Added protein translation practice exercise

config.json

@@ -866,6 +866,14 @@
           "variables"
         ]
       },
+      {
+        "slug": "protein-translation",
+        "name": "Protein Translation",
+        "uuid": "98b2f717-2630-4f28-a5f2-e51047b59a56",
+        "practices": [],
+        "prerequisites": [],
+        "difficulty": 2
+      },
       {
         "slug": "space-age",
         "name": "Space Age",

exercises/practice/protein-translation/.docs/instructions.append.md

@@ -0,0 +1,19 @@
+# Instructions append
+
+## Bonus
+
+You might like to use this exercise as an excuse to experiment with [non-standard string literals][nssl].
+A short introduction to non-standard string literals can be found in this [blog post][nssl-blog].
+
+To pass the bonus tests, define a macro `rna_str` as explained in the links above, then your users could write code like this:
+
+```julia
+rna"AUGUGU" == ["Methionine", "Cysteine"]
+
+rna"""
+AUGUUUUCUUAAAUG
+""" == ["Methionine", "Phenylalanine", "Serine"]
+```
+
+[nssl]: https://docs.julialang.org/en/v1/manual/metaprogramming/#meta-non-standard-string-literals
+[nssl-blog]: https://web.archive.org/web/20170625222109/https://iaindunning.com/blog/julia-unicode.html

exercises/practice/protein-translation/.docs/instructions.md

@@ -0,0 +1,45 @@
+# 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)

exercises/practice/protein-translation/.meta/config.json

@@ -0,0 +1,16 @@
+{
+  "authors": [],
+  "files": {
+    "solution": [
+      "protein-translation.jl"
+    ],
+    "test": [
+      "runtests.jl"
+    ],
+    "example": [
+      ".meta/example.jl"
+    ]
+  },
+  "blurb": "Translate RNA sequences into proteins.",
+  "source": "Tyler Long"
+}

exercises/practice/protein-translation/.meta/example.jl

@@ -0,0 +1,48 @@
+const codon_protein_dict = Dict(
+    "AUG" => "Methionine",
+    "UUU" => "Phenylalanine",
+    "UUC" => "Phenylalanine",
+    "UUA" => "Leucine",
+    "UUG" => "Leucine",
+    "UCU" => "Serine",
+    "UCC" => "Serine",
+    "UCA" => "Serine",
+    "UCG" => "Serine",
+    "UAU" => "Tyrosine",
+    "UAC" => "Tyrosine",
+    "UGU" => "Cysteine",
+    "UGC" => "Cysteine",
+    "UGG" => "Tryptophan",
+    "UAA" => "STOP",
+    "UAG" => "STOP",
+    "UGA" => "STOP"
+)
+
+struct TranslationError <: Exception
+    message::String
+end
+
+
+function rna_to_amino_acids(str)
+    n = 3
+    result = []
+    for i=1:n:length(str)
+        substring = try
+            SubString(str, i, i+n-1)
+        catch
+            throw(TranslationError("invalid rna string"))
+        end
+        protein = string_to_protein(substring)
+        protein == "STOP" && break
+        push!(result, protein)
+    end
+    result
+
+end
+
+
+function string_to_protein(str)
+    p = get(codon_protein_dict, str, nothing)
+    p === nothing && throw(TranslationError("invalid codon"))
+    return p
+end

