Introduction to the Unix Shell

Published

2025-01-24

Questions

Objectives
  • What is a command shell and why would I use one?
  • Explain how the shell relates to the keyboard, the screen, the operating system, and users’ programs.
  • Explain when and why command-line interfaces should be used instead of graphical interfaces.

About this tutorial

This tutorial was heavily adapted from the Shell Novice tutorial created by Software Carpentry. It has been shortened to fit our time frame.

Background

We interact with computers in many different ways, such as through a keyboard and mouse, and touch screen interfaces. The most widely used way to interact with personal computers is called a graphical user interface (GUI). With a GUI, we give instructions by clicking a mouse and using menu-driven interactions.

While the visual aid of a GUI makes it intuitive to use, this way of delivering instructions to a computer scales very poorly. Imagine the following task: you have to copy the third line of one thousand text files in one thousand different directories and paste it into a single file. Using a GUI, you would not only be clicking at your desk for several hours, but you could potentially also commit an error in the process of completing this repetitive task. This is where we take advantage of the Unix shell. The Unix shell is both a command-line interface (CLI) and a scripting language, allowing such repetitive tasks to be done automatically and fast. With the proper commands, the shell can repeat tasks with or without some modification as many times as we want. Using the shell, the task in the literature example can be accomplished in seconds.

The Shell

The shell is a program where users can type commands. With the shell, it’s possible to invoke complicated programs or simple commands with only one line of code. The most popular Unix shell is Bash (the Bourne Again SHell — so-called because it’s derived from a shell written by Stephen Bourne). Bash is the default shell on most implementations of Unix (Mac computers running macOS Catalina or later releases, the default Unix Shell is “Zsh”) and in most packages that provide Unix-like tools for Windows. Note that ‘Git Bash’ is a piece of software that enables Windows users to use a Bash-like interface when interacting with Git.

Using the shell will take some effort and some time to learn. While a GUI presents you with choices to select, CLI choices are not automatically presented to you, so you must learn a few commands like new vocabulary in a language you’re studying. Luckily, a small number of “words” (i.e. commands) gets you a long way, and we’ll cover those essential few today.

The grammar of a shell allows you to combine existing tools into powerful pipelines and handle large volumes of data automatically. Sequences of commands can be written into a script, improving the reproducibility of workflows.

In addition, the command line is often the easiest way to interact with remote machines and supercomputers. Familiarity with the shell is near essential to run a variety of specialized tools and resources including high-performance computing systems. As clusters and cloud computing systems become more popular for scientific data crunching, being able to interact with the shell is becoming a necessary skill. We can build on the command-line skills covered here to tackle a wide range of scientific questions and computational challenges.

Let’s get started.

The prompt

When the shell is first opened, you are presented with a prompt, indicating that the shell is waiting for input.

$

The shell typically uses $ as the prompt, but may use a different symbol. In the examples for this lesson, we’ll show the prompt as $. Most importantly, do not type the prompt when typing commands. Only type the command that follows the prompt. This rule applies both in these lessons and in lessons from other sources. 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, for example.

Note that your prompt might look a little different. In particular, most popular shell environments by default put your user name and the host name before the $. Such a prompt might look like, e.g.:

sklucas@localhost $

The prompt might even include more than this. Do not worry if your prompt is not just a short $. This lesson does not depend on this additional information and it should also not get in your way. The only important item to focus on is the $ character itself and we will see later why.

OPTIONAL: Change your prompt to $

If you’d like to simplify your prompt for the purposes of this tutorial, copy and paste the code below into your terminal:

PS1='$ '

So let’s try our first command, ls, which is short for listing. This command will list the contents of the current directory:

$ ls
Desktop     Downloads   Movies      Pictures
Documents   Library     Music       Public
Command not found

If the shell can’t find a program whose name is the command you typed, it will print an error message such as:

$ ks
ks: command not found

This might happen if the command was mis-typed or if the program corresponding to that command is not installed.

A Typical Problem

You are a marine biologist who has just returned from a six-month survey of the North Pacific Gyre, where you have sampled gelatinous marine life in the Great Pacific Garbage Patch. You have 1520 samples that you’ve run through an assay machine to measure the relative abundance of 300 proteins. You need to run these 1520 files through an imaginary program called goostats.sh. In addition to this huge task, you have to write up results by the end of the month, so your paper can appear in a special issue of Aquatic Goo Letters.

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

The next few lessons will explore the ways you can achieve this. More specifically, the lessons explain how you can use a command shell to run the goostats.sh program, using loops to automate the repetitive steps of entering file names, so that your computer can work while you write your paper.

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

In order to achieve your task, you need to know how to:

  • navigate to a file/directory
  • create a file/directory
  • check the length of a file
  • chain commands together
  • retrieve a set of files
  • iterate over files
  • run a shell script containing your pipeline

Download files:

You need to download some files to follow this lesson.

  1. Download shell-lesson-data.zip and move the file to your Desktop.

  2. Unzip/extract the file. Let your instructor know if you need help with this step. You should end up with a new folder called shell-lesson-data on your Desktop.

Key Points
  • A shell is a program whose primary purpose is to read commands and run other programs.
  • This lesson uses Bash, the default shell in many implementations of Unix.
  • Programs can be run in Bash by entering commands at the command-line prompt.
  • The shell’s main advantages are its high action-to-keystroke ratio, its support for automating repetitive tasks, and its capacity to access networked machines.
  • A significant challenge when using the shell can be knowing what commands need to be run and how to run them.

Creating, moving, removing

Questions Objectives
  • How can I navigate my filesystem at the CLI
  • How can I create, copy, and delete files and directories?
  • How can I edit files?
  • Create a new directory hierarchy
  • Create files in that hierarchy using a text editor
  • Delete, copy, and move files and/or directories

Creating Directories and Files

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

In this episode we will learn about creating and moving files and directories, using the exercise-data/writing directory as an example.

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

We should still be in the shell-lesson-data directory on the Desktop, which we can check using:

$ pwd
/Users/sklucas/Desktop/shell-lesson-data

Next we’ll move to the exercise-data/writing directory and see what it contains:

$ cd exercise-data/writing/
$ ls -F
haiku.txt  LittleWomen.txt

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
haiku.txt  LittleWomen.txt  thesis/

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

$ ls -F thesis

Note that mkdir is not limited to creating single directories one at a time. The -p option allows mkdir to create a directory with nested subdirectories in a single operation:

$ mkdir -p ../project/data ../project/results

The -R option to the ls command will list all nested subdirectories within a directory. Let’s use ls -FR to recursively list the new directory hierarchy we just created in the project directory:

$ ls -FR ../project
../project/:
data/  results/

../project/data:

../project/results:
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 and directories.

  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/). To test this out, try typing mkdir north pacific gyre and see what directory (or directories!) are made when you check with ls -F.

  1. Don’t begin the name with - (dash).

Commands treat names starting with - as options.

  1. 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 single quotes ('').

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 draft.txt:

$ cd thesis
$ nano draft.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 need to do after this workshop. On Unix systems (such as Linux and macOS), many programmers use Emacs or Vim (both of which require more time to learn), or a graphical editor such as Gedit or VScode. 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 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 will be asked to provide a name for the file that will contain our text. Press Return to accept the suggested default of draft.txt.

Once our file is saved, we can use Ctrl+X to quit the editor and return to the shell.

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 draft.txt:

$ ls
draft.txt
Challenge: 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.

To avoid confusion later on, we suggest removing the file you’ve just created before proceeding with the rest of the episode, otherwise future outputs may vary from those given in the lesson. To do this, use the following command:

$ rm my_file.txt

What’s in a name?

