2  Before you begin

This chapter serves to get the practicalities out of the way so you can start programming. Read the whole chapter once carefully before you install anything

Install Python

In this course, we use the Python programming language and need the Python program to run the code we will write. We will use a Python distribution called Anaconda. Anaconda is the easiest way to install Python on Windows, Mac OS (Mac), and Linux. To install Anaconda, head to this site. Click “Download”. When the download has been completed, double-click the file you just downloaded and follow the instructions on the screen. You must accept all the suggested installation settings.

The text editor

You will also need a text editor. A text editor is where you write your Python code. For this course, we will use Visual Studio Code - or VScode for short. You can download it from this page. If you open VScode, you should see something like Figure 2.1. You may wonder why we cannot use Word to create and edit files with programming code. The reason is that a text editor made for programming, such as VScode, only saves the actual characters you type. So, unlike Word, it does not silently save all kinds of formatting, like margins, boldface text, headers, etc. With VScode, what you type is exactly in the file when you save it. In addition, where Word is made for prose, VScode is made for programming and has many features that will make your programming life easier.

Figure 2.1: Visual Studio Code (VScode)

The terminal

The last thing you need is a tool to make Python run the programs you write. Fortunately, that is already installed. On OSX, this is an application called Terminal. You can find it by typing “Terminal” in Spotlight Search. When you start, you will see something like Figure 2.2. You may be presented with the following text:

The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.

Figure 2.2: The Terminal app on Mac

Figure 2.3: Anaconda Powershell Prompt app on Windows

Do not update your account after you install Anaconda (see below). If you do, Terminal will not be able to find the Anaconda Python (If you did so by mistake, you change back using this command: chsh -s /bin/bash.

On Windows, the tool you need is called the Anaconda Powershell Prompt, which was installed along with Anaconda Python. You should be able to find it from the Start menu. Ensure you open Anaconda Powershell Prompt and not Anaconda Powershell Prompt. They are different programs. If you open Anaconda Powershell Prompt, you should see something like Figure 2.3.

What is Anaconda Powershell Prompt and this Terminal thing? Both programs are what we call terminal emulators. They are used to run other programs, like the ones you will write yourself. I will informally refer to both Terminal and Anaconda Powershell Prompt as “the terminal.” So if I write something like “open the terminal,” you should open Anaconda Powershell Prompt if you are running Windows and the Terminal application if you are running OS X.

The terminal is a very useful tool. However, to use it, you need to know a few basics. First of all, a terminal lets you execute commands on your computer. You type the command you want and then hit enter. The place where you type is called a prompt (or command prompt), and it may look a little different depending on which terminal emulator you use. In this book, we represent the prompt with the character $. So, a command in the examples below is the line of text to the left of the $. When you open the terminal, you’ll be redirected to a folder. You can see which folder you are in by typing pwd, and then press Enter on the keyboard. When you press Enter, you tell the terminal to execute your written command. In this case, the command you typed tells you the path to the folder we are in. If I do it, I get:

Terminal

$ pwd
/Users/kasper/programming

If I had been on a Windows machine, it would have looked something like this:

Terminal

$ cd
C:\Users\kasper\programming

So, right now, I am in the programming folder. /Users/kasper/programming is the folder’s path or “full address” with dashes (or backslashes on Windows) separating nested folders. So programming is a subfolder of kasper, a subfolder of Users. That way, you know which folder you are in and where that folder is. Let us see what is in this folder. You can use the ls command (l as in Lima and s as in Sierra). When I do that and press Enter I get the following:

Terminal

$ ls
notes projects

There seem to be two other folders, one called notes and another called projects. If you are curious about what is inside the notes folder, you can “walk” into the folder with the cd command. To use this command, you must specify which folder you want to walk into (in this case, notes). We do this by typing cd, then a space, and then the folder’s name. When I press Enter I get the following:

Terminal

$ cd notes
$

It seems that nothing really happened, but if I run the pwd command now to see which folder I am in, I get the following:

