Introduction to Computational Genomics

Section 1

Objectives

Questions

How to access the terminal if you’re on a windows PC

For mac and linux computers, the terminal program is pre-installed, but for windows users you will need to install it. Follow this link and click on the “windows” tab. Then follow the instructions there to download and install git for windows, which includes a bash shell.

How to access the remote server

All students will be accessing the server using their UVic Netlink ID. You will use the ssh or Secure Shell command to login to the remote server, while logged into the UVic VPN. The VPN is called “Cisco AnyConnect Secure Mobile Client”. Open it and fill in “vpn.uvic.ca” into the connection box. It will then tell you to select a group, please select “3 - Student”. This will then prompt you to fill in your netlink ID and then request a Duo Push notification.

ssh your_id@indri.rcs.uvic.ca

You will be prompted to use Duo, two-factor authentication before you enter your password. After approving the authentication on your phone, you will use your netlink ID to login.

(base) p165-072:~ gregoryowens$ ssh grego@indri.rcs.uvic.ca
*
* Acceptable Use of Electronic Information Resources
*
* Access to this system is prohibited except for authorized University of
* Victoria students, faculty, and staff.
*
* All activity may be logged/monitored and unauthorized access will be handled
* per the provisions of UVic's Policy IM7200: Acceptable Use of Electronic
* Information Resources.
*
* https://www.uvic.ca/universitysecretary/assets/docs/policies/IM7200_6030_.pdf
*
(grego@fossa.rcs.uvic.ca) Duo two-factor login for grego

Enter a passcode or select one of the following options:

 1. Duo Push to XXX-XXX-XXXX

Passcode or option (1-1):

After logging in, you will see a screen showing something like this:

To access CVMFS modules please source the appropriate profile.
For example: 'source /cvmfs/soft.computecanada.ca/config/profile/bash.sh'

Last failed login: Thu Oct  5 10:44:07 PDT 2023 from 142.104.165.72 on ssh:notty
There was 1 failed login attempt since the last successful login.
Last login: Thu Oct  5 09:48:45 2023 from 142.104.165.72

Sourcing our programs

We want to access a variety of programs on the server. To do that, we are going to source a file to bring it into our profile. This will tell the computer where all your programs are stored. NOTE: You have to run this command whenever you login.

source /cvmfs/soft.computecanada.ca/config/profile/bash.sh

Creating directories

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

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

We can get this data by downloading it from a git repository:

[grego@indri ~]$ git clone https://github.com/owensgl/shell_data.git

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

First we should return to the home directory:

$ cd ~/shell_data

Then enter the lab_2_data directory:

$ cd lab_2_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

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:

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 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 in a few lines of text.

Once we’re happy with our text, we can press Ctrl+O (press the Ctrl or Control key and, while holding it down, press the O key) to write our data to disk. We 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:

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?

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 the 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-data/lab_2_data/exercise-data/writing directory,

$ cd ~shell_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

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 ____/____

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 .

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

Removing files and directories

Returning to the shell-data/lab_2_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.

Using rm Safely

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

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 files and directories

Oftentimes one needs to copy or move several files at once. This can be done by providing a list of individual filenames, or specifying a naming pattern using wildcards. 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-data/lab_2_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

Wildcards

* is a wildcard, which represents zero or more other characters. Let’s consider the shell-data/lab_2_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.*

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

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

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

Keypoints

Rest Break

Section 2

Objectives

Questions

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-data/lab_2_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: Ctrl+C. Then release both keys.

Capturing output from commands

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

Output Page by Page

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.

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-data/lab_2_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.

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.

Challenge: Appending Data

Consider the file shell-data/lab_2_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

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

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-data/lab_2_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

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 a 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)?