You may have noticed that all of your files 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 merely 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.

Naming a PNG image of a whale as whale.mp3 doesn’t somehow magically turn it into a recording of whale song, though it might cause the operating system to associate the file with a music player program. In this case, if someone double-clicked whale.mp3 in a file explorer program, the music player will automatically (and erroneously) attempt to open the whale.mp3 file.

Moving Files and Directories

Returning to the shell-lesson-data/exercise-data/writing directory,

$ cd ~/Desktop/shell-lesson-data/exercise-data/writing

In our thesis directory we have a file draft.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/draft.txt thesis/quotes.txt

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

$ ls thesis
quotes.txt

One must 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. By default, mv will not ask for confirmation before overwriting files. However, an additional option, mv -i (or mv --interactive), will cause mv to request such confirmation.

Note that mv also works on directories.

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

Alternatively, we can confirm the file quotes.txt is no longer present in the thesis directory by explicitly trying to list it:

$ ls thesis/quotes.txt
ls: cannot access 'thesis/quotes.txt': No such file or directory

ls with a filename or directory as an argument only lists the requested file or directory. If the file given as the argument doesn’t exist, the shell returns an error as we saw above. We can use this to see that quotes.txt is now present in our current directory:

$ ls quotes.txt
quotes.txt
Challenge: Moving files to a new folder

After running the following commands, Jamie realizes that she put the files sucrose.dat and maltose.dat into the wrong folder. The files should have been placed in the raw folder.

$ ls -F
 analyzed/ raw/
$ ls -F analyzed
fructose.dat glucose.dat maltose.dat sucrose.dat
$ cd analyzed

Fill in the blanks to move these files to the raw/ folder (i.e. the one she forgot to put them in)

$ mv sucrose.dat maltose.dat ____/____
$ mv sucrose.dat maltose.dat ../raw

Recall that .. refers to the parent directory (i.e. one above the current directory) and that . refers to the current directory.

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 quotes.txt thesis/quotations.txt
$ ls quotes.txt thesis/quotations.txt
quotes.txt   thesis/quotations.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:
quotations.txt

thesis_backup:
quotations.txt

It is important to include the -r flag. If you want to copy a directory and you omit this option you will see a message that the directory has been omitted because -r not specified.

$ cp thesis thesis_backup
cp: -r not specified; omitting directory 'thesis'
Challenge: 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 of the following commands 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.
Challenge: Moving and copying

What is the output of the closing ls command in the sequence shown below?

$ pwd
/Users/jamie/data
$ ls
proteins.dat
$ mkdir recombined
$ mv proteins.dat recombined/
$ cp recombined/proteins.dat ../proteins-saved.dat
$ ls
  1. proteins-saved.dat recombined
  2. recombined
  3. proteins.dat recombined
  4. proteins-saved.dat

We start in the /Users/jamie/data directory, and create a new folder called recombined. The second line moves (mv) the file proteins.dat to the new folder (recombined). 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 /Users/jamie. 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 /Users/jamie/data) is the recombined folder.

  1. No, see explanation above. proteins-saved.dat is located at /Users/jamie
  2. Yes
  3. No, see explanation above. proteins.dat is located at /Users/jamie/data/recombined
  4. No, see explanation above. proteins-saved.dat is located at /Users/jamie

Removing files and directories

Returning to the shell-lesson-data/exercise-data/writing directory, let’s tidy up this directory by removing the quotes.txt file we created. The Unix command we’ll use for this is rm (short for ‘remove’):

$ rm quotes.txt

We can confirm the file has gone using ls:

$ ls quotes.txt
ls: cannot access 'quotes.txt': No such file or directory
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’s no guarantee they’ll work in any particular situation, since the computer may recycle the file’s disk space right away.

Challenge: Using rm Safely

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

rm: remove regular file 'thesis_backup/quotations.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).

Operations with Multiple Filenames

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. Wildcards are special characters that can be used to represent unknown characters or sets of characters when navigating the Unix file system.

Challenge: Copy with Multiple Filenames

For this exercise, you can test the commands in the shell-lesson-data/exercise-data directory.

In the example below, what does cp do when given several filenames and a directory name?

$ mkdir backup
$ cp creatures/minotaur.dat creatures/unicorn.dat backup/

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

$ cd creatures
$ ls -F
basilisk.dat  minotaur.dat  unicorn.dat
$ cp minotaur.dat unicorn.dat basilisk.dat

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 'basilisk.dat' is not a directory

Using Wildcards for Accessing Multiple Files at Once

* is a wildcard, which represents zero or more other characters. Let’s consider the shell-lesson-data/exercise-data/alkanes directory: *.pdb represents ethane.pdb, propane.pdb, and every file that ends with ‘.pdb’. On the other hand, p*.pdb only represents pentane.pdb and propane.pdb, because the ‘p’ at the front can only represent filenames that begin with the letter ‘p’.

? is also a wildcard, but it represents exactly one character. So ?ethane.pdb could represent methane.pdb whereas *ethane.pdb represents both ethane.pdb and methane.pdb.

Wildcards can be used in combination with each other. For example, ???ane.pdb indicates 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 preceding command. 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 alkanes 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 expands the wildcards.

Challenge: List filenames matching a pattern

When run in the alkanes 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 solution 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..

Challenge: More on wildcards

Sam has a directory containing calibration data, datasets, and descriptions of the datasets:

.
├── 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
│   └── datasets
└── send_to_bob
    ├── all_datasets_created_on_a_23rd
    └── all_november_files

Before heading off to another field trip, she wants to back up her data and send some datasets to her colleague Bob. Sam uses the following commands to get the job done:

$ cp *dataset* backup/datasets
$ cp ____calibration____ backup/calibration
$ cp 2015-____-____ send_to_bob/all_november_files/
$ cp ____ send_to_bob/all_datasets_created_on_a_23rd/

Help Sam by filling in the blanks.

The resulting directory structure should look like this

.
├── 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
$ cp *calibration.txt backup/calibration
$ cp 2015-11-* send_to_bob/all_november_files/
$ cp *-23-dataset* send_to_bob/all_datasets_created_on_a_23rd/
Challenge: Organizing directories and files

Jamie is working on a project, and she sees that her files aren’t very well organized:

$ ls -F
analyzed/  fructose.dat    raw/   sucrose.dat

The fructose.dat and sucrose.dat files contain output from her data analysis. What command(s) covered in this lesson does she need to run so that the commands below will produce the output shown?

$ ls -F
analyzed/   raw/
$ ls analyzed
fructose.dat    sucrose.dat
mv *.dat analyzed

Jamie needs to move her files fructose.dat and sucrose.dat to the analyzed directory. The shell will expand *.dat to match all .dat files in the current directory. The mv command then moves the list of .dat files to the ‘analyzed’ directory.

Challenge: 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 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?

$ mkdir 2016-05-20
$ mkdir 2016-05-20/data
$ mkdir 2016-05-20/data/processed
$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20
$ cd 2016-05-20
$ mkdir data
$ cd data
$ mkdir raw processed
$ mkdir 2016-05-20/data/raw
$ mkdir 2016-05-20/data/processed
$ mkdir -p 2016-05-20/data/raw
$ mkdir -p 2016-05-20/data/processed
$ 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 the default behavior of mkdir won’t create a subdirectory of a non-existent directory: the intermediate level folders must be created first.

The fourth set of commands achieve this objective. Remember, the -p option, followed by a path of one or more directories, will cause mkdir to create any intermediate subdirectories as required.

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

Key Points
  • 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.
  • Use of the Control key may be described in many ways, including Ctrl-X, Control-X, and ^X.
  • 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.
  • Depending on the type of work you do, you may need a more powerful text editor than Nano.

