Introduction to Shell: Bioinformatics

Open the Ubuntu app or any other distributor of choice having the Linux.

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Previous: Why Learn Unix/Shell/Bash/Linux for Bioinformatics?

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$

The shell typically uses $ as the prompt, but may use a different symbol. Most importantly: when typing commands, do not type the prompt, only the commands that follow it. Also note that after you type a command, you have to press the Enter key to execute it.

The prompt is followed by a text cursor, a character that indicates the position where your typing will appear. The cursor is usually a flashing or solid block, but it can also be an underscore or a pipe. You may have seen it in a text editor program or word processor, for example.

First Shell Command

So let’s try our first command, ls which is short for listing. This command will list the contents of the current directory. This is written in small letters. The output will be a list of files in the current directory.

If you confuse and write ks, the output will be ks: command not found.

A Typical Problem

You have 1520 samples run through an assay machine to measure the relative abundance of 300 proteins from a field survey. You need to run these 1520 files through an imaginary program called goostats.

If you have to run goostats by hand using a GUI, you’ll have to select and open a file 1520 times. If goostats takes 30 seconds to run each file, the whole process will take more than 12 hours of your attention. With the shell, you can instead assign your computer this mundane task while she focuses her attention on something.

The next few lessons will explore the ways you can achieve this using a command shell to run the goostats program, using loops to automate the repetitive steps of entering file names, so that you computer can work while you do something else.

As a bonus, once you have put a processing pipeline together, she will be able to use it again whenever you collect more data.

Navigating Files and Directories

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.

Second Shell Command

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:

For example: /home/newbiochemist

This is my current home directory.

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

To understand what a ‘home directory’ is, let’s have a look at how the file system as a whole is organized.

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 /Users/newbiochemist.

Inside that directory are several other directories: bin (which is where some built-in programs are stored), data (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 /Users/newbiochemist is stored inside /Users because /Users is the first part of its name. Similarly, we know that /Users is stored inside the root directory / because its name begins with /.

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 path, it’s just a separator.

ls

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

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 Commands

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, 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:

$ ls -s Desktop/data-shell/data
total 116
 4 amino-acids.txt   4 animals.txt   4 morse.txt  12 planets.txt  76 sunspot.txt
 4 animal-counts     4 elements      4 pdb         4 salmon.txt
$ ls -S Desktop/data-shell/data
sunspot.txt  animal-counts  pdb        amino-acids.txt  salmon.txt
planets.txt  elements       morse.txt  animals.txt

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:

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

Depending on your environment you might find that only one of these works (either man or --help, eg. man works for macOS and --help typically works for Git Bash).

We’ll describe both ways below.

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
...        ...        ...

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.

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.

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.

Solution

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 flags? Hint: You may need to use the -l flag to see the last changed dates.

Solution

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

data-shell/

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 data-shell directory you downloaded at the setup for this lesson. 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 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 data-shell 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 to ls:

$ ls -F Desktop/data-shell

creatures/          molecules/          notes.txt           solar.pdf
data/               north-pacific-gyre/ pizza.cfg           writing/

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. 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. The cd command is akin to double clicking a folder in a graphical interface to get into a folder.

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

$ cd Desktop
$ cd data-shell
$ cd data

These commands will move us from our home directory into our Desktop directory, then into the data-shell directory, then into the 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 /Users/nelle/Desktop/data-shell/data. If we run ls -F without arguments now, it lists the contents of /Users/nelle/Desktop/data-shell/data, because that’s where we now are:

$ pwd

/Users/nelle/Desktop/data-shell/data

$ 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 (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 data-shell

-bash: cd: data-shell: 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 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 /Users/nelle/Desktop/data-shell:

$ pwd

/Users/nelle/Desktop/data-shell

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

$ ls -F -a

./   .bash_profile  data/       north-pacific-gyre/  pizza.cfg  thesis/
../  creatures/     molecules/  notes.txt            solar.pdf  writing/

-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 /Users/nelle, refers to the /Users 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’ll see some uses for it soon.

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 .bash_profile. 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.

Orthogonality

The special names . and .. don’t belong to cd; they are interpreted the same way by every program. For example, if we are in /Users/nelle/data, the command ls .. will give us a listing of /Users/nelle. When the meanings of the parts are the same no matter how they’re combined, programmers say they are orthogonal: Orthogonal systems tend to be easier for people to learn because there are fewer special cases and exceptions to keep track of.

These then, 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/nelle

It turns out that cd without an argument will return you to your home directory, which is great if you’ve gotten lost in your own filesystem.

Let’s try returning to the data directory from before. Last time, we used three commands, but we can actually string together the list of directories to move to data in one step:

$ cd Desktop/data-shell/data

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 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 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 data-shell directory from anywhere on the filesystem (including from inside data). To find the absolute path we’re looking for, we can use pwd and then extract the piece we need to move to data-shell.

$ pwd

/Users/nelle/Desktop/data-shell/data

$ cd /Users/nelle/Desktop/data-shell

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

Two More Shortcuts

The shell interprets the character ~ (tilde) at the start of a path to mean “the current user’s home directory”. For example, if Nelle’s home directory is /Users/nelle, then ~/data is equivalent to /Users/nelle/data. This only works if it is the first character in the path: here/there/~/elsewhere is not here/there/Users/nelle/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 directories. The difference between cd .. and cd - is that the former brings you up, while the latter brings you back. You can think of it as the Last Channel button on a TV remote.

Absolute vs Relative Paths

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

1. cd .
2. cd /
3. cd /home/amanda
4. cd ../..
5. cd ~
6. cd home
7. cd ~/data/..
8. cd
9. cd ..

Solution

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/

Solution

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/

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

Solution

Nelle’s Pipeline: Organizing Files

Knowing this much about files and directories, Nelle is ready to organize the files that the protein assay machine will create. First, she creates a directory called north-pacific-gyre (to remind herself where the data came from). Inside that, she creates a directory called 2012-07-03, which is the date she started processing the samples. She used to use names like conference-paper and revised-results, but she found them hard to understand after a couple of years. (The final straw was when she found herself creating a directory called revised-revised-results-3.)

Sorting Output

Nelle names her directories ‘year-month-day’, with leading zeroes for months and days, because the shell displays file and directory names in alphabetical order. If she used month names, December would come before July; if she didn’t use leading zeroes, November (‘11’) would come before July (‘7’). Similarly, putting the year first means that June 2012 will come before June 2013.

Each of her physical samples is labelled according to her lab’s convention with a unique ten-character ID, such as ‘NENE01729A’. This 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 as part of each data file’s name. Since the assay machine’s output is plain text, she will call her files NENE01729A.txt, NENE01812A.txt, and so on. All 1520 files will go into the same directory.

Now in her current directory data-shell, Nelle can see what files she has using the command:

$ ls north-pacific-gyre/2012-07-03/

This 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/

If she presses Tab again, Bash will add 2012-07-03/ to the command, since it’s the only possible completion. Pressing Tab again does nothing, since there are 19 possibilities; pressing Tab twice brings up a list of all the files, and so on. This is called tab completion, and we will see it in many other tools as we go on.