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
Execute the tests with:
$ mix test
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
If you're stuck on something, it may help to look at some of the available resources out there where answers might be found.
Tyler Long
It's possible to submit an incomplete solution so you can see how others have completed the exercise.
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
ExUnit.start()
ExUnit.configure(exclude: :pending, trace: true)
defmodule ProteinTranslation do
@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(rna) do
case do_of_rna(rna, []) do
{:error, _} -> {:error, "invalid RNA"}
{:ok, translation} -> {:ok, Enum.reverse(translation)}
end
end
defp do_of_rna("", acc), do: {:ok, acc}
defp do_of_rna(<<codon::binary-size(3), rest::binary>>, acc) do
case of_codon(codon) do
{:ok, "STOP"} -> {:ok, acc}
{:ok, translation} -> do_of_rna(rest, [translation | acc])
{:error, reason} -> {:error, reason}
end
end
defp do_of_rna(_, _), do: {:error, "malformed input"}
@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
"""
@spec of_codon(String.t()) :: { atom, String.t() }
def of_codon(codon) do
case codon do
codon when codon in ~w(UGU UGC) -> {:ok, "Cysteine"}
codon when codon in ~w(UUA UUG) -> {:ok, "Leucine"}
codon when codon in ~w(AUG) -> {:ok, "Methionine"}
codon when codon in ~w(UUU UUC) -> {:ok, "Phenylalanine"}
codon when codon in ~w(UCU UCC UCA UCG) -> {:ok, "Serine"}
codon when codon in ~w(UGG) -> {:ok, "Tryptophan"}
codon when codon in ~w(UAU UAC) -> {:ok, "Tyrosine"}
codon when codon in ~w(UAA UAG UGA) -> {:ok, "STOP"}
_ -> { :error, "invalid codon" }
end
end
end
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Community comments
I like a lot those guard clauses in of_codon.