Terminal

$ pwd
/Users/kasper/programming/notes

Just to keep track of what is happening: before we ran the cd command, we were in the directory /Users/kasper/programming folder, and now we’re in /Users/kasper/programming/notes. This means that we can now use the ls command to see what is in the notes folder:

Terminal

$ ls
$

Again, it seems like nothing happened. Well, ls and dir do not show anything if the folder we are in is empty. So notes must be empty. Let us go back to where we came from. To walk “back” or “up” to /Users/kasper/programming, we again use the cd command, but we do not need to name a folder this time. Instead, we use the special name .. to say that we wish to go to the parent folder called programming, i.e., the folder we just came from:

Terminal

$ cd ..
$ pwd
/Users/kasper/programming

When we run the pwd command, we see that we are back where we started. Let us see if the two folders are still there:

Terminal

$ ls
notes projects

They are!

Hopefully, you can now navigate your folders and see what is in them. You will need this later to access the folders with the code you write for the exercises and projects during the course.

Action	OSX
Show current folder	pwd
List folder content	ls
Go to subfolder “notes”	cd notes
Go to parent folder	cd ..

Create a conda environment for the course

In bioinformatics, we install packages and programs to use them in our analyses and pipelines. Sometimes, however, the packages you need for one project conflict with the ones you need for other projects you work on in parallel. Such conflicts seem like an unsolvable problem. If only you could create a small insulated world for each project that only contained the packages you needed for that particular project. If each project lived in an isolated world, then there would be no such version conflicts. Fortunately, a tool lets you do just that, and its name is Conda.

Conda is an open-source environment management system for installing multiple versions of software packages and their dependencies and easily switching between them.

The small worlds that Conda creates are called “environments”. You can create as many environments as you like and then use each for a separate bioinformatics project, a course, a bachelor project, or whatever you want to insulate from everything else. Conda also downloads and installs the packages for you, ensuring that the software packages you install in each environment are compatible. It even makes sure that packages needed by packages (dependencies) are also installed. Conda is truly awesome.

When you install Anaconda, Conda makes a single base environment for you. It is called “base”, and this is why it says “(base)” on your terminal.

In this course, you must install programs and Python libraries that could conflict with the packages you need for other courses or future projects. So, we will create an isolated Conda environment for Bioinformatics and Programming to avoid such conflicts. Conda is a program you run from the command line, like python or cd. So open your terminal (i.e., the “Terminal” program if you are on a Mac and the “Anaconda Powershell Prompt” program if you are on Windows). Now copy/paste these command lines into the terminal one at a time and press return (enter) after pasting each one:

Terminal

conda create -y -n bioprog
conda activate bioprog
conda config --env --add channels conda-forge
conda config --env --add channels sepandhaghighi
conda config --env --add channels kaspermunch
conda install -y 'python=3.9' pygments textual rich art bp-help

This command runs the Conda program and tells it to create a new environment named “bioprog” and install the packages we need in that environment. Once you hit enter on the last command, Conda works for some time and then writes a long list of packages in your terminal. These are all the packages and dependencies required in versions that fit together.

Notice how the command prompt changed from “(base)” to “(bioprog)” to show that you are now in the bioprog environment. It looks like nothing has changed, but now you can access unavailable terminal commands in the base environment. You’ll be able to learn about these later. Try this command:

conda deactivate

Notice how it again says “(base)” on your command prompt. That is because you are back in your base environment. When you start a new terminal window, you must run conda activate bioprog to activate the environment and access the course tools.

You are all set

Well done! You are all set to start the course. Have a cup of coffee, and look forward to your first program. While you sip your coffee, I need you to take an oath (one of three you will take during this course). Raise your right hand! (put the coffee on your left).

Oath 1: I swear never to copy and paste code examples from this book into my text editor. I will always read the examples and then type them into my editor.

This serves three purposes (as if one was not enough):

1. You will be fully aware of every bit of each example.
2. You will learn to write code correctly and without omissions and mistakes.
3. You will get Python “into your fingers”. It sounds silly, but it will get into your fingers.