Pipes and Filters

Questions

Objectives
  • How can I combine existing commands to produce a desired output?
  • How can I show only part of the output?
  • Explain the advantage of linking commands with pipes and filters.
  • Combine sequences of commands to get new output
  • Redirect a command’s output to a file.
  • Explain what usually happens if a program or pipeline isn’t given any input to process.

Now that we know a few basic commands, we can finally look at the shell’s most powerful feature: the ease with which it lets us combine existing programs in new ways. We’ll start with the directory shell-lesson-data/exercise-data/alkanes that contains six files describing some simple organic molecules. The .pdb extension indicates that these files are in Protein Data Bank format, a simple text format that specifies the type and position of each atom in the molecule.

$ ls
cubane.pdb    methane.pdb    pentane.pdb
ethane.pdb    octane.pdb     propane.pdb

Let’s run an example command:

$ wc cubane.pdb
20  156 1158 cubane.pdb

wc is the ‘word count’ command: it counts the number of lines, words, and characters in files (returning the values in that order from left to right).

If we run the command wc *.pdb, the * in *.pdb matches zero or more characters, so the shell turns *.pdb into a list of all .pdb files in the current directory:

$ wc *.pdb
  20  156  1158  cubane.pdb
  12  84   622   ethane.pdb
   9  57   422   methane.pdb
  30  246  1828  octane.pdb
  21  165  1226  pentane.pdb
  15  111  825   propane.pdb
 107  819  6081  total

Note that wc *.pdb also shows the total number of all lines in the last line of the output.

If we run wc -l instead of just wc, the output shows only the number of lines per file:

$ wc -l *.pdb
  20  cubane.pdb
  12  ethane.pdb
   9  methane.pdb
  30  octane.pdb
  21  pentane.pdb
  15  propane.pdb
 107  total

The -m and -w options can also be used with the wc command to show only the number of characters or the number of words, respectively.

Why isn’t it doing anything?

What happens if a command is supposed to process a file, but we don’t give it a filename? For example, what if we type:

$ wc -l

but don’t type *.pdb (or anything else) after the command? Since it doesn’t have any filenames, wc assumes it is supposed to process input given at the command prompt, so it just sits there and waits for us to give it some data interactively. From the outside, though, all we see is it sitting there, and the command doesn’t appear to do anything.

If you make this kind of mistake, you can escape out of this state by holding down the control key (Ctrl) and pressing the letter C once: . Then release both keys.

Capturing output from commands

Output page by page with less

We’ll continue to use cat in this lesson, for convenience and consistency, but it has the disadvantage that it always dumps the whole file onto your screen. More useful in practice is the command less (e.g. less lengths.txt). This displays a screenful of the file, and then stops. You can go forward one screenful by pressing the spacebar, or back one by pressing b. Press q to quit.

Which of these files contains the fewest lines? It’s an easy question to answer when there are only six files, but what if there were 6000? Our first step toward a solution is to run the command:

$ wc -l *.pdb > lengths.txt

The greater than symbol, >, tells the shell to redirect the command’s output to a file instead of printing it to the screen. This command prints no screen output, because everything that wc would have printed has gone into the file lengths.txt instead. If the file doesn’t exist prior to issuing the command, the shell will create the file. If the file exists already, it will be silently overwritten, which may lead to data loss. Thus, redirect commands require caution.

ls lengths.txt confirms that the file exists:

$ ls lengths.txt
lengths.txt

We can now send the content of lengths.txt to the screen using cat lengths.txt. The cat command gets its name from ‘concatenate’ i.e. join together, and it prints the contents of files one after another. There’s only one file in this case, so cat just shows us what it contains:

$ cat lengths.txt
  20  cubane.pdb
  12  ethane.pdb
   9  methane.pdb
  30  octane.pdb
  21  pentane.pdb
  15  propane.pdb
 107  total

Filtering output

Next we’ll use the sort command to sort the contents of the lengths.txt file. But first we’ll do an exercise to learn a little about the sort command:

Challenge: What does sort -n do?

The file shell-lesson-data/exercise-data/numbers.txt contains the following lines:

10
2
19
22
6

If we run sort on this file, the output is:

10
19
2
22
6

If we run sort -n on the same file, we get this instead:

2
6
10
19
22

Explain why -n has this effect.

The -n option specifies a numerical rather than an alphanumerical sort.

We will also use the -n option to specify that the sort is numerical instead of alphanumerical. This does not change the file; instead, it sends the sorted result to the screen:

$ sort -n lengths.txt
  9  methane.pdb
 12  ethane.pdb
 15  propane.pdb
 20  cubane.pdb
 21  pentane.pdb
 30  octane.pdb
107  total

We can put the sorted list of lines in another temporary file called sorted-lengths.txt by putting > sorted-lengths.txt after the command, just as we used > lengths.txt to put the output of wc into lengths.txt. Once we’ve done that, we can run another command called head to get the first few lines in sorted-lengths.txt:

$ sort -n lengths.txt > sorted-lengths.txt
$ head -n 1 sorted-lengths.txt
  9  methane.pdb

Using -n 1 with head tells it that we only want the first line of the file; -n 20 would get the first 20, and so on. Since sorted-lengths.txt contains the lengths of our files ordered from least to greatest, the output of head must be the file with the fewest lines.

Redirecting to the same file

It’s a very bad idea to try redirecting the output of a command that operates on a file to the same file. For example:

$ sort -n lengths.txt > lengths.txt

Doing something like this may give you incorrect results and/or delete the contents of lengths.txt.

Challenge: What Does >> Mean?

We have seen the use of >, but there is a similar operator >> which works slightly differently. We’ll learn about the differences between these two operators by printing some strings. We can use the echo command to print strings e.g.

$ echo The echo command prints text
The echo command prints text

Now test the commands below to reveal the difference between the two operators:

$ echo hello > testfile01.txt

and:

$ echo hello >> testfile02.txt

Hint: Try executing each command twice in a row and then examining the output files.

In the first example with >, the string ‘hello’ is written to testfile01.txt, but the file gets overwritten each time we run the command.

We see from the second example that the >> operator also writes ‘hello’ to a file (in this case testfile02.txt), but appends the string to the file if it already exists (i.e. when we run it for the second time).

Challenge: appending data

We have already met the head command, which prints lines from the start of a file. tail is similar, but prints lines from the end of a file instead.

Consider the file shell-lesson-data/exercise-data/animal-counts/animals.csv. After these commands, select the answer that corresponds to the file animals-subset.csv:

$ head -n 3 animals.csv > animals-subset.csv
$ tail -n 2 animals.csv >> animals-subset.csv
  1. The first three lines of animals.csv
  2. The last two lines of animals.csv
  3. The first three lines and the last two lines of animals.csv
  4. The second and third lines of animals.csv

Option 3 is correct. For option 1 to be correct we would only run the head command. For option 2 to be correct we would only run the tail command. For option 4 to be correct we would have to pipe the output of head into tail -n 2 by doing head -n 3 animals.csv | tail -n 2 > animals-subset.csv

Passing output to another command

In our example of finding the file with the fewest lines, we are using two intermediate files lengths.txt and sorted-lengths.txt to store output. This is a confusing way to work because even once you understand what wc, sort, and head do, those intermediate files make it hard to follow what’s going on. We can make it easier to understand by running sort and head together:

$ sort -n lengths.txt | head -n 1
  9  methane.pdb

The vertical bar, |, between the two commands is called a pipe. It tells the shell that we want to use the output of the command on the left as the input to the command on the right.

This has removed the need for the sorted-lengths.txt file.

