nucleotide_count
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{
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"authors": [
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"rubysolo"
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],
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"contributors": [
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"andrewsardone",
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"angelikatyborska",
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"Cohen-Carlisle",
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"dalexj",
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"dantswain",
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"devonestes",
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"henrik",
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"jinyeow",
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"kytrinyx",
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"leikind",
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"lpil",
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"MarcosX",
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"neenjaw",
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"nimser",
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"parkerl",
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"rud",
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"sotojuan",
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"Teapane",
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"toriejw",
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"waiting-for-dev"
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],
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"files": {
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"solution": [
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"lib/nucleotide_count.ex"
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],
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"test": [
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"test/nucleotide_count_test.exs"
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],
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"example": [
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".meta/example.ex"
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]
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},
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"blurb": "Given a DNA string, compute how many times each nucleotide occurs in the string.",
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"source": "The Calculating DNA Nucleotides_problem at Rosalind",
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"source_url": "https://rosalind.info/problems/dna/"
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}
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{"track":"elixir","exercise":"nucleotide-count","id":"fb05458eec1d47cb957f302624413711","url":"https://exercism.org/tracks/elixir/exercises/nucleotide-count","handle":"negrienko","is_requester":true,"auto_approve":false}
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# Used by "mix format"
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[
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inputs: ["{mix,.formatter}.exs", "{config,lib,test}/**/*.{ex,exs}"]
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]
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# The directory Mix will write compiled artifacts to.
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/_build/
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# If you run "mix test --cover", coverage assets end up here.
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/cover/
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# The directory Mix downloads your dependencies sources to.
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/deps/
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# Where third-party dependencies like ExDoc output generated docs.
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/doc/
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# Ignore .fetch files in case you like to edit your project deps locally.
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/.fetch
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# If the VM crashes, it generates a dump, let's ignore it too.
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erl_crash.dump
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# Also ignore archive artifacts (built via "mix archive.build").
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*.ez
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# Ignore package tarball (built via "mix hex.build").
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nucleotide_count-*.tar
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# Help
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## Running the tests
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From the terminal, change to the base directory of the exercise then execute the tests with:
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```bash
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$ mix test
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```
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This will execute the test file found in the `test` subfolder -- a file ending in `_test.exs`
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Documentation:
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* [`mix test` - Elixir's test execution tool](https://hexdocs.pm/mix/Mix.Tasks.Test.html)
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* [`ExUnit` - Elixir's unit test library](https://hexdocs.pm/ex_unit/ExUnit.html)
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## Pending tests
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In test suites of practice exercises, all but the first test have been tagged to be skipped.
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Once you get a test passing, you can unskip the next one by commenting out the relevant `@tag :pending` with a `#` symbol.
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For example:
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```elixir
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# @tag :pending
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test "shouting" do
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assert Bob.hey("WATCH OUT!") == "Whoa, chill out!"
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end
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```
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If you wish to run all tests at once, you can include all skipped test by using the `--include` flag on the `mix test` command:
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```bash
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$ mix test --include pending
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```
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Or, you can enable all the tests by commenting out the `ExUnit.configure` line in the file `test/test_helper.exs`.
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```elixir
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# ExUnit.configure(exclude: :pending, trace: true)
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```
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## Useful `mix test` options
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* `test/<FILE>.exs:LINENUM` - runs only a single test, the test from `<FILE>.exs` whose definition is on line `LINENUM`
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* `--failed` - runs only tests that failed the last time they ran
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* `--max-failures` - the suite stops evaluating tests when this number of test failures
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is reached
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* `--seed 0` - disables randomization so the tests in a single file will always be ran
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in the same order they were defined in
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## Submitting your solution
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You can submit your solution using the `exercism submit lib/nucleotide_count.ex` command.
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This command will upload your solution to the Exercism website and print the solution page's URL.
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It's possible to submit an incomplete solution which allows you to:
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- See how others have completed the exercise
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- Request help from a mentor
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## Need to get help?
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If you'd like help solving the exercise, check the following pages:
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- The [Elixir track's documentation](https://exercism.org/docs/tracks/elixir)
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- The [Elixir track's programming category on the forum](https://forum.exercism.org/c/programming/elixir)
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- [Exercism's programming category on the forum](https://forum.exercism.org/c/programming/5)
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- The [Frequently Asked Questions](https://exercism.org/docs/using/faqs)
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Should those resources not suffice, you could submit your (incomplete) solution to request mentoring.
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If you're stuck on something, it may help to look at some of the [available resources](https://exercism.org/docs/tracks/elixir/resources) out there where answers might be found.
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# Nucleotide Count
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Welcome to Nucleotide Count on Exercism's Elixir Track.
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If you need help running the tests or submitting your code, check out `HELP.md`.
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## Instructions
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Each of us inherits from our biological parents a set of chemical instructions known as DNA that influence how our bodies are constructed.
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All known life depends on DNA!
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> Note: You do not need to understand anything about nucleotides or DNA to complete this exercise.
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DNA is a long chain of other chemicals and the most important are the four nucleotides, adenine, cytosine, guanine and thymine.
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A single DNA chain can contain billions of these four nucleotides and the order in which they occur is important!
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We call the order of these nucleotides in a bit of DNA a "DNA sequence".
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We represent a DNA sequence as an ordered collection of these four nucleotides and a common way to do that is with a string of characters such as "ATTACG" for a DNA sequence of 6 nucleotides.
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'A' for adenine, 'C' for cytosine, 'G' for guanine, and 'T' for thymine.
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Given a string representing a DNA sequence, count how many of each nucleotide is present.
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If the string contains characters that aren't A, C, G, or T then it is invalid and you should signal an error.
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For example:
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```text
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"GATTACA" -> 'A': 3, 'C': 1, 'G': 1, 'T': 2
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"INVALID" -> error
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```
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## Elixir-specific changes
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Error handling has been omitted from this exercise for the sake of simplicity.
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## Source
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### Created by
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- @rubysolo
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### Contributed to by
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- @andrewsardone
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- @angelikatyborska
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- @Cohen-Carlisle
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- @dalexj
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- @dantswain
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- @devonestes
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- @henrik
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- @jinyeow
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- @kytrinyx
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- @leikind
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- @lpil
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- @MarcosX
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- @neenjaw
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- @nimser
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- @parkerl
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- @rud
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- @sotojuan
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- @Teapane
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- @toriejw
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- @waiting-for-dev
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### Based on
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The Calculating DNA Nucleotides_problem at Rosalind - https://rosalind.info/problems/dna/
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defmodule NucleotideCount do
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@nucleotides [?A, ?C, ?G, ?T]
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@doc """
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Counts individual nucleotides in a DNA strand.
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## Examples
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iex> NucleotideCount.count(~c"AATAA", ?A)
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4
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iex> NucleotideCount.count(~c"AATAA", ?T)
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1
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"""
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@spec count(charlist(), char()) :: non_neg_integer()
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def count(strand, nucleotide), do: Enum.count(strand, &(&1 == nucleotide))
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@doc """
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Returns a summary of counts by nucleotide.
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## Examples
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iex> NucleotideCount.histogram(~c"AATAA")
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%{?A => 4, ?T => 1, ?C => 0, ?G => 0}
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"""
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@spec histogram(charlist()) :: map()
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def histogram(strand) do
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for nucleotide <- @nucleotides, into: %{}, do: {nucleotide, count(strand, nucleotide)}
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end
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end
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defmodule NucleotideCount.MixProject do
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use Mix.Project
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def project do
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[
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app: :nucleotide_count,
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version: "0.1.0",
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# elixir: "~> 1.8",
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start_permanent: Mix.env() == :prod,
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deps: deps()
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]
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end
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# Run "mix help compile.app" to learn about applications.
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def application do
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[
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extra_applications: [:logger]
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]
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end
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# Run "mix help deps" to learn about dependencies.
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defp deps do
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[
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# {:dep_from_hexpm, "~> 0.3.0"},
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# {:dep_from_git, git: "https://github.com/elixir-lang/my_dep.git", tag: "0.1.0"}
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]
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end
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end
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defmodule NucleotideCountTest do
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use ExUnit.Case
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describe "count" do
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test "empty dna string has no adenine" do
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assert NucleotideCount.count(~c"", ?A) == 0
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end
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test "one nucleotide" do
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assert NucleotideCount.count(~c"G", ?G) == 1
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end
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test "repetitive cytosine gets counted" do
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assert NucleotideCount.count(~c"CCCCC", ?C) == 5
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end
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test "counts only thymine" do
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assert NucleotideCount.count(~c"GGGGGTAACCCGG", ?T) == 1
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end
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end
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describe "histogram" do
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test "empty dna string has no nucleotides" do
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expected = %{?A => 0, ?T => 0, ?C => 0, ?G => 0}
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assert NucleotideCount.histogram(~c"") == expected
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end
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test "one nucleotide" do
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expected = %{?A => 0, ?T => 0, ?C => 0, ?G => 1}
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assert NucleotideCount.histogram(~c"G") == expected
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end
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test "repetitive sequence has only guanine" do
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expected = %{?A => 0, ?T => 0, ?C => 0, ?G => 8}
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assert NucleotideCount.histogram(~c"GGGGGGGG") == expected
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end
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test "counts all nucleotides" do
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s = ~c"AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC"
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expected = %{?A => 20, ?T => 21, ?C => 12, ?G => 17}
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assert NucleotideCount.histogram(s) == expected
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end
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end
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end
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ExUnit.start()
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ExUnit.configure(exclude: :pending, trace: true)
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