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to Hamming in the Go Track

Published at Oct 17 2019 · 0 comments
Instructions
Test suite
Solution

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.

You may be wondering about the cases_test.go file. We explain it in the leap exercise.

Running the tests

To run the tests run the command go test from within the exercise directory.

If the test suite contains benchmarks, you can run these with the --bench and --benchmem flags:

go test -v --bench . --benchmem

Keep in mind that each reviewer will run benchmarks on a different machine, with different specs, so the results from these benchmark tests may vary.

Further information

For more detailed information about the Go track, including how to get help if you're having trouble, please visit the exercism.io Go language page.

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.

cases_test.go

package hamming

// Source: exercism/problem-specifications
// Commit: 4119671 Hamming: Add a tests to avoid wrong recursion solution (#1450)
// Problem Specifications Version: 2.3.0

var testCases = []struct {
	s1          string
	s2          string
	want        int
	expectError bool
}{
	{ // empty strands
		"",
		"",
		0,
		false,
	},
	{ // single letter identical strands
		"A",
		"A",
		0,
		false,
	},
	{ // single letter different strands
		"G",
		"T",
		1,
		false,
	},
	{ // long identical strands
		"GGACTGAAATCTG",
		"GGACTGAAATCTG",
		0,
		false,
	},
	{ // long different strands
		"GGACGGATTCTG",
		"AGGACGGATTCT",
		9,
		false,
	},
	{ // disallow first strand longer
		"AATG",
		"AAA",
		0,
		true,
	},
	{ // disallow second strand longer
		"ATA",
		"AGTG",
		0,
		true,
	},
	{ // disallow left empty strand
		"",
		"G",
		0,
		true,
	},
	{ // disallow right empty strand
		"G",
		"",
		0,
		true,
	},
}

hamming_test.go

package hamming

import "testing"

func TestHamming(t *testing.T) {
	for _, tc := range testCases {
		got, err := Distance(tc.s1, tc.s2)
		if tc.expectError {
			// check if err is of error type
			var _ error = err

			// we expect error
			if err == nil {
				t.Fatalf("Distance(%q, %q); expected error, got nil.",
					tc.s1, tc.s2)
			}
		} else {
			// we do not expect error
			if err != nil {
				t.Fatalf("Distance(%q, %q) returned unexpected error: %v",
					tc.s1, tc.s2, err)
			}
			if got != tc.want {
				t.Fatalf("Distance(%q, %q) = %d, want %d.",
					tc.s1, tc.s2, got, tc.want)
			}

		}
	}
}

func BenchmarkHamming(b *testing.B) {
	// bench combined time to run through all test cases
	for i := 0; i < b.N; i++ {
		for _, tc := range testCases {
			// ignoring errors and results because we're just timing function execution
			_, _ = Distance(tc.s1, tc.s2)
		}
	}
}
package hamming

import "errors"

// Distance refers to the number of points at which two lines of string differ
func Distance(a, b string) (int, error) {
	countMistake := 0
	ar, br := []rune(a), []rune(b)
	if len(ar) != len(br) {
		return countMistake, errors.New("error: the two secuences are differents sizes")
	}
	for i := range ar {
		if ar[i] != br[i] {
			countMistake++
		}
	}
	return countMistake, nil
}

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