Combining multiple commands

Nothing prevents us from chaining pipes consecutively. We can for example send the output of wc directly to sort, and then send the resulting output to head. This removes the need for any intermediate files.

We’ll start by using a pipe to send the output of wc to sort:

$ wc -l *.pdb | sort -n
   9 methane.pdb
  12 ethane.pdb
  15 propane.pdb
  20 cubane.pdb
  21 pentane.pdb
  30 octane.pdb
 107 total

We can then send that output through another pipe, to head, so that the full pipeline becomes:

$ wc -l *.pdb | sort -n | head -n 1
   9  methane.pdb

This is exactly like a mathematician nesting functions like log(3x) and saying ‘the log of three times x’. In our case, the algorithm is ‘head of sort of line count of *.pdb’.

The redirection and pipes used in the last few commands are illustrated below:

Challenge: Piping commands together

In our current directory, we want to find the 3 files which have the least number of lines. Which command listed below would work?

  1. wc -l * > sort -n > head -n 3
  2. wc -l * | sort -n | head -n 1-3
  3. wc -l * | head -n 3 | sort -n
  4. wc -l * | sort -n | head -n 3

Option 4 is the solution. The pipe character | is used to connect the output from one command to the input of another. > is used to redirect standard output to a file. Try it in the shell-lesson-data/exercise-data/alkanes directory!

Tools designed to work together

This idea of linking programs together is why Unix has been so successful. Instead of creating enormous programs that try to do many different things, Unix programmers focus on creating lots of simple tools that each do one job well, and that work well with each other. This programming model is called ‘pipes and filters’. We’ve already seen pipes; a filter is a program like wc or sort that transforms a stream of input into a stream of output. Almost all of the standard Unix tools can work this way. Unless told to do otherwise, they read from standard input, do something with what they’ve read, and write to standard output.

The key is that any program that reads lines of text from standard input and writes lines of text to standard output can be combined with every other program that behaves this way as well. You can and should write your programs this way so that you and other people can put those programs into pipes to multiply their power.

Challenge: Pipe Reading Comprehension

A file called animals.csv (in the shell-lesson-data/exercise-data/animal-counts folder) contains the following data:

2012-11-05,deer,5
2012-11-05,rabbit,22
2012-11-05,raccoon,7
2012-11-06,rabbit,19
2012-11-06,deer,2
2012-11-06,fox,4
2012-11-07,rabbit,16
2012-11-07,bear,1

What text passes through each of the pipes and the final redirect in the pipeline below? Note, the sort -r command sorts in reverse order.

$ cat animals.csv | head -n 5 | tail -n 3 | sort -r > final.txt

Hint: build the pipeline up one command at a time to test your understanding

The head command extracts the first 5 lines from animals.csv. Then, the last 3 lines are extracted from the previous 5 by using the tail command. With the sort -r command those 3 lines are sorted in reverse order. Finally, the output is redirected to a file: final.txt. The content of this file can be checked by executing cat final.txt. The file should contain the following lines:

2012-11-06,rabbit,19
2012-11-06,deer,2
2012-11-05,raccoon,7
Challenge: Pipe Construction

For the file animals.csv from the previous exercise, consider the following command:

$ cut -d , -f 2 animals.csv

The cut command is used to remove or ‘cut out’ certain sections of each line in the file, and cut expects the lines to be separated into columns by a Tab character. A character used in this way is called a delimiter. In the example above we use the -d option to specify the comma as our delimiter character. We have also used the -f option to specify that we want to extract the second field (column). This gives the following output:

deer
rabbit
raccoon
rabbit
deer
fox
rabbit
bear

The uniq command filters out adjacent matching lines in a file. How could you extend this pipeline (using uniq and another command) to find out what animals the file contains (without any duplicates in their names)?

$ cut -d , -f 2 animals.csv | sort | uniq
Challenge: Which Pipe?

The file animals.csv contains 8 lines of data formatted as follows:

2012-11-05,deer,5
2012-11-05,rabbit,22
2012-11-05,raccoon,7
2012-11-06,rabbit,19
...

The uniq command has a -c option which gives a count of the number of times a line occurs in its input. Assuming your current directory is shell-lesson-data/exercise-data/animal-counts, what command would you use to produce a table that shows the total count of each type of animal in the file?

  1. sort animals.csv | uniq -c
  2. sort -t, -k2,2 animals.csv | uniq -c
  3. cut -d, -f 2 animals.csv | uniq -c
  4. cut -d, -f 2 animals.csv | sort | uniq -c
  5. cut -d, -f 2 animals.csv | sort | uniq -c | wc -l

Option 4. is the correct answer. If you have difficulty understanding why, try running the commands, or sub-sections of the pipelines (make sure you are in the shell-lesson-data/exercise-data/animal-counts directory).

Your Pipeline: Checking Files

You have run your samples through the assay machines and created 17 files in the north-pacific-gyre directory described earlier. As a quick check, starting from the shell-lesson-data directory, you type:

$ cd north-pacific-gyre
$ wc -l *.txt

The output is 18 lines that look like this:

300 NENE01729A.txt
300 NENE01729B.txt
300 NENE01736A.txt
300 NENE01751A.txt
300 NENE01751B.txt
300 NENE01812A.txt
... ...

Now you type this:

$ wc -l *.txt | sort -n | head -n 5
 240 NENE02018B.txt
 300 NENE01729A.txt
 300 NENE01729B.txt
 300 NENE01736A.txt
 300 NENE01751A.txt

Whoops: one of the files is 60 lines shorter than the others. When you go back and check it, you see that you did that assay at 8:00 on a Monday morning — someone was probably in using the machine on the weekend, and you forgot to reset it. Before re-running that sample, you check to see if any files have too much data:

$ wc -l *.txt | sort -n | tail -n 5
 300 NENE02040B.txt
 300 NENE02040Z.txt
 300 NENE02043A.txt
 300 NENE02043B.txt
5040 total

Those numbers look good — but what’s that ‘Z’ doing there in the third-to-last line? All of your samples should be marked ‘A’ or ‘B’; by convention, your lab uses ‘Z’ to indicate samples with missing information. To find others like it, you do this:

$ ls *Z.txt
NENE01971Z.txt    NENE02040Z.txt

Sure enough, when you check the log on your laptop, there’s no depth recorded for either of those samples. Since it’s too late to get the information any other way, you must exclude those two files from your analysis. You could delete them using rm, but there are actually some analyses you might do later where depth doesn’t matter, so instead, you’ll have to be careful later on to select files using the wildcard expressions NENE*A.txt NENE*B.txt.

Key Points
  • wc counts lines, words, and characters in its inputs.
  • cat displays the contents of its inputs.
  • sort sorts its inputs.
  • head displays the first 10 lines of its input by default without additional arguments.
  • tail displays the last 10 lines of its input by default without additional arguments.
  • command > [file] redirects a command’s output to a file (overwriting any existing content).
  • command >> [file] appends a command’s output to a file.
  • [first] | [second] is a pipeline: the output of the first command is used as the input to the second.
  • The best way to use the shell is to use pipes to combine simple single-purpose programs (filters).’ll have to be careful later on to select files using the wildcard expressions NENE*A.txt NENE*B.txt.

Repeating commands using loops

Loops are a programming construct which allow us to repeat a command or set of commands for each item in a list. As such they are key to productivity improvements through automation. Similar to wildcards and tab completion, using loops also reduces the amount of typing required (and hence reduces the number of typing mistakes).

Suppose we have several hundred genome data files named basilisk.dat, minotaur.dat, and unicorn.dat. For this example, we’ll use the exercise-data/creatures directory which only has three example files, but the principles can be applied to many many more files at once.

