Bash exercise using GitHub’s codespace

Follow the instructions below to complete this exercise, and put your answers to the questions into the Exercise 2 quiz on Canvas.

Your project repository

Make your copy and open your codespace

Go to the Comp Bio project template on GitHub, and follow the instructions in its README under the following two sections ONLY:
- “Make your own copy of this repository”: Name your repository bash-intro, and choose Public
- “Open your codespace”: When you get a “Do you trust the authors of the files in this folder?” pop-up, click “Trust Folder & Continue”
Stop and come back here once you get to “Set up your project environment” (don’t set up the environment; we don’t need it for this exercise).
Once your codespace is ready, you should see your files on the left side of VS Code and a terminal at the bottom. Click in the terminal and check that you’re in your project’s folder:
```
Terminal
```
```
pwd
ls -a
```
pwd (print working directory) tells you what directory (“folder”) you are in, which should be /workspaces/comp-bio-project. This folder you are in is called your working directory. ls -a lists all files and directories in your working directory. When you run this command, you should see README.md and a folder named .devcontainer (plus a folder named .git; more on that below).

The terminal is the Bash command line running on a Linux computer in the cloud. All of the commands in this exercise are typed in the terminal.

Creating a new directory and copying files into it

Using the terminal, navigate to your home directory:
```
Terminal
```
```
cd ~
```
Create a new directory called “exercise2”
```
Terminal
```
```
mkdir exercise2
```

Use the curl command to download an answer1.txt file from our class GitHub repo into your new exercise2 directory:

Terminal

curl -L -o exercise2/answer1.txt https://raw.githubusercontent.com/phyletica/intro-to-comp-bio/refs/heads/main/notebooks/data/answer1.txt

Use the curl command again to download the SARS-CoV-2.fasta file from our class GitHub repo into your new exercise2 directory:

Terminal

curl -L -o exercise2/SARS-CoV-2.fasta https://raw.githubusercontent.com/phyletica/intro-to-comp-bio/refs/heads/main/notebooks/data/SARS-CoV-2.fasta

Now, move into the “exercise2” directory and confirm the files you downloaded are there:
```
Terminal
```
```
cd exercise2
ls
```

Question 1

Use the command line (terminal) to see what is in the answer1.txt file. Enter what you find in the file into Question 1 of the Exercise 2 quiz on Canvas.

Hint: The commands cat or less would be useful. I would normally encourage you to use the man command to learn more about these commands, but man doesn’t work by default in GitHub’s Codespaces. As an alternative, go to the Linux man pages online and use the search bar near the bottom of the page to search for the commands cat and less.

Save your work to GitHub at the end of every part

Your GitHub codespace is temporary. It stops on its own after 30 minutes of inactivity, and GitHub deletes codespaces that haven’t been used for 30 days, even if they contain work you haven’t pushed to GitHub. Your work is only safe once you have committed it and pushed it to GitHub (you’ll learn how in Part 1).

Manipulating sequence data

The “SARS-CoV-2.fasta” file contains nucleotide sequence data from different strains of the SARS-CoV-2 virus. The sequences are in a format called FASTA. The FASTA format looks like:

>Name1
AATCGGCTA
>Name2
ATTCGCCTA

Question 2

Use the command line to determine the number of sequences in the “SARS-CoV-2.fasta” file.

Notice all sequences start with a “>” character to specify the seqence’s name. We can use that to count the sequences efficiently. Try:
```
Terminal
```
```
grep ">" SARS-CoV-2.fasta
```
NOTE: Putting quotes around the > character is important, because in the Bash language, this character is normally used to redirect output!

grep is a very useful command for finding string patterns. You can learn more about it by searching for grep at the Linux man pages online.
grep works okay for this small FASTA file, but what if there were 1000s of sequences in the file? You wouldn’t want to count them “by hand!”

We can use the wc command (word count) for counting the sequences. Try:
```
Terminal
```
```
grep ">" SARS-CoV-2.fasta | wc -l
```
The pipe (|) character converts, or “pipes”, the output of one command to input to another command. wc -l will count the number of lines output by grep

Put the number of sequences into Question 2 of the Exercise 2 quiz on Canvas.

Question 3

What does the -l flag in the wc -l do? Hint: use the Linux man pages online to find out!

Question 4

What is your output for the following command?

Terminal

whoami

Question 5

What is your output for the following command?

Terminal

echo $MACHTYPE

Question 6

What is your output for the following command?

Terminal

uname -a

Question 7

What does the -a flag do in the uname -a command? Hint: use the Linux man pages online to find out!