exercism/lisp/hamming

Hamming

Write a program that can calculate the Hamming difference between two DNA strands.

A mutation is simply a mistake that occurs during the creation or copying of a nucleic acid, in particular DNA. Because nucleic acids are vital to cellular functions, mutations tend to cause a ripple effect throughout the cell. Although mutations are technically mistakes, a very rare mutation may equip the cell with a beneficial attribute. In fact, the macro effects of evolution are attributable by the accumulated result of beneficial microscopic mutations over many generations.

The simplest and most common type of nucleic acid mutation is a point mutation, which replaces one base with another at a single nucleotide.

By counting the number of differences between two homologous DNA strands taken from different genomes with a common ancestor, we get a measure of the minimum number of point mutations that could have occurred on the evolutionary path between the two strands.

This is called the 'Hamming distance'.

It is found by comparing two DNA strands and counting how many of the nucleotides are different from their equivalent in the other string.

GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^  ^ ^    ^^

The Hamming distance between these two DNA strands is 7.

Implementation notes

The Hamming distance is only defined for sequences of equal length. This means that based on the definition, each language could deal with getting sequences of equal length differently.

Setup

Check out Exercism Help for instructions to get started writing Common Lisp. That page will explain how to install and setup a Lisp implementation and how to run the tests.

Formatting

While Common Lisp doesn't care about indentation and layout of code, nor whether you use spaces or tabs, this is an important consideration for submissions to exercism.io. Excercism.io's code widget cannot handle mixing of tab and space characters well so using only spaces is recommended to make the code more readable to the human reviewers. Please review your editors settings on how to accomplish this. Below are instructions for popular editors for Common Lisp.

VIM

Use the following commands to ensure VIM uses only spaces for indentation:

:set tabstop=2
:set shiftwidth=2
:set expandtab

(or as a oneliner :set tabstop=2 shiftwidth=2 expandtab). This can be added to your ~/.vimrc file to use it all the time.

Emacs

Emacs is very well suited for editing Common Lisp and has many powerful add-on packages available. The only thing that one needs to do with a stock emacs to make it work well with exercism.io is to evaluate the following code:

(setq indent-tab-mode nil)

This can be placed in your ~/.emacs (or ~/.emacs.d/init.el) in order to have it set whenever Emacs is launched.

One suggested add-on for Emacs and Common Lisp is SLIME which offers tight integration with the REPL; making iterative coding and testing very easy.

Source

The Calculating Point Mutations problem at Rosalind http://rosalind.info/problems/hamm/

Submitting Incomplete Problems

It's possible to submit an incomplete solution so you can see how others have completed the exercise.