diff --git a/config.json b/config.json index c6540cc0..41933333 100644 --- a/config.json +++ b/config.json @@ -873,6 +873,14 @@ "practices": [], "prerequisites": [], "difficulty": 2 + }, + { + "slug": "protein-translation", + "name": "Protein Translation", + "uuid": "53835da9-e270-4fba-9fcd-b81050ebf764", + "practices": [], + "prerequisites": [], + "difficulty": 2 } ] }, diff --git a/exercises/practice/protein-translation/.docs/instructions.md b/exercises/practice/protein-translation/.docs/instructions.md new file mode 100644 index 00000000..7dc34d2e --- /dev/null +++ b/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) diff --git a/exercises/practice/protein-translation/.meta/config.json b/exercises/practice/protein-translation/.meta/config.json new file mode 100644 index 00000000..f1a16c9b --- /dev/null +++ b/exercises/practice/protein-translation/.meta/config.json @@ -0,0 +1,18 @@ +{ + "authors": [ + "BNAndras" + ], + "files": { + "solution": [ + "protein-translation.jl" + ], + "test": [ + "runtests.jl" + ], + "example": [ + ".meta/example.jl" + ] + }, + "blurb": "Translate RNA sequences into proteins.", + "source": "Tyler Long" +} diff --git a/exercises/practice/protein-translation/.meta/example.jl b/exercises/practice/protein-translation/.meta/example.jl new file mode 100644 index 00000000..2b1d34f0 --- /dev/null +++ b/exercises/practice/protein-translation/.meta/example.jl @@ -0,0 +1,35 @@ +function proteins(strand) + results = [] + for codon in join.(Iterators.partition(strand, 3)) + if !haskey(MAPPINGS, codon) + throw(DomainError("Invalid codon")) + end + + protein = MAPPINGS[codon] + if protein == "STOP" + return results + end + + push!(results, protein) + end + + results +end + +MAPPINGS = 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") diff --git a/exercises/practice/protein-translation/.meta/tests.toml b/exercises/practice/protein-translation/.meta/tests.toml new file mode 100644 index 00000000..adcb83c4 --- /dev/null +++ b/exercises/practice/protein-translation/.meta/tests.toml @@ -0,0 +1,101 @@ +# 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" +include = false \ No newline at end of file diff --git a/exercises/practice/protein-translation/protein-translation.jl b/exercises/practice/protein-translation/protein-translation.jl new file mode 100644 index 00000000..faa0281c --- /dev/null +++ b/exercises/practice/protein-translation/protein-translation.jl @@ -0,0 +1,3 @@ +function proteins(strand) + +end diff --git a/exercises/practice/protein-translation/runtests.jl b/exercises/practice/protein-translation/runtests.jl new file mode 100644 index 00000000..2e714fc5 --- /dev/null +++ b/exercises/practice/protein-translation/runtests.jl @@ -0,0 +1,121 @@ +using Test + +include("protein-translation.jl") + +@testset verbose = true "Protein Translation" begin + @testset "Empty RNA sequence results in no proteins" begin + @test proteins("") == [] + end + + @testset "Methionine RNA sequence" begin + @test proteins("AUG") == ["Methionine"] + end + + @testset "Phenylalanine RNA sequence 1" begin + @test proteins("UUU") == ["Phenylalanine"] + end + + @testset "Phenylalanine RNA sequence 2" begin + @test proteins("UUC") == ["Phenylalanine"] + end + + @testset "Leucine RNA sequence 1" begin + @test proteins("UUA") == ["Leucine"] + end + + @testset "Leucine RNA sequence 2" begin + @test proteins("UUG") == ["Leucine"] + end + + @testset "Serine RNA sequence 1" begin + @test proteins("UCU") == ["Serine"] + end + + @testset "Serine RNA sequence 2" begin + @test proteins("UCC") == ["Serine"] + end + + @testset "Serine RNA sequence 3" begin + @test proteins("UCA") == ["Serine"] + end + + @testset "Serine RNA sequence 4" begin + @test proteins("UCG") == ["Serine"] + end + + @testset "Tyrosine RNA sequence 1" begin + @test proteins("UAC") == ["Tyrosine"] + end + + @testset "Tyrosine RNA sequence 2" begin + @test proteins("UAC") == ["Tyrosine"] + end + + @testset "Cysteine RNA sequence 1" begin + @test proteins("UGU") == ["Cysteine"] + end + + @testset "Cysteine RNA sequence 2" begin + @test proteins("UGC") == ["Cysteine"] + end + + @testset "Tryptophan RNA sequence" begin + @test proteins("UGG") == ["Tryptophan"] + end + + @testset "STOP codon RNA sequence 1" begin + @test proteins("UAA") == [] + end + + @testset "STOP codon RNA sequence 2" begin + @test proteins("UAG") == [] + end + + @testset "STOP codon RNA sequence 3" begin + @test proteins("UGA") == [] + end + + @testset "Sequence of two protein codons translates into proteins" begin + @test proteins("UUUUUU") == ["Phenylalanine", "Phenylalanine"] + end + + @testset "Sequence of two different protein codons translates into proteins" begin + @test proteins("UUAUUG") == ["Leucine", "Leucine"] + end + + @testset "Translate RNA strand into correct protein list" begin + @test proteins("AUGUUUUGG") == ["Methionine", "Phenylalanine", "Tryptophan"] + end + + @testset "Translation stops if STOP codon is at beginning of sequence" begin + @test proteins("UAGUGG") == [] + end + + @testset "Translation stops if STOP codon is at end of two-codon sequence" begin + @test proteins("UGGUAG") == ["Tryptophan"] + end + + @testset "Translation stops if STOP codon is at end of three-codon sequence" begin + @test proteins("AUGUUUUAA") == ["Methionine", "Phenylalanine"] + end + + @testset "Translation stops if STOP codon is in middle of three-codon sequence" begin + @test proteins("UGGUAGUGG") == ["Tryptophan"] + end + + @testset "Translation stops if STOP codon is in middle of six-codon sequence" begin + @test proteins("UGGUGUUAUUAAUGGUUU") == ["Tryptophan", "Cysteine", "Tyrosine"] + end + + @testset "Non-existing codon can't translate" begin + @test_throws DomainError proteins("AAA") + end + + @testset "Unknown amino acids, not