Summary and Schedule
Do you often work with lots of data files on the computer? Are you often trying to spot particular files or lines of text in them that are important for you?
If so, then using regular expressions could save you a lot of time and frustration!
Regular expressions (regex/REs) are a method for describing patterns
of characters that you want to match in a body of text. A knowledge of
regular expressions can be extremely helpful in computational biology
and when combined with text editors and common tools (grep,
sed, awk, etc) used in command line
computing.
These course materials are designed to give an introduction to using regular regular expressions. Working through the materials, you will learn how to quickly find and replace text in large files, controlling the types and numbers of characters matched, handling repeats, keeping certain parts of a matched pattern during replacement, and constructing sets of different options to be matched.
The course does not provide a comprehensive overview of the regex syntax or engine. Instead, they reflect the vast majority of use cases that the authors encounter. The background of the authors is represented in many of the examples chosen, which often focus on biological contexts and file formats.
For a comprehensive overview of regular expressions, we highly recommend the excellent regular-expressions.info.
Prerequisites
To follow this lesson, learners should know how to open a text file on their computer, and some familiarity with the Find/Replace functionality available in most text editing tools will be beneficial. The examples used will feel most relevant to those who are familiar with common file formats used to represent biological data, and some knowledge of sequence biology (DNA/RNA and protein sequences) is assumed.
| Setup Instructions | Download files required for the lesson | |
| Duration: 00h 00m | 1. Introduction |
What is a regular expression? In what programs can I use regular expessions? |
| Duration: 00h 00m | 2. Regex Fundamentals |
How can I search for sets of characters in a text file? How can I specify ranges of characters in a search? |
| Duration: 00h 00m | 3. Tokens and Wildcards |
How can I specify that patterns should only match as whole words or
whole lines? How can I only match patterns that appear at the very beginning or very end of a line? How can I specify positions in a pattern that could match any character? ::: |
| Duration: 00h 00m | 4. Repeated Matches |
How can I define a character or set that appears multiple times in a
pattern? How can I define the maximum and minimum number of times a character or set should appear in the pattern? |
| Duration: 00h 00m | 5. Capture Groups and References |
How can I reuse parts of the matched pattern when I replace it? ::: |
| Duration: 00h 00m | 6. Alternative Matches | How can I define multiple possible strings that can be matched in a regular expression? |
| Duration: 00h 00m | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.
Text Editor
If you already have a preferred text editor you can probably continue to use that to follow this lesson. Open the “Find/Replace” interface and look for an option with a label like “mode”, “grep-like”, “regular expression” or “regex.”
If you are installing a text editor for the first time, here are a few recommendations:
- For Windows, try the freely-available editor ‘Notepad++’, available at https://notepad-plus-plus.org.
- For Mac, TextWrangler is a good generic text editor, available free from http://www.barebones.com/products/TextWrangler/ or the App Store.
- Sublime Text is another good option, available on all operating systems from https://www.sublimetext.com.
Exercise Files
Download a ZIP of all of the exercise files here.