before overwriting.

Note that mv also works on directories.

Let’s move second_draft.txt into the current working directory. We use mv once again, but this time we’ll just use 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.

mv thesis/second_draft.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:

ls thesis

Further, ls with a filename or directory name as an argument only lists that file or directory. We can use this to see that second_draft.txt is still in our current directory:

ls second_draft.txt
second_draft.txt

2.2.5 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:

cp second_draft.txt thesis/third_draft.txt
ls second_draft.txt thesis/third_draft.txt
second_draft.txt   thesis/third_draft.txt

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

cp -r thesis thesis_backup

We can check the result by listing the contents of both the thesis and thesis_backup directory:

ls thesis thesis_backup
thesis:
third_draft.txt

thesis_backup:
third_draft.txt
Exercise 2.2.5.1: 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 command 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 .
  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.
Exercise 2.2.5.2: Moving and Copying

What is the output of the closing ls command in the sequence shown below? You can try the commands starting from /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro/mycobacteria_rpob.

pwd
/home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro/mycobacteria_rpob
ls
Mycobacterium_tuberculosis_H37Rv_rpob.fasta
mkdir recombine
mv Mycobacterium_tuberculosis_H37Rv_rpob.fasta recombine/
cp recombine/Mycobacterium_tuberculosis_H37Rv_rpob.fasta ../Mycobacterium_tuberculosis_H37Rv_rpob-saved.fasta
ls
  1. Mycobacterium_tuberculosis_H37Rv_rpob-saved.fasta recombine
  2. recombine
  3. Mycobacterium_tuberculosis_H37Rv_rpob.fasta recombine
  4. Mycobacterium_tuberculosis_H37Rv_rpob-saved.fasta
  • We start in the /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro/mycobacteria_rpob directory, and create a new folder called recombine.
  • The second line moves (mv) the file Mycobacterium_tuberculosis_H37Rv_rpob.fasta to the new folder (recombine).
  • 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 /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro. - 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 /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro/mycobacteria_rpob) is the recombine folder.

  1. No, see explanation above. Mycobacterium_tuberculosis_H37Rv_rpob-saved.fasta is located in /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro
  2. Yes
  3. No, see explanation above. Mycobacterium_tuberculosis_H37Rv_rpob.fasta is located at /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro/mycobacteria_rpob/recombine
  4. No, see explanation above. Mycobacterium_tuberculosis_H37Rv_rpob-saved.fasta is located at /home/ubuntu/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro

2.2.6 Removing files and directories

Returning to the workshop_files_Bact_Genomics_2023 directory, let’s tidy up this directory by removing the second_draft.txt file we created. The Unix command we will use for this is rm (short for ‘remove’):

rm second_draft.txt

We can confirm the file has gone using ls:

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

You can also check by simply executing ls

ls
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 is no guarantee they will work in any particular situation, since the computer may recycle the file’s disk space right away.

Exercise 2.2.6.1: Using rm Safely

What happens when we execute rm -i thesis_backup/third_draft.txt? Why would we want this protection when using rm?

rm: remove regular file 'thesis_backup/third_draft.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:

rm thesis
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:

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).

2.2.7 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.

Exercise 2.2.7.1: Copy with Multiple Filenames

For this exercise, you can test the commands in the workshop_files_Bact_Genomics_2023/02_unix_intro directory. In the example below, what does cp do when given several filenames and a directory name?

mkdir backup
cp nucleotides.txt bacteria.txt backup/

In the example below, what does cp do when given three or more file names?

ls -F
nucleotides.txt  bacteria.txt  backup/  elements/  morse.txt  
pdb/  planets.txt  salmon.txt  sunspot.txt
cp nucleotides.txt bacteria.txt morse.txt

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.

cp: target ‘morse.txt’ is not a directory

Using wildcards for accessing multiple files at once

Wildcards

*

* is a wildcard, which matches zero or more characters. Let’s consider the workshop_files_Bact_Genomics_2023/02_unix_intro/molecules directory: *.pdb matches ethane.pdb, propane.pdb, and every file that ends with ‘.pdb’. On the other hand, p*.pdb only matches pentane.pdb and propane.pdb, because the ‘p’ at the front only matches filenames that begin with the letter ‘p’.

?

? is also a wildcard, but it matches exactly one character. So ?ethane.pdb would match methane.pdb whereas *ethane.pdb matches both ethane.pdb, and methane.pdb.

Wildcards can be used in combination with each other e.g. ???ane.pdb matches 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 command that was asked for. 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 molecules 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 deals with expanding wildcards, and this is an example of orthogonal design.

Exercise 2.2.7.2: List filenames matching a pattern

When run in the molecules 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.*

The answer 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..

Exercise 2.2.7.3: More on Wildcards

Look into the exp directory in ~/Desktop/workshop_files_Bact_Genomics_2023/02_unix_intro/exp that has the following structure:

exp
├── 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

Suppose you want to:

  1. backup all dataset file to backup/datasets and all calibration files to backup/calibration

  2. copy all the dataset files created on the 23rd to send_to_bob/all_datasets_created_on_a_23rd and all November files (calibration) and dataset) to send_to_bob/all_november_files so you can send to a colleague.

Which commands would you use to do that?

The resulting directory structure should look like this

exp
├── 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

Solution is scheduled to be released after class.

Exercise 2.2.7.4: Reproduce a folder structure

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-data folder into a folder called 2016-05-20 so that your final directory structure looks like this:

2016-05-20/
└── data
    ├── processed
    └── raw

Which of the following set of commands would achieve this objective? What would the other commands do? Try them out in the workshop_files_Bact_Genomics_2023/02_unix_intro directory.

1.

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

2.

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

3.

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

4.

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

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 mkdir won’t create a subdirectory of a non-existent directory: the intermediate level folders must be created first.

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

2.2.8 Credit

Information on this page has been adapted and modified from the following source(s):

  • Gabriel A. Devenyi (Ed.), Gerard Capes (Ed.), Colin Morris (Ed.), Will Pitchers (Ed.),Greg Wilson, Gerard Capes, Gabriel A. Devenyi, Christina Koch, Raniere Silva, Ashwin Srinath, … Vikram Chhatre. (2019, July). swcarpentry/shell-novice: Software Carpentry: the UNIX shell, June 2019 (Version v2019.06.1).

  • https://github.com/cambiotraining/UnixIntro