exercises/practice/protein-translation/.meta/tests.toml

@@ -0,0 +1,100 @@
+# This is an auto-generated file.
+#
+# Regenerating this file via `configlet sync` will:
+# - Recreate every `description` key/value pair
+# - Recreate every `reimplements` key/value pair, where they exist in problem-specifications
+# - Remove any `include = true` key/value pair (an omitted `include` key implies inclusion)
+# - Preserve any other key/value pair
+#
+# As user-added comments (using the # character) will be removed when this file
+# is regenerated, comments can be added via a `comment` key.
+
+[2c44f7bf-ba20-43f7-a3bf-f2219c0c3f98]
+description = "Empty RNA sequence results in no proteins"
+
+[96d3d44f-34a2-4db4-84cd-fff523e069be]
+description = "Methionine RNA sequence"
+
+[1b4c56d8-d69f-44eb-be0e-7b17546143d9]
+description = "Phenylalanine RNA sequence 1"
+
+[81b53646-bd57-4732-b2cb-6b1880e36d11]
+description = "Phenylalanine RNA sequence 2"
+
+[42f69d4f-19d2-4d2c-a8b0-f0ae9ee1b6b4]
+description = "Leucine RNA sequence 1"
+
+[ac5edadd-08ed-40a3-b2b9-d82bb50424c4]
+description = "Leucine RNA sequence 2"
+
+[8bc36e22-f984-44c3-9f6b-ee5d4e73f120]
+description = "Serine RNA sequence 1"
+
+[5c3fa5da-4268-44e5-9f4b-f016ccf90131]
+description = "Serine RNA sequence 2"
+
+[00579891-b594-42b4-96dc-7ff8bf519606]
+description = "Serine RNA sequence 3"
+
+[08c61c3b-fa34-4950-8c4a-133945570ef6]
+description = "Serine RNA sequence 4"
+
+[54e1e7d8-63c0-456d-91d2-062c72f8eef5]
+description = "Tyrosine RNA sequence 1"
+
+[47bcfba2-9d72-46ad-bbce-22f7666b7eb1]
+description = "Tyrosine RNA sequence 2"
+
+[3a691829-fe72-43a7-8c8e-1bd083163f72]
+description = "Cysteine RNA sequence 1"
+
+[1b6f8a26-ca2f-43b8-8262-3ee446021767]
+description = "Cysteine RNA sequence 2"
+
+[1e91c1eb-02c0-48a0-9e35-168ad0cb5f39]
+description = "Tryptophan RNA sequence"
+
+[e547af0b-aeab-49c7-9f13-801773a73557]
+description = "STOP codon RNA sequence 1"
+
+[67640947-ff02-4f23-a2ef-816f8a2ba72e]
+description = "STOP codon RNA sequence 2"
+
+[9c2ad527-ebc9-4ace-808b-2b6447cb54cb]
+description = "STOP codon RNA sequence 3"
+
+[f4d9d8ee-00a8-47bf-a1e3-1641d4428e54]
+description = "Sequence of two protein codons translates into proteins"
+
+[dd22eef3-b4f1-4ad6-bb0b-27093c090a9d]
+description = "Sequence of two different protein codons translates into proteins"
+
+[d0f295df-fb70-425c-946c-ec2ec185388e]
+description = "Translate RNA strand into correct protein list"
+
+[e30e8505-97ec-4e5f-a73e-5726a1faa1f4]
+description = "Translation stops if STOP codon at beginning of sequence"
+
+[5358a20b-6f4c-4893-bce4-f929001710f3]
+description = "Translation stops if STOP codon at end of two-codon sequence"
+
+[ba16703a-1a55-482f-bb07-b21eef5093a3]
+description = "Translation stops if STOP codon at end of three-codon sequence"
+
+[4089bb5a-d5b4-4e71-b79e-b8d1f14a2911]
+description = "Translation stops if STOP codon in middle of three-codon sequence"
+
+[2c2a2a60-401f-4a80-b977-e0715b23b93d]
+description = "Translation stops if STOP codon in middle of six-codon sequence"
+
+[1e75ea2a-f907-4994-ae5c-118632a1cb0f]
+description = "Non-existing codon can't translate"
+
+[9eac93f3-627a-4c90-8653-6d0a0595bc6f]
+description = "Unknown amino acids, not part of a codon, can't translate"
+
+[9d73899f-e68e-4291-b1e2-7bf87c00f024]
+description = "Incomplete RNA sequence can't translate"
+
+[43945cf7-9968-402d-ab9f-b8a28750b050]
+description = "Incomplete RNA sequence can translate if valid until a STOP codon"

