protein-translation

elixir/protein-translation/.exercism/config.json

@@ -0,0 +1,26 @@
+{
+  "authors": [
+    "DoggettCK"
+  ],
+  "contributors": [
+    "angelikatyborska",
+    "Cohen-Carlisle",
+    "devonestes",
+    "neenjaw",
+    "nwshane",
+    "sotojuan"
+  ],
+  "files": {
+    "solution": [
+      "lib/protein_translation.ex"
+    ],
+    "test": [
+      "test/protein_translation_test.exs"
+    ],
+    "example": [
+      ".meta/example.ex"
+    ]
+  },
+  "blurb": "Translate RNA sequences into proteins.",
+  "source": "Tyler Long"
+}

elixir/protein-translation/.exercism/metadata.json

@@ -0,0 +1 @@
+{"track":"elixir","exercise":"protein-translation","id":"b19fcedc09cb4e6ab1ed560eaeb5cdec","url":"https://exercism.org/tracks/elixir/exercises/protein-translation","handle":"negrienko","is_requester":true,"auto_approve":false}

elixir/protein-translation/.formatter.exs

@@ -0,0 +1,4 @@
+# Used by "mix format"
+[
+  inputs: ["{mix,.formatter}.exs", "{config,lib,test}/**/*.{ex,exs}"]
+]

elixir/protein-translation/.gitignore

@@ -0,0 +1,24 @@
+# The directory Mix will write compiled artifacts to.
+/_build/
+
+# If you run "mix test --cover", coverage assets end up here.
+/cover/
+
+# The directory Mix downloads your dependencies sources to.
+/deps/
+
+# Where third-party dependencies like ExDoc output generated docs.
+/doc/
+
+# Ignore .fetch files in case you like to edit your project deps locally.
+/.fetch
+
+# If the VM crashes, it generates a dump, let's ignore it too.
+erl_crash.dump
+
+# Also ignore archive artifacts (built via "mix archive.build").
+*.ez
+
+# Ignore package tarball (built via "mix hex.build").
+protein_translation-*.tar
+

elixir/protein-translation/HELP.md

@@ -0,0 +1,75 @@
+# Help
+
+## Running the tests
+
+From the terminal, change to the base directory of the exercise then execute the tests with:
+
+```bash
+$ mix test
+```
+
+This will execute the test file found in the `test` subfolder -- a file ending in `_test.exs`
+
+Documentation:
+
+* [`mix test` - Elixir's test execution tool](https://hexdocs.pm/mix/Mix.Tasks.Test.html)
+* [`ExUnit` - Elixir's unit test library](https://hexdocs.pm/ex_unit/ExUnit.html)
+
+## Pending tests
+
+In test suites of practice exercises, all but the first test have been tagged to be 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:
+
+```elixir
+# @tag :pending
+test "shouting" do
+  assert Bob.hey("WATCH OUT!") == "Whoa, chill out!"
+end
+```
+
+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:
+
+```bash
+$ mix test --include pending
+```
+
+Or, you can enable all the tests by commenting out the `ExUnit.configure` line in the file `test/test_helper.exs`.
+
+```elixir
+# ExUnit.configure(exclude: :pending, trace: true)
+```
+
+## Useful `mix test` options
+
+* `test/<FILE>.exs:LINENUM` - runs only a single test, the test from `<FILE>.exs` whose definition is on line `LINENUM`
+* `--failed` - runs only tests that failed the last time they ran
+* `--max-failures` - the suite stops evaluating tests when this number of test failures
+is reached
+* `--seed 0` - disables randomization so the tests in a single file will always be ran
+in the same order they were defined in
+
+## Submitting your solution
+
+You can submit your solution using the `exercism submit lib/protein_translation.ex` command.
+This command will upload your solution to the Exercism website and print the solution page's URL.
+
+It's possible to submit an incomplete solution which allows you to:
+
+- See how others have completed the exercise
+- Request help from a mentor
+
+## Need to get help?
+
+If you'd like help solving the exercise, check the following pages:
+
+- The [Elixir track's documentation](https://exercism.org/docs/tracks/elixir)
+- The [Elixir track's programming category on the forum](https://forum.exercism.org/c/programming/elixir)
+- [Exercism's programming category on the forum](https://forum.exercism.org/c/programming/5)
+- The [Frequently Asked Questions](https://exercism.org/docs/using/faqs)
+
+Should those resources not suffice, you could submit your (incomplete) solution to request mentoring.
+
+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.

elixir/protein-translation/README.md

@@ -0,0 +1,69 @@
+# Protein Translation
+
+Welcome to Protein Translation on Exercism's Elixir Track.
+If you need help running the tests or submitting your code, check out `HELP.md`.
+
+## Instructions
+
+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", "UAA", "AUG"` =>
+
+Protein: `"Methionine", "Phenylalanine", "Serine"`
+
+Note the stop codon `"UAA"` 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][protein-translation].
+
+[protein-translation]: https://en.wikipedia.org/wiki/Translation_(biology)
+
+## Source
+
+### Created by
+
+- @DoggettCK
+
+### Contributed to by
+
+- @angelikatyborska
+- @Cohen-Carlisle
+- @devonestes
+- @neenjaw
+- @nwshane
+- @sotojuan
+
+### Based on
+
+Tyler Long

elixir/protein-translation/lib/protein_translation.ex

@@ -0,0 +1,68 @@
+defmodule ProteinTranslation do
+  @doc """
+  Given an RNA string, return a list of proteins specified by codons, in order.
+  """
+  @spec of_rna(String.t()) :: {:ok, list(String.t())} | {:error, String.t()}
+  def of_rna(""), do: {:ok, []}
+
+  def of_rna(rna) do
+    rna
+    |> String.graphemes()
+    |> Enum.chunk_every(3)
+    |> Enum.map(&Enum.join/1)
+    |> Enum.reduce_while([], &reducer/2)
+    |> case do
+      proteines when is_list(proteines) -> {:ok, Enum.reverse(proteines)}
+      {:error, error} -> {:error, error}
+    end
+  end
+
+  defp reducer(codon, proteines) do
+    case of_codon(codon) do
+      {:error, _error} -> {:halt, {:error, "invalid RNA"}}
+      {:ok, "STOP"} -> {:halt, proteines}
+      {:ok, proteine} -> {:cont, [proteine | proteines]}
+    end
+  end
+
+  @doc """
+  Given a codon, return the corresponding protein
+
+  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
+  """
+  @cysteines ~w(UGU UGC)
+  @leucines ~w(UUA UUG)
+  @tyrosines ~w(UAU UAC)
+  @phenylalanines ~w(UUU UUC)
+  @serines ~w(UCU UCC UCA UCG)
+  @methionines ~w(AUG)
+  @tryptophans ~w(UGG)
+  @stops ~w(UAA UAG UGA)
+
+  @spec of_codon(String.t()) :: {:ok, String.t()} | {:error, String.t()}
+  def of_codon(cysteine) when cysteine in @cysteines, do: {:ok, "Cysteine"}
+  def of_codon(leucine) when leucine in @leucines, do: {:ok, "Leucine"}
+  def of_codon(tyrosine) when tyrosine in @tyrosines, do: {:ok, "Tyrosine"}
+  def of_codon(phenylalanine) when phenylalanine in @phenylalanines, do: {:ok, "Phenylalanine"}
+  def of_codon(serine) when serine in @serines, do: {:ok, "Serine"}
+  def of_codon(methionine) when methionine in @methionines, do: {:ok, "Methionine"}
+  def of_codon(tryptophan) when tryptophan in @tryptophans, do: {:ok, "Tryptophan"}
+  def of_codon(stop) when stop in @stops, do: {:ok, "STOP"}
+  def of_codon(_invalid), do: {:error, "invalid codon"}
+end

elixir/protein-translation/mix.exs

@@ -0,0 +1,28 @@
+defmodule ProteinTranslation.MixProject do
+  use Mix.Project
+
+  def project do
+    [
+      app: :protein_translation,
+      version: "0.1.0",
+      # elixir: "~> 1.8",
+      start_permanent: Mix.env() == :prod,
+      deps: deps()
+    ]
+  end
+
+  # Run "mix help compile.app" to learn about applications.
+  def application do
+    [
+      extra_applications: [:logger]
+    ]
+  end
+
+  # Run "mix help deps" to learn about dependencies.
+  defp deps do
+    [
+      # {:dep_from_hexpm, "~> 0.3.0"},
+      # {:dep_from_git, git: "https://github.com/elixir-lang/my_dep.git", tag: "0.1.0"}
+    ]
+  end
+end

elixir/protein-translation/test/protein_translation_test.exs

@@ -0,0 +1,139 @@
+defmodule ProteinTranslationTest do
+  use ExUnit.Case
+
+  describe "of_codon" do
+    test "AUG translates to methionine" do
+      assert ProteinTranslation.of_codon("AUG") == {:ok, "Methionine"}
+    end
+
+    test "identifies Phenylalanine codons" do
+      assert ProteinTranslation.of_codon("UUU") == {:ok, "Phenylalanine"}
+      assert ProteinTranslation.of_codon("UUC") == {:ok, "Phenylalanine"}
+    end
+
+    test "identifies Leucine codons" do
+      assert ProteinTranslation.of_codon("UUA") == {:ok, "Leucine"}
+      assert ProteinTranslation.of_codon("UUG") == {:ok, "Leucine"}
+    end
+
+    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
+
+    test "identifies Tyrosine codons" do
+      assert ProteinTranslation.of_codon("UAU") == {:ok, "Tyrosine"}
+      assert ProteinTranslation.of_codon("UAC") == {:ok, "Tyrosine"}
+    end
+
+    test "identifies Cysteine codons" do
+      assert ProteinTranslation.of_codon("UGU") == {:ok, "Cysteine"}
+      assert ProteinTranslation.of_codon("UGC") == {:ok, "Cysteine"}
+    end
+
+    test "identifies Tryptophan codons" do
+      assert ProteinTranslation.of_codon("UGG") == {:ok, "Tryptophan"}
+    end
+
+    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
+
+    test "incomplete codon" do
+      assert ProteinTranslation.of_codon("UG") == {:error, "invalid codon"}
+    end
+
+    test "too long, invalid codon" do
+      assert ProteinTranslation.of_codon("UGGG") == {:error, "invalid codon"}
+    end
+
+    test "known amino acids, but invalid codon" do
+      assert ProteinTranslation.of_codon("AAA") == {:error, "invalid codon"}
+    end
+
+    test "unknown amino acids, not part of a codon" do
+      assert ProteinTranslation.of_codon("XYZ") == {:error, "invalid codon"}
+    end
+  end
+
+  describe "of_rna" do
+    test "empty RNA sequence results in no proteins" do
+      strand = ""
+      assert ProteinTranslation.of_rna(strand) == {:ok, []}
+    end
+
+    test "translates rna strand into correct protein" do
+      strand = "AUGUUUUGG"
+      assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Methionine Phenylalanine Tryptophan)}
+    end
+
+    test "sequence of two identical protein codons translates into two identical proteins" do
+      strand = "UUUUUU"
+      assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Phenylalanine Phenylalanine)}
+    end
+
+    test "sequence of two different protein codons translates into two identical proteins" do
+      strand = "UUAUUG"
+      assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Leucine Leucine)}
+    end
+
+    test "stops translation if stop codon preset at beginning of sequence" do
+      strand = "UAGUGG"
+      assert ProteinTranslation.of_rna(strand) == {:ok, ~w()}
+    end
+
+    test "stops translation if stop codon present at end of two-codon sequence" do
+      strand = "UGGUAG"
+      assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Tryptophan)}
+    end
+
+    test "stops translation if stop codon present at end of three-codon sequence" do
+      strand = "AUGUUUUAA"
+      assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Methionine Phenylalanine)}
+    end
+
+    test "stops translation if stop codon present in middle of three-codon sequence" do
+      strand = "UGGUAGUGG"
+      assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Tryptophan)}
+    end
+
+    test "stops translation if stop codon present in middle of six-codon sequence" do
+      strand = "UGGUGUUAUUAAUGGUUU"
+      assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Tryptophan Cysteine Tyrosine)}
+    end
+
+    test "incomplete codon, invalid RNA" do
+      strand = "UG"
+      assert ProteinTranslation.of_rna(strand) == {:error, "invalid RNA"}
+    end
+
+    test "known amino acids, but invalid codon, invalid RNA" do
+      strand = "AAA"
+      assert ProteinTranslation.of_rna(strand) == {:error, "invalid RNA"}
+    end
+
+    test "unknown amino acids, not part of a codon, invalid RNA" do
+      strand = "XYZ"
+      assert ProteinTranslation.of_rna(strand) == {:error, "invalid RNA"}
+    end
+
+    test "invalid codon at end of RNA" do
+      strand = "UUUROT"
+      assert ProteinTranslation.of_rna(strand) == {:error, "invalid RNA"}
+    end
+
+    test "incomplete RNA" do
+      strand = "AUGU"
+      assert ProteinTranslation.of_rna(strand) == {:error, "invalid RNA"}
+    end
+
+    test "incomplete RNA valid until a STOP codon" do
+      strand = "UUCUUCUAAUGGU"
+      assert ProteinTranslation.of_rna(strand) == {:ok, ~w(Phenylalanine Phenylalanine)}
+    end
+  end
+end

elixir/protein-translation/test/test_helper.exs

@@ -0,0 +1,2 @@
+ExUnit.start()
+ExUnit.configure(exclude: :pending, trace: true)