 shmibs's solution

to Hamming in the Crystal Track

Published at Nov 17 2018 · 0 comments
Instructions
Test suite
Solution

Note:

This exercise has changed since this solution was written.

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, so an attempt to calculate it between sequences of different lengths should not work. The general handling of this situation (e.g., raising an exception vs returning a special value) may differ between languages.

Setup

Follow the setup instructions for Crystal here:

http://exercism.io/languages/crystal

More help installing can be found here:

http://crystal-lang.org/docs/installation/index.html

Making the Test Suit Pass

Execute the tests with:

\$ crystal spec

In each test suite all but the first test have been skipped.

Once you get a test passing, you can unskip the next one by changing pending to it.

Source

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

Submitting Incomplete Solutions

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

hamming_spec.cr

require "spec"
require "../src/*"

describe "Hamming" do
describe "#compute" do
it "computes no difference for identical single nucleotide strands" do
Hamming.compute("A", "A").should eq 0
end

pending "computes a distance for single nucleotide strands" do
Hamming.compute("A", "G").should eq 1
end

pending "computes a distance for small strands" do
Hamming.compute("AG", "CT").should eq 2
end

pending "computes a distance for medium strands" do
Hamming.compute("GGACG", "GGTCG").should eq 1
end

pending "computes a distance for large strands" do
Hamming.compute("GGACGGATTCTG", "AGGACGGATTCT").should eq 9
end

pending "raises an exception when strands aren't of equal length" do
expect_raises(ArgumentError) { Hamming.compute("GCC", "A") }
end
end
end
module Hamming
extend self

CHARSET = Set{'A'.bytes, 'T'.bytes, 'C'.bytes, 'G'.bytes}

def compute(nlist_1 : String, nlist_2 : String)

# lengths must match
if nlist_1.bytesize != nlist_2.bytesize
raise ArgumentError.new
end

(0...nlist_1.bytesize).count { |i|
c1 = nlist_1.unsafe_byte_at(i)
c2 = nlist_2.unsafe_byte_at(i)

# err on bad char
unless CHARSET === c1 && CHARSET === c2
raise ArgumentError.new
end

c1 != c2
}

end

end