The structure of these files is the same: the common name, classification, and updated date are presented on the first three lines, with DNA sequences on the following lines. Let’s look at the files:

$ head -n 5 basilisk.dat minotaur.dat unicorn.dat

We would like to print out the classification for each species, which is given on the second line of each file. For each file, we would need to execute the command head -n 2 and pipe this to tail -n 1. We’ll use a loop to solve this problem, but first let’s look at the general form of a loop, using the pseudo-code below:

# The word "for" indicates the start of a "For-loop" command
for thing in list_of_things 
#The word "do" indicates the start of job execution list
do 
    # Indentation within the loop is not required, but aids legibility
    operation_using/command $thing 
# The word "done" indicates the end of a loop
done

and we can apply this to our example like this:

$ for filename in basilisk.dat minotaur.dat unicorn.dat
> do
>     echo $filename
>     head -n 2 $filename | tail -n 1
> done
basilisk.dat
CLASSIFICATION: basiliscus vulgaris
minotaur.dat
CLASSIFICATION: bos hominus
unicorn.dat
CLASSIFICATION: equus monoceros
Follow the prompt

The shell prompt changes from $ to > and back again as we were typing in our loop. The second prompt, >, is different to remind us that we haven’t finished typing a complete command yet. A semicolon, ;, can be used to separate two commands written on a single line.

When the shell sees the keyword for, it knows to repeat a command (or group of commands) once for each item in a list. Each time the loop runs (called an iteration), an item in the list is assigned in sequence to the variable, and the commands inside the loop are executed, before moving on to the next item in the list. Inside the loop, we call for the variable’s value by putting $ in front of it. The $ tells the shell interpreter to treat the variable as a variable name and substitute its value in its place, rather than treat it as text or an external command.

In this example, the list is three filenames: basilisk.dat, minotaur.dat, and unicorn.dat. Each time the loop iterates, we first use echo to print the value that the variable $filename currently holds. This is not necessary for the result, but beneficial for us here to have an easier time to follow along. Next, we will run the head command on the file currently referred to by $filename. The first time through the loop, $filename is basilisk.dat. The interpreter runs the command head on basilisk.dat and pipes the first two lines to the tail command, which then prints the second line of basilisk.dat. For the second iteration, $filename becomes minotaur.dat. This time, the shell runs head on minotaur.dat and pipes the first two lines to the tail command, which then prints the second line of minotaur.dat. For the third iteration, $filename becomes unicorn.dat, so the shell runs the head command on that file, and tail on the output of that. Since the list was only three items, the shell exits the for loop.

Same symbols, different meanings

Here we see > being used as a shell prompt, whereas > is also used to redirect output. Similarly, $ is used as a shell prompt, but, as we saw earlier, it is also used to ask the shell to get the value of a variable.

If the shell prints > or $ then it expects you to type something, and the symbol is a prompt.

If you type > or $ yourself, it is an instruction from you that the shell should redirect output or get the value of a variable.

When using variables it is also possible to put the names into curly braces to clearly delimit the variable name: $filename is equivalent to ${filename}, but is different from ${file}name. You may find this notation in other people’s programs.

We have called the variable in this loop filename in order to make its purpose clearer to human readers. The shell itself doesn’t care what the variable is called; if we wrote this loop as:

$ for x in basilisk.dat minotaur.dat unicorn.dat
> do
>     head -n 2 $x | tail -n 1
> done

or:

$ for temperature in basilisk.dat minotaur.dat unicorn.dat
> do
>     head -n 2 $temperature | tail -n 1
> done

it would work exactly the same way. Don’t do this. Programs are only useful if people can understand them, so meaningless names (like x) or misleading names (like temperature) increase the odds that the program won’t do what its readers think it does.

In the above examples, the variables (thing, filename, x and temperature) could have been given any other name, as long as it is meaningful to both the person writing the code and the person reading it.

Note also that loops can be used for other things than filenames, like a list of numbers or a subset of data.

Challenge: Write your own loop

How would you write a loop that echoes all 10 numbers from 0 to 9?

$ for loop_variable in 0 1 2 3 4 5 6 7 8 9
> do
>     echo $loop_variable
> done

output:

0
1
2
3
4
5
6
7
8
9
Challenge: Variables in loops

This exercise refers to the shell-lesson-data/exercise-data/alkanes directory. ls *.pdb gives the following output:

cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb

What is the output of the following code?

$ for datafile in *.pdb
> do
>     ls *.pdb
> done

Now, what is the output of the following code?

$ for datafile in *.pdb
> do
>     ls $datafile
> done

Why do these two loops give different outputs?

The first code block gives the same output on each iteration through the loop. Bash expands the wildcard *.pdb within the loop body (as well as before the loop starts) to match all files ending in .pdb and then lists them using ls. The expanded loop would look like this:

$ for datafile in cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
> do
>     ls cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
> done
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb
cubane.pdb  ethane.pdb  methane.pdb  octane.pdb  pentane.pdb  propane.pdb

The second code block lists a different file on each loop iteration. The value of the datafile variable is evaluated using $datafile, and then listed using ls.

cubane.pdb
ethane.pdb
methane.pdb
octane.pdb
pentane.pdb
propane.pdb
Challenge: Limiting sets of files

What would be the output of running the following loop in the shell-lesson-data/exercise-data/alkanes directory?

$ for filename in c*
> do
>     ls $filename
> done

  1. No files are listed.

  2. All files are listed.

  3. Only cubane.pdb, octane.pdb and pentane.pdb are listed.

  4. Only cubane.pdb is listed.

4 is the correct answer. * matches zero or more characters, so any file name starting with the letter c, followed by zero or more other characters will be matched.

Challenge: Limiting sets of files (continued)

How would the output differ from using this command instead?

$ for filename in *c*
> do
>     ls $filename
> done

  1. The same files would be listed.

  2. All the files are listed this time.

  3. No files are listed this time.

  4. The files cubane.pdb and octane.pdb will be listed.

  5. Only the file octane.pdb will be listed.

4 is the correct answer. * matches zero or more characters, so a file name with zero or more characters before a letter c and zero or more characters after the letter c will be matched.

Challenge: Saving to a file in a loop - part one

In the shell-lesson-data/exercise-data/alkanes directory, what is the effect of this loop?

for alkanes in *.pdb
do
    echo $alkanes
    cat $alkanes > alkanes.pdb
done

  1. Prints cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and propane.pdb, and the text from propane.pdb will be saved to a file called alkanes.pdb.

  2. Prints cubane.pdb, ethane.pdb, and methane.pdb, and the text from all three files would be concatenated and saved to a file called alkanes.pdb.

  3. Prints cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, and pentane.pdb, and the text from propane.pdb will be saved to a file called alkanes.pdb.

  4. None of the above.

    1. The text from each file in turn gets written to the alkanes.pdb file. However, the file gets overwritten on each loop iteration, so the final content of alkanes.pdb is the text from the propane.pdb file.
Challenge: Saving to a file in a loop - part two

Also in the shell-lesson-data/exercise-data/alkanes directory, what would be the output of the following loop?

for datafile in *.pdb
do
    cat $datafile >> all.pdb
done

  1. All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, and pentane.pdb would be concatenated and saved to a file called all.pdb.

  2. The text from ethane.pdb will be saved to a file called all.pdb.

  3. All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and propane.pdb would be concatenated and saved to a file called all.pdb.

  4. All of the text from cubane.pdb, ethane.pdb, methane.pdb, octane.pdb, pentane.pdb and propane.pdb would be printed to the screen and saved to a file called all.pdb.

