Chapter 9 Next Steps

Congratulations! You’ve successfully completed all the exercises and practiced creating multiple Python scripts and running them at the UNIX command line. In addition to these practical skills, you got a taste of how Python works, and how it can be used to parse through text files line by line. We hope this helps demystify ever so slightly how UNIX commands can, and often are, Python scripts. As a reminder, here’s what we covered in each chapter:

Set up Compute: Join SciServer, start Jupyter
Running Programs: Run UNIX commands, wrap UNIX commands in a Bash script, run a Bash script
Hello, World!: Python “Hello, World!” example and run a Python script
Command line arguments: Print all command line arguments, understanding lists, accessing specific arguments, and arguments are strings
Parsing files line by line: Create a text file, open a file stream, add a for loop
Replicating the head command: Practice the head command, designing the head algorithm, coding step by step

You should now have all the tools you need to follow a full fledged Python tutorial. Here is one recommendation from Software Carpentry:

Programming with Python

As you continue your journey with Python, try replicating these two additional UNIX commands that are commonly used to filter and subset text files:

grep.py - Print only lines that match a given string (hint: if pattern in line:)
cut.py - For tab delimited files, print a specific column (hint: fields = line.split())