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to Hamming in the Go Track

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

Calculate the Hamming Distance between two DNA strands.

Your body is made up of cells that contain DNA. Those cells regularly wear out and need replacing, which they achieve by dividing into daughter cells. In fact, the average human body experiences about 10 quadrillion cell divisions in a lifetime!

When cells divide, their DNA replicates too. Sometimes during this process mistakes happen and single pieces of DNA get encoded with the incorrect information. If we compare two strands of DNA and count the differences between them we can see how many mistakes occurred. This is known as the "Hamming Distance".

We read DNA using the letters C,A,G and T. Two strands might look like this:

GAGCCTACTAACGGGAT
CATCGTAATGACGGCCT
^ ^ ^  ^ ^    ^^

They have 7 differences, and therefore the Hamming Distance is 7.

The Hamming Distance is useful for lots of things in science, not just biology, so it's a nice phrase to be familiar with :)

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.

Coding the solution

Look for a stub file having the name hamming.go and place your solution code in that file.

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"

func Distance(a, b string) (int, error) {
  if len(a) != len(b) {
    return 0, errors.New("Strings are unequal length")
  }
  ham := 0
  for x, d1 := range a {
    if d1 != rune(b[x]) {
      ham++
    }
  }
  return ham, nil
}

What can you learn from this solution?

A huge amount can be learned from reading other people’s code. This is why we wanted to give exercism users the option of making their solutions public.

Here are some questions to help you reflect on this solution and learn the most from it.

  • What compromises have been made?
  • Are there new concepts here that you could read more about to improve your understanding?