3 is the correct answer. >> appends to a file, rather than overwriting it with the redirected output from a command. Given the output from the cat command has been redirected, nothing is printed to the screen.

Let’s continue with our example in the shell-lesson-data/exercise-data/creatures directory. Here’s a slightly more complicated loop:

$ for filename in *.dat
> do
>     echo $filename
>     head -n 100 $filename | tail -n 20
> done

The shell starts by expanding *.dat to create the list of files it will process. The loop body then executes two commands for each of those files. The first command, echo, prints its command-line arguments to standard output. For example:

$ echo hello there

prints:

hello there

In this case, since the shell expands $filename to be the name of a file, echo $filename prints the name of the file. Note that we can’t write this as:

$ for filename in *.dat
> do
>     $filename
>     head -n 100 $filename | tail -n 20
> done

because then the first time through the loop, when $filename expanded to basilisk.dat, the shell would try to run basilisk.dat as a program. Finally, the head and tail combination selects lines 81-100 from whatever file is being processed (assuming the file has at least 100 lines).

Spaces in names

Spaces are used to separate the elements of the list that we are going to loop over. If one of those elements contains a space character, we need to surround it with quotes, and do the same thing to our loop variable. Suppose our data files are named:

red dragon.dat
purple unicorn.dat

To loop over these files, we would need to add double quotes like so:

$ for filename in "red dragon.dat" "purple unicorn.dat"
> do
>     head -n 100 "$filename" | tail -n 20
> done

It is simpler to avoid using spaces (or other special characters) in filenames.

The files above don’t exist, so if we run the above code, the head command will be unable to find them; however, the error message returned will show the name of the files it is expecting:

head: cannot open ‘red dragon.dat' for reading: No such file or directory
head: cannot open ‘purple unicorn.dat' for reading: No such file or directory

Try removing the quotes around $filename in the loop above to see the effect of the quote marks on spaces. Note that we get a result from the loop command for unicorn.dat when we run this code in the creatures directory:

head: cannot open ‘red' for reading: No such file or directory
head: cannot open ‘dragon.dat' for reading: No such file or directory
head: cannot open ‘purple' for reading: No such file or directory
CGGTACCGAA
AAGGGTCGCG
CAAGTGTTCC
...

We would like to modify each of the files in shell-lesson-data/exercise-data/creatures, but also save a version of the original files. We want to copy the original files to new files named original-basilisk.dat and original-unicorn.dat, for example. We can’t use:

$ cp *.dat original-*.dat

because that would expand to:

$ cp basilisk.dat minotaur.dat unicorn.dat original-*.dat

This wouldn’t back up our files, instead we get an error:

cp: target `original-*.dat' is not a directory

This problem arises when cp receives more than two inputs. When this happens, it expects the last input to be a directory where it can copy all the files it was passed. Since there is no directory named original-*.dat in the creatures directory, we get an error.

Instead, we can use a loop:

$ for filename in *.dat
> do
>     cp $filename original-$filename
> done

This loop runs the cp command once for each filename. The first time, when $filename expands to basilisk.dat, the shell executes:

cp basilisk.dat original-basilisk.dat

The second time, the command is:

cp minotaur.dat original-minotaur.dat

The third and last time, the command is:

cp unicorn.dat original-unicorn.dat

Since the cp command does not normally produce any output, it’s hard to check that the loop is working correctly. However, we learned earlier how to print strings using echo, and we can modify the loop to use echo to print our commands without actually executing them. As such we can check what commands would be run in the unmodified loop.

The following diagram shows what happens when the modified loop is executed and demonstrates how the judicious use of echo is a good debugging technique.

Your pipeline: Processing files

You are now ready to process your data files using goostats.sh — a shell script written by your supervisor. This calculates some statistics from a protein sample file and takes two arguments:

  1. an input file (containing the raw data)

  2. an output file (to store the calculated statistics)

Since you are still learning how to use the shell, you decides to build up the required commands in stages. Your first step is to make sure that you can select the right input files — remember, these are ones whose names end in ‘A’ or ‘B’, rather than ‘Z’. Moving to the north-pacific-gyre directory, you type:

$ cd
$ cd Desktop/shell-lesson-data/north-pacific-gyre
$ for datafile in NENE*A.txt NENE*B.txt
> do
>     echo $datafile
> done
NENE01729A.txt
NENE01736A.txt
NENE01751A.txt

...
NENE02040B.txt
NENE02043B.txt

Your next step is to decide what to call the files that the goostats.sh analysis program will create. Prefixing each input file’s name with ‘stats’ seems simple, so you modify your loop to do that:

$ for datafile in NENE*A.txt NENE*B.txt
> do
>     echo $datafile stats-$datafile
> done
NENE01729A.txt stats-NENE01729A.txt
NENE01736A.txt stats-NENE01729A.txt
NENE01751A.txt stats-NENE01729A.txt
...
NENE02040B.txt stats-NENE02040B.txt
NENE02043B.txt stats-NENE02043B.txt

You haven’t actually run goostats.sh yet, but now you’re sure you can select the right files and generate the right output filenames.

Typing in commands over and over again is becoming tedious, though, and you are worried about making mistakes, so instead of re-entering your loop, you press ↑. In response, the shell re-displays the whole loop on one line (using semi-colons to separate the pieces):

$ for datafile in NENE*A.txt NENE*B.txt; do echo $datafile stats-$datafile; done

Using the ←, you navigate to the echo command and change it to bash goostats.sh:

$ for datafile in NENE*A.txt NENE*B.txt; do bash goostats.sh $datafile stats-$datafile; done

When you press Enter, the shell runs the modified command. However, nothing appears to happen — there is no output. After a moment, you realize that since your script doesn’t print anything to the screen any longer, you has no idea whether it is running, much less how quickly. You kill the running command by typing Ctrl+C, uses ↑ to repeat the command, and edit it to read:

$ for datafile in NENE*A.txt NENE*B.txt; do echo $datafile;
bash goostats.sh $datafile stats-$datafile; done
Beginning and end

We can move to the beginning of a line in the shell by typing Ctrl+A and to the end using Ctrl+E.

When you run your program now, it produces one line of output every five seconds or so:

NENE01729A.txt
NENE01736A.txt
NENE01751A.txt
...

1518 times 5 seconds, divided by 60, tells her that her script will take about two hours to run. As a final check, you open another terminal window, go into north-pacific-gyre, and uses cat stats-NENE01729B.txt to examine one of the output files. It looks good, so you decides to get some coffee and catch up on your reading.

Those who know history can choose to repeat it

Another way to repeat previous work is to use the history command to get a list of the last few hundred commands that have been executed, and then to use !123 (where ‘123’ is replaced by the command number) to repeat one of those commands. For example, if you types this:

$ history | tail -n 5
456  for datafile in NENE*A.txt NENE*B.txt; do   echo $datafile stats-$datafile; done
457  for datafile in NENE*A.txt NENE*B.txt; do echo $datafile stats-$datafile; done
458  for datafile in NENE*A.txt NENE*B.txt; do bash goostats.sh $datafile stats-$datafile; done
459  for datafile in NENE*A.txt NENE*B.txt; do echo $datafile; bash goostats.sh $datafile
stats-$datafile; done
460  history | tail -n 5

then you can re-run goostats.sh on the files simply by typing !459.

More history commands

There are a number of other shortcut commands for getting at the history.

  • Ctrl+R enters a history search mode ‘reverse-i-search’ and finds the most recent command in your history that matches the text you enter next. Press Ctrl+R one or more additional times to search for earlier matches. You can then use the left and right arrow keys to choose that line and edit it then hit Return to run the command.

