thekeele's solution to Protein Translation on the Elixir track

Instructions

Test suite

Solution

Note:

This solution was written on an old version of Exercism. The tests below might not correspond to the solution code, and the exercise may have changed since this code was written.

Translate RNA sequences into proteins.

RNA can be broken into three nucleotide sequences called codons, and then translated to a polypeptide like so:

RNA: "AUGUUUUCU" => translates to

Codons: "AUG", "UUU", "UCU" => which become a polypeptide with the following sequence =>

Protein: "Methionine", "Phenylalanine", "Serine"

There are 64 codons which in turn correspond to 20 amino acids; however, all of the codon sequences and resulting amino acids are not important in this exercise. If it works for one codon, the program should work for all of them. However, feel free to expand the list in the test suite to include them all.

There are also three terminating codons (also known as 'STOP' codons); if any of these codons are encountered (by the ribosome), all translation ends and the protein is terminated.

All subsequent codons after are ignored, like this:

RNA: "AUGUUUUCUUAAAUG" =>

Codons: "AUG", "UUU", "UCU", "UAG", "AUG" =>

Protein: "Methionine", "Phenylalanine", "Serine"

Note the stop codon terminates the translation and the final methionine is not translated into the protein sequence.

Below are the codons and resulting Amino Acids needed for the exercise.

Codon	Protein
AUG	Methionine
UUU, UUC	Phenylalanine
UUA, UUG	Leucine
UCU, UCC, UCA, UCG	Serine
UAU, UAC	Tyrosine
UGU, UGC	Cysteine
UGG	Tryptophan
UAA, UAG, UGA	STOP

Learn more about protein translation on Wikipedia

Running tests

Execute the tests with:

$ elixir protein_translation_test.exs

Pending tests

In the test suites, all but the first test have been skipped.

Once you get a test passing, you can unskip the next one by commenting out the relevant @tag :pending with a # symbol.

For example:

# @tag :pending
test "shouting" do
  assert Bob.hey("WATCH OUT!") == "Whoa, chill out!"
end

Or, you can enable all the tests by commenting out the ExUnit.configure line in the test suite.

# ExUnit.configure exclude: :pending, trace: true

For more detailed information about the Elixir track, please see the help page.

Source

Tyler Long

Submitting Incomplete Solutions

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

protein_translation_test.exs

if !System.get_env("EXERCISM_TEST_EXAMPLES") do
  Code.load_file("protein_translation.exs", __DIR__)
end

ExUnit.start()
ExUnit.configure(exclude: :pending, trace: true)

defmodule ProteinTranslationTest do
  use ExUnit.Case

  # @tag :pending
  test "AUG translates to methionine" do
    assert ProteinTranslation.of_codon("AUG") == {:ok, "Methionine"}
  end

  @tag :pending
  test "identifies Phenylalanine codons" do
    assert ProteinTranslation.of_codon("UUU") == {:ok, "Phenylalanine"}
    assert ProteinTranslation.of_codon("UUC") == {:ok, "Phenylalanine"}
  end

  @tag :pending
  test "identifies Leucine codons" do
    assert ProteinTranslation.of_codon("UUA") == {:ok, "Leucine"}
    assert ProteinTranslation.of_codon("UUG") == {:ok, "Leucine"}
  end

  @tag :pending
  test "identifies Serine codons" do
    assert ProteinTranslation.of_codon("UCU") == {:ok, "Serine"}
    assert ProteinTranslation.of_codon("UCC") == {:ok, "Serine"}
    assert ProteinTranslation.of_codon("UCA") == {:ok, "Serine"}
    assert ProteinTranslation.of_codon("UCG") == {:ok, "Serine"}
  end

  @tag :pending
  test "identifies Tyrosine codons" do
    assert ProteinTranslation.of_codon("UAU") == {:ok, "Tyrosine"}
    assert ProteinTranslation.of_codon("UAC") == {:ok, "Tyrosine"}
  end

  @tag :pending
  test "identifies Cysteine codons" do
    assert ProteinTranslation.of_codon("UGU") == {:ok, "Cysteine"}
    assert ProteinTranslation.of_codon("UGC") == {:ok, "Cysteine"}
  end

  @tag :pending
  test "identifies Tryptophan codons" do
    assert ProteinTranslation.of_codon("UGG") == {:ok, "Tryptophan"}
  end

  @tag :pending
  test "identifies stop codons" do
    assert ProteinTranslation.of_codon("UAA") == {:ok, "STOP"}
    assert ProteinTranslation.of_codon("UAG") == {:ok, "STOP"}
    assert ProteinTranslation.of_codon("UGA") == {:ok, "STOP"}
  end

  @tag :pending
  test "translates rna strand into correct protein" do
    strand = "AUGUUUUGG"
    assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Methionine Phenylalanine Tryptophan)}
  end

  @tag :pending
  test "stops translation if stop codon present" do
    strand = "AUGUUUUAA"
    assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Methionine Phenylalanine)}
  end

  @tag :pending
  test "stops translation of longer strand" do
    strand = "UGGUGUUAUUAAUGGUUU"
    assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Tryptophan Cysteine Tyrosine)}
  end

  @tag :pending
  test "invalid RNA" do
    assert ProteinTranslation.of_rna("CARROT") == {:error, "invalid RNA"}
  end

  @tag :pending
  test "invalid codon at end of RNA" do
    assert ProteinTranslation.of_rna("UUUROT") == {:error, "invalid RNA"}
  end

  @tag :pending
  test "invalid codon" do
    assert ProteinTranslation.of_codon("INVALID") == {:error, "invalid codon"}
  end
end

defmodule ProteinTranslation do
  @proteins %{
    "UGU" => "Cysteine",
    "UGC" => "Cysteine",
    "UUA" => "Leucine",
    "UUG" => "Leucine",
    "AUG" => "Methionine",
    "UUU" => "Phenylalanine",
    "UUC" => "Phenylalanine",
    "UCU" => "Serine",
    "UCC" => "Serine",
    "UCA" => "Serine",
    "UCG" => "Serine",
    "UGG" => "Tryptophan",
    "UAU" => "Tyrosine",
    "UAC" => "Tyrosine",
    "UAA" => "STOP",
    "UAG" => "STOP",
    "UGA" => "STOP"
  }
  @doc """
  Given an RNA string, return a list of proteins specified by codons, in order.
  """
  @spec of_rna(String.t()) :: { atom,  list(String.t()) }
  def of_rna(nil), do: {:error, "invalid RNA"}
  def of_rna(rna) do
    proteins = for <<codon::binary-size(3) <- rna>>, do: @proteins[codon]
    proteins = Enum.take_while(proteins, &(&1 != "STOP"))

    if nil in proteins, do: of_rna(nil), else: {:ok, proteins}
  end

  @doc """
  Given a codon, return the corresponding protein
  """
  @spec of_codon(String.t()) :: { atom, String.t() }
  def of_codon(codon) when byte_size(codon) == 3 do
    case @proteins[codon] do
      nil -> of_codon("")

      protein -> {:ok, protein}
    end
  end
  def of_codon(_), do: {:error, "invalid codon"}
end

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thekeele's solution

to Protein Translation in the Elixir Track