exercises/practice/protein-translation/protein-translation.jl

@@ -0,0 +1,3 @@
+function rna_to_amino_acids(rna::String)
+    # I'm a ribosome function!
+end

exercises/practice/protein-translation/runtests.jl

@@ -0,0 +1,88 @@
+using Test
+
+include("protein-translation.jl")
+
+@testset "Protein Translation" begin
+
+    @testset "Empty RNA sequence returns an empty list" begin
+        @test rna_to_amino_acids("") == []
+    end
+
+    @testset "Methionine RNA sequence is decoded as Methionine" begin
+        @test rna_to_amino_acids("AUG") == ["Methionine"]
+    end
+
+    @testset "Phenylalanine RNA sequence is decoded as Phenylalanine" begin
+        @test rna_to_amino_acids("UUUUUC") == ["Phenylalanine", "Phenylalanine"]
+    end
+
+    @testset "Leucine RNA sequence is decoded as Leucine" begin
+        @test rna_to_amino_acids("UUA") == ["Leucine"]
+    end
+
+    @testset "Leucine RNA sequence is decoded as Leucine" begin
+        @test rna_to_amino_acids("UUG") == ["Leucine"]
+    end
+
+    @testset "Serine RNA sequence is decoded as Serine" begin
+        @test rna_to_amino_acids("UCUUCCUCAUCG") == ["Serine", "Serine", "Serine", "Serine"]
+    end
+
+    @testset "Tyrosine RNA sequence is decoded as Tyrosine" begin
+        @test rna_to_amino_acids("UAUUAC") == ["Tyrosine", "Tyrosine"]
+    end
+
+    @testset "Cysteine RNA sequence is decoded as Cysteine" begin
+        @test rna_to_amino_acids("UGUUGC") == ["Cysteine", "Cysteine"]
+    end
+
+    @testset "Tryptophan RNA sequence is decoded as Tryptophan" begin
+        @test rna_to_amino_acids("UGG") == ["Tryptophan"]
+    end
+
+    @testset "STOP codon terminates translation" begin
+        @test rna_to_amino_acids("UAA") == []
+        @test rna_to_amino_acids("UAG") == []
+        @test rna_to_amino_acids("UGA") == []
+    end
+
+    @testset "Sequence of two codons translates into proteins" begin
+        @test rna_to_amino_acids("UUUUUUUGA") == ["Phenylalanine", "Phenylalanine"]
+    end
+
+    @testset "Sequence of two different codons translates into proteins" begin
+        @test rna_to_amino_acids("UUAUUUUAG") == ["Leucine", "Phenylalanine"]
+    end
+
+    @testset "Translation stops if STOP codon appears in middle of sequence" begin
+        @test rna_to_amino_acids("UGGUAAUGCAUG") == ["Tryptophan"]
+    end
+
+    @testset "Translation stops if STOP codon appears at beginning of sequence" begin
+        @test rna_to_amino_acids("UAGUAUUCGUCAUCU") == []
+    end
+
+    @testset "Translation stops if STOP codon appears at end of two-codon sequence" begin
+        @test rna_to_amino_acids("UGGUGUUGA") == ["Tryptophan", "Cysteine"]
+    end
+
+    @testset "Non existent codon causes translation exception" begin
+        @test_throws ArgumentError rna_to_amino_acids("AAA")
+    end
+
+    @testset "Incomplete codon causes translation exception" begin
+        @test_throws ArgumentError rna_to_amino_acids("UGUU")
+    end
+
+    @testset "Incomplete RNA sequence can translate if given a stop codon" begin
+        @test rna_to_amino_acids("UGGUGAUG") == ["Tryptophan"]
+    end
+
+    # Bonus
+    if isdefined(@__MODULE__, Symbol("@rna_str"))
+        @eval @testset "Bonus: rna string macro" begin
+            @test rna"AUGUUUUUAUGGUACUAG" == ["Methionine", "Phenylalanine", "Leucine", "Tryptophan", "Tyrosine"]
+        end
+    end
+
+end