Lesson 5: Absolute and Relative Paths

In bioinformatics, you will often need to reference files located in various places: your home directory, a shared lab drive, or a specific project folder. Understanding how to precisely tell the computer where a file is located is critical.

There are two ways to specify a file’s location: Absolute Paths and Relative Paths.

1. The File System Tree and Root (`/`)

Linux organizes files in a hierarchical tree structure.

Root (/): The very top of the tree is called the “root” directory and is represented by a single forward slash /.
Everything on your system lives under root. There are no drive letters like C: or D: at the top level in Linux.

2. Mounted Drives (`/mnt`)

If you are using WSL (Windows Subsystem for Linux) or accessing external hard drives on a Linux machine, these drives are often “mounted” inside the /mnt directory.

WSL Users: Your C: drive is typically accessible at /mnt/c/.
Example: If your Bioinformatic_Fridays folder is in your Windows Documents folder, the path might look like:
Terminal window
```
/mnt/c/Users/YourName/Documents/Bioinformatic_Fridays/
```

3. Absolute Paths

An Absolute Path is the full address of a file, starting from the root (/). It is unambiguous; it points to the same location no matter where your current working directory is.

Key Rule: An absolute path always starts with a /.

Examples

Let’s find the absolute path to the attendees.csv file in our Training folder.

Navigate to the Training folder (wherever it is on your system).
Run the pwd (Print Working Directory) command:
Terminal window
```
pwd
```
Output (example for a Linux user):
```
/home/bodeoni/Bioinformatic_Fridays/Training
```
Output (example for a WSL user):
```
/mnt/c/Users/WAVECU001/Documents/Bioinformatic_Fridays/Training
```

The Absolute Path to the file is that full folder path plus the filename:

/home/bodeoni/Bioinformatic_Fridays/Training/attendees.csv

When to use Absolute Paths:

In scripts/code (so they run correctly from anywhere).
When configuring tools that need to find a reference file (e.g., a genome index).

4. Relative Paths

A Relative Path describes the location of a file relative to where you are right now. It never starts with a /.

Symbols:

. (dot): The current directory.
.. (dot dot): The parent directory (one level up).

Scenarios

Scenario A: You are inside Bioinformatic_Fridays/

To list the files in Training/long_reads without leaving your current spot:
Terminal window
```
ls Training/long_reads
```
(This is a relative path. We didn’t start with /, so Linux looks for Training inside the current folder.)

Scenario B: You are inside Training/short_reads/

You want to see the attendees.csv file, which is one level up (in Training/).
Path: ../attendees.csv
Terminal window
```
ls ../attendees.csv
```

Scenario C: You are inside Training/short_reads/ and want to go to Training/long_reads/

You need to go up one level (to Training), and then down into long_reads.
Path: ../long_reads
Terminal window
```
cd ../long_reads
```

5. The Home Shortcut (`~`)

The tilde character ~ is a shortcut for your home directory.

On standard Linux: usually /home/your_username
On WSL: usually /home/your_linux_username (Note: this is your Linux home, not your Windows User folder).
Example: cd ~ takes you home.
Example: ls ~/Downloads lists your Downloads folder (if it exists in your Linux home).

Practice Exercise

Navigate to the Training/long_reads directory.
Use pwd to find the Absolute Path of this directory.
List the contents of the short_reads directory using a Relative Path (hint: you need to go up, then down).
Try to list the attendees.csv file using an Absolute Path (use the output from step 2 to help you construct it).