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
Execute the tests with:
$ elixir protein_translation_test.exs
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.
Tyler Long
It's possible to submit an incomplete solution so you can see how others have completed the exercise.
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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