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-data/lab_2_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

Nelle’s Pipeline: Checking Files

Nelle has run her 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-data/lab_2_data directory, Nelle types:

$ 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 she types 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 she goes back and checks it, she sees that she did that assay at 8:00 on a Monday morning — someone was probably in using the machine on the weekend, and she forgot to reset it. Before re-running that sample, she checks 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 her samples should be marked ‘A’ or ‘B’; by convention, her lab uses ‘Z’ to indicate samples with missing information. To find others like it, she does this:

$ ls *Z.txt

NENE01971Z.txt    NENE02040Z.txt

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

Challenge: Removing Unneeded Files

Suppose you want to delete your processed data files, and only keep your raw files and processing script to save storage. The raw files end in .dat and the processed files end in .txt. Which of the following would remove all the processed data files, and only the processed data files?

  1. rm ?.txt
  2. rm *.txt
  3. rm * .txt
  4. rm *.*

Keypoints

Rest Break

Section 3

Objectives

Questions

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 assign a file name to the variable filename and run the head command. 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?

Challenge: Variables in Loops

This exercise refers to the shell-data/lab_2_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?

Challenge: Limiting Sets of Files

What would be the output of running the following loop in the shell-data/lab_2_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.

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.

Challenge: Saving to a File in a Loop - Part One

In the shell-data/lab_2_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.

Challenge: Saving to a File in a Loop - Part Two

Also in the shell-data/lab_2_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.

Let’s continue with our example in the shell-data/lab_2_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-data/lab_2_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.

Nelle’s Pipeline: Processing Files

Nelle is now ready to process her data files using goostats.sh — a shell script written by her 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 she’s still learning how to use the shell, she decides to build up the required commands in stages. Her first step is to make sure that she 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, Nelle types:

$ cd
$ cd shell-data/lab_2_data/north-pacific-gyre
$ for datafile in NENE*A.txt NENE*B.txt
> do
>     echo $datafile
> done

NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
...
NENE02043A.txt
NENE02043B.txt

Her 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 she modifies her loop to do that:

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

NENE01729A.txt stats-NENE01729A.txt
NENE01729B.txt stats-NENE01729B.txt
NENE01736A.txt stats-NENE01736A.txt
...
NENE02043A.txt stats-NENE02043A.txt
NENE02043B.txt stats-NENE02043B.txt

She hasn’t actually run goostats.sh yet, but now she’s sure she can select the right files and generate the right output filenames.

Typing in commands over and over again is becoming tedious, though, and Nelle is worried about making mistakes, so instead of re-entering her loop, she presses ↑. In response, the shell redisplays 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 ←, Nelle navigates to the echo command and changes it to bash goostats.sh:

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

When she presses Enter, the shell runs the modified command. However, nothing appears to happen — there is no output. After a moment, Nelle realizes that since her script doesn’t print anything to the screen any longer, she has no idea whether it is running, much less how quickly. She kills the running command by typing Ctrl+C, uses ↑ to repeat the command, and edits 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 she runs her program now, it produces one line of output every five seconds or so:

NENE01729A.txt
NENE01729B.txt
NENE01736A.txt
...

1518 times 5 seconds, divided by 60, tells her that her script will take about two hours to run. As a final check, she opens another terminal window, goes into north-pacific-gyre, and uses cat stats-NENE01729B.txt to examine one of the output files. It looks good, so she decides to get some coffee and catch up on her 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 Nelle 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 she can re-run goostats.sh on the files simply by typing !459.

Other History Commands

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

Challenge: Doing a Dry Run

A loop is a way to do many things at once — or to make many mistakes at once if it does the wrong thing. One way to check what a loop would do is to echo the commands it would run instead of actually running them.

Suppose we want to preview the commands the following loop will execute without actually running those commands:

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

What is the difference between the two loops below, and which one would we want to run?

# Version 1
$ for datafile in *.pdb
> do
>     echo cat $datafile >> all.pdb
> done

# Version 2
$ for datafile in *.pdb
> do
>     echo "cat $datafile >> all.pdb"
> done

Challenge: Nested Loops

Suppose we want to set up a directory structure to organize some experiments measuring reaction rate constants with different compounds and different temperatures. What would be the result of the following code:

$ for species in cubane ethane methane
> do
>     for temperature in 25 30 37 40
>     do
>         mkdir $species-$temperature
>     done
> done

Keypoints