  • !! retrieves the immediately preceding command (you may or may not find this more convenient than using ↑)

  • !$ retrieves the last word of the last command. That’s useful more often than you might expect: after bash goostats.sh NENE01729B.txt stats-NENE01729B.txt, you can type less !$ to look at the file stats-NENE01729B.txt, which is quicker than doing ↑ and editing the command-line.

Key Points

  • A for loop repeats commands once for every thing in a list.

  • Every for loop needs a variable to refer to the thing it is currently operating on.

  • Use $name to expand a variable (i.e., get its value). ${name} can also be used.

  • Do not use spaces, quotes, or wildcard characters such as ‘*’ or ‘?’ in filenames, as it complicates variable expansion.

  • Give files consistent names that are easy to match with wildcard patterns to make it easy to select them for looping.

  • Use the up-arrow key to scroll up through previous commands to edit and repeat them.

  • Use Ctrl+R to search through the previously entered commands.

  • Use history to display recent commands, and ![number] to repeat a command by number.

Shell Scripts

We are finally ready to see what makes the shell such a powerful programming environment. We are going to take the commands we repeat frequently and save them in files so that we can re-run all those operations again later by typing a single command. For historical reasons, a bunch of commands saved in a file is usually called a shell script, but make no mistake — these are actually small programs.

Not only will writing shell scripts make your work faster, but also you won’t have to retype the same commands over and over again. It will also make it more accurate (fewer chances for typos) and more reproducible. If you come back to your work later (or if someone else finds your work and wants to build on it), you will be able to reproduce the same results simply by running your script, rather than having to remember or retype a long list of commands.

Let’s start by going back to alkanes/ and creating a new file, middle.sh which will become our shell script:

$ cd alkanes
$ nano middle.sh

The command nano middle.sh opens the file middle.sh within the text editor ‘nano’ (which runs within the shell). If the file does not exist, it will be created. We can use the text editor to directly edit the file by inserting the following line:

head -n 15 octane.pdb | tail -n 5

This is a variation on the pipe we constructed earlier, which selects lines 11-15 of the file octane.pdb. Remember, we are not running it as a command just yet; we are only incorporating the commands in a file.

Then we save the file (Ctrl-O in nano) and exit the text editor (Ctrl-X in nano). Check that the directory alkanes now contains a file called middle.sh.

Once we have saved the file, we can ask the shell to execute the commands it contains. Our shell is called bash, so we run the following command:

$ bash middle.sh
ATOM      9  H           1      -4.502   0.681   0.785  1.00  0.00
ATOM     10  H           1      -5.254  -0.243  -0.537  1.00  0.00
ATOM     11  H           1      -4.357   1.252  -0.895  1.00  0.00
ATOM     12  H           1      -3.009  -0.741  -1.467  1.00  0.00
ATOM     13  H           1      -3.172  -1.337   0.206  1.00  0.00

Sure enough, our script’s output is exactly what we would get if we ran that pipeline directly.

What if we want to select lines from an arbitrary file? We could edit middle.sh each time to change the filename, but that would probably take longer than typing the command out again in the shell and executing it with a new file name. Instead, let’s edit middle.sh and make it more versatile:

$ nano middle.sh

Now, within “nano”, replace the text octane.pdb with the special variable called $1:

head -n 15 "$1" | tail -n 5

Inside a shell script, $1 means ‘the first filename (or other argument) on the command line’. We can now run our script like this:

$ bash middle.sh octane.pdb
ATOM      9  H           1      -4.502   0.681   0.785  1.00  0.00
ATOM     10  H           1      -5.254  -0.243  -0.537  1.00  0.00
ATOM     11  H           1      -4.357   1.252  -0.895  1.00  0.00
ATOM     12  H           1      -3.009  -0.741  -1.467  1.00  0.00
ATOM     13  H           1      -3.172  -1.337   0.206  1.00  0.00

or on a different file like this:

$ bash middle.sh pentane.pdb
ATOM      9  H           1       1.324   0.350  -1.332  1.00  0.00
ATOM     10  H           1       1.271   1.378   0.122  1.00  0.00
ATOM     11  H           1      -0.074  -0.384   1.288  1.00  0.00
ATOM     12  H           1      -0.048  -1.362  -0.205  1.00  0.00
ATOM     13  H           1      -1.183   0.500  -1.412  1.00  0.00
Double-quotes around arguments

For the same reason that we put the loop variable inside double-quotes, in case the filename happens to contain any spaces, we surround $1 with double-quotes.

Currently, we need to edit middle.sh each time we want to adjust the range of lines that is returned. Let’s fix that by configuring our script to instead use three command-line arguments. After the first command-line argument ($1), each additional argument that we provide will be accessible via the special variables $1, $2, $3, which refer to the first, second, third command-line arguments, respectively.

Knowing this, we can use additional arguments to define the range of lines to be passed to head and tail respectively:

$ nano middle.sh
head -n "$2" "$1" | tail -n "$3"

We can now run:

$ bash middle.sh pentane.pdb 15 5
ATOM      9  H           1       1.324   0.350  -1.332  1.00  0.00
ATOM     10  H           1       1.271   1.378   0.122  1.00  0.00
ATOM     11  H           1      -0.074  -0.384   1.288  1.00  0.00
ATOM     12  H           1      -0.048  -1.362  -0.205  1.00  0.00
ATOM     13  H           1      -1.183   0.500  -1.412  1.00  0.00

By changing the arguments to our command, we can change our script’s behaviour:

$ bash middle.sh pentane.pdb 20 5
ATOM     14  H           1      -1.259   1.420   0.112  1.00  0.00
ATOM     15  H           1      -2.608  -0.407   1.130  1.00  0.00
ATOM     16  H           1      -2.540  -1.303  -0.404  1.00  0.00
ATOM     17  H           1      -3.393   0.254  -0.321  1.00  0.00
TER      18              1

This works, but it may take the next person who reads middle.sh a moment to figure out what it does. We can improve our script by adding some comments at the top:

$ nano middle.sh
# Select lines from the middle of a file.
# Usage: bash middle.sh filename end_line num_lines
head -n "$2" "$1" | tail -n "$3"

A comment starts with a # character and runs to the end of the line. The computer ignores comments, but they’re invaluable for helping people (including your future self) understand and use scripts. The only caveat is that each time you modify the script, you should check that the comment is still accurate. An explanation that sends the reader in the wrong direction is worse than none at all.

What if we want to process many files in a single pipeline? For example, if we want to sort our .pdb files by length, we would type:

$ wc -l *.pdb | sort -n

because wc -l lists the number of lines in the files (recall that wc stands for ‘word count’, adding the -l option means ‘count lines’ instead) and sort -n sorts things numerically. We could put this in a file, but then it would only ever sort a list of .pdb files in the current directory. If we want to be able to get a sorted list of other kinds of files, we need a way to get all those names into the script. We can’t use $1, $2, and so on because we don’t know how many files there are. Instead, we use the special variable $@, which means, ‘All of the command-line arguments to the shell script’. We also should put $@ inside double-quotes to handle the case of arguments containing spaces ("$@" is special syntax and is equivalent to "$1" "$2" …).

Here’s an example:

$ nano sorted.sh
# Sort files by their length.
# Usage: bash sorted.sh one_or_more_filenames
wc -l "$@" | sort -n
$ bash sorted.sh *.pdb ../creatures/*.dat
9 methane.pdb
12 ethane.pdb
15 propane.pdb
20 cubane.pdb
21 pentane.pdb
30 octane.pdb
163 ../creatures/basilisk.dat
163 ../creatures/minotaur.dat
163 ../creatures/unicorn.dat
596 total
Challenge: List unique species

Leah has several hundred data files, each of which is formatted like this:

2013-11-05,deer,5
2013-11-05,rabbit,22
2013-11-05,raccoon,7
2013-11-06,rabbit,19
2013-11-06,deer,2
2013-11-06,fox,1
2013-11-07,rabbit,18
2013-11-07,bear,1

An example of this type of file is given in shell-lesson-data/exercise-data/animal-counts/animals.csv.

We can use the command cut -d , -f 2 animals.csv | sort | uniq to produce the unique species in animals.csv. In order to avoid having to type out this series of commands every time, a scientist may choose to write a shell script instead.

Write a shell script called species.sh that takes any number of filenames as command-line arguments and uses a variation of the above command to print a list of the unique species appearing in each of those files separately.

# Script to find unique species in csv files where species is the second data field
# This script accepts any number of file names as command line arguments

# Loop over all files
for file in $@
do
    echo "Unique species in $file:"
    # Extract species names
    cut -d , -f 2 $file | sort | uniq
done

Suppose we have just run a series of commands that did something useful — for example, creating a graph we’d like to use in a paper. We’d like to be able to re-create the graph later if we need to, so we want to save the commands in a file. Instead of typing them in again (and potentially getting them wrong) we can do this:

$ history | tail -n 5 > redo-figure-3.sh

The file redo-figure-3.sh now contains:

297 bash goostats.sh NENE01729B.txt stats-NENE01729B.txt
298 bash goodiff.sh stats-NENE01729B.txt /data/validated/01729.txt > 01729-differences.txt
299 cut -d ',' -f 2-3 01729-differences.txt > 01729-time-series.txt
300 ygraph --format scatter --color bw --borders none 01729-time-series.txt figure-3.png
301 history | tail -n 5 > redo-figure-3.sh

After a moment’s work in an editor to remove the serial numbers on the commands, and to remove the final line where we called the history command, we have a completely accurate record of how we created that figure.

Challenge: Why record commands in the history before running them?

If you run the command:

$ history | tail -n 5 > recent.sh

the last command in the file is the history command itself, i.e., the shell has added history to the command log before actually running it. In fact, the shell always adds commands to the log before running them. Why do you think it does this?

If a command causes something to crash or hang, it might be useful to know what that command was, in order to investigate the problem. Were the command only be recorded after running it, we would not have a record of the last command run in the event of a crash.

In practice, most people develop shell scripts by running commands at the shell prompt a few times to make sure they’re doing the right thing, then saving them in a file for re-use. This style of work allows people to recycle what they discover about their data and their workflow with one call to history and a bit of editing to clean up the output and save it as a shell script.

Your pipeline: Creating a script

Your supervisor insisted that all your analytics must be reproducible. The easiest way to capture all the steps is in a script.

First we return to your project directory:

$ cd ../../north-pacific-gyre/

You create a file using nano …

$ nano do-stats.sh

…which contains the following:

# Calculate stats for data files.
for datafile in "$@"
do
    echo $datafile
    bash goostats.sh $datafile stats-$datafile
done

You save this in a file called do-stats.sh so that you can now re-do the first stage of your analysis by typing:

$ bash do-stats.sh NENE*A.txt NENE*B.txt

You can also do this:

$ bash do-stats.sh NENE*A.txt NENE*B.txt | wc -l

so that the output is just the number of files processed rather than the names of the files that were processed.

One thing to note about your script is that it lets the person running it decide what files to process. You could have written it as:

# Calculate stats for Site A and Site B data files.
for datafile in NENE*A.txt NENE*B.txt
do
    echo $datafile
    bash goostats.sh $datafile stats-$datafile
done

The advantage is that this always selects the right files: you doesn’t have to remember to exclude the ‘Z’ files. The disadvantage is that it always selects just those files — you can’t run it on all files (including the ‘Z’ files), or on the ‘G’ or ‘H’ files your colleagues in Antarctica are producing, without editing the script. If you wanted to be more adventurous, you could modify your script to check for command-line arguments, and use NENE*A.txt NENE*B.txt if none were provided. Of course, this introduces another tradeoff between flexibility and complexity.

Challenge: Variables in shell scripts

In the alkanes directory, imagine you have a shell script called script.sh containing the following commands:

head -n $2 $1
tail -n $3 $1

While you are in the alkanes directory, you type the following command:

$ bash script.sh '*.pdb' 1 1

Which of the following outputs would you expect to see?

  1. All of the lines between the first and the last lines of each file ending in .pdb in the alkanes directory

  2. The first and the last line of each file ending in .pdb in the alkanes directory

  3. The first and the last line of each file in the alkanes directory

  4. An error because of the quotes around *.pdb

The correct answer is 2.

The special variables $1, $2 and $3 represent the command line arguments given to the script, such that the commands run are:

$ head -n 1 cubane.pdb ethane.pdb octane.pdb pentane.pdb propane.pdb
$ tail -n 1 cubane.pdb ethane.pdb octane.pdb pentane.pdb propane.pdb

The shell does not expand '*.pdb' because it is enclosed by quote marks. As such, the first argument to the script is '*.pdb' which gets expanded within the script by head and tail

Challenge: Find the longest file with a given extension

Write a shell script called longest.sh that takes the name of a directory and a filename extension as its arguments, and prints out the name of the file with the most lines in that directory with that extension. For example:

$ bash longest.sh shell-lesson-data/exercise-data/alkanes pdb

would print the name of the .pdb file in shell-lesson-data/exercise-data/alkanes that has the most lines.

Feel free to test your script on another directory e.g.

$ bash longest.sh shell-lesson-data/exercise-data/writing txt
# Shell script which takes two arguments:
#    1. a directory name
#    2. a file extension
# and prints the name of the file in that directory
# with the most lines which matches the file extension.

wc -l $1/*.$2 | sort -n | tail -n 2 | head -n 1

The first part of the pipeline, wc -l $1/*.$2 | sort -n, counts the lines in each file and sorts them numerically (largest last). When there’s more than one file, wc also outputs a final summary line, giving the total number of lines across all files. We use tail -n 2 | head -n 1 to throw away this last line.

With wc -l $1/*.$2 | sort -n | tail -n 1 we’ll see the final summary line: we can build our pipeline up in pieces to be sure we understand the output.

Challenge: Script reading comprehension

For this question, consider the shell-lesson-data/exercise-data/alkanes directory once again. This contains a number of .pdb files in addition to any other files you may have created. Explain what each of the following three scripts would do when run as bash script1.sh *.pdb, bash script2.sh *.pdb, and bash script3.sh *.pdb respectively.

# Script 1
echo *.*
# Script 2
for filename in $1 $2 $3
do
    cat $filename
done
# Script 3
echo $@.pdb

In each case, the shell expands the wildcard in *.pdb before passing the resulting list of file names as arguments to the script.

Script 1 would print out a list of all files containing a dot in their name. The arguments passed to the script are not actually used anywhere in the script.

Script 2 would print the contents of the first 3 files with a .pdb file extension. $1, $2, and $3 refer to the first, second, and third argument respectively.

Script 3 would print all the arguments to the script (i.e. all the .pdb files), followed by .pdb. $@ refers to all the arguments given to a shell script.

cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb.pdb
Key Points

  • Save commands in files (usually called shell scripts) for re-use.

  • bash [filename] runs the commands saved in a file.

  • $@ refers to all of a shell script’s command-line arguments.

  • $1, $2, etc., refer to the first command-line argument, the second command-line argument, etc.

  • Place variables in quotes if the values might have spaces in them.

  • Letting users decide what files to process is more flexible and more consistent with built-in Unix commands.

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