MatMoore / rosalind-problems

Solutions to bioinformatics problems

Rosalind problems

This repo contains my solutions to the bioinformatics problems at https://rosalind.info/problems

To run the solutions

• ruby runner.rb runs all the solutions.
• ruby runner.rb PROBLEM_ID runs a single solution.
• ruby runner.rb -o PROBLEM_ID copies an input from ~/Downloads, then runs the solution.

Some fun ruby stuff I used along the way

Zeitwerk

The runner module uses the Zeitwerk autoloader to eager load all the code for the project, based on the directory structure. This saves me writing lots of 'require' statements.

Characterization testing

The runner uses characertization testing to ensure my previous solutions don't break when refactoring code.

This works great for exercises like this, since my definition of working code is simply: "does it produce a solution that was marked correct?".

Data classes

Ruby 3.2 added a new data class for defining immutable value objects. I use it in the GeneticString module for modelling DNA and RNA.

I made the classes themselves private and provided factory methods to make sure sequences are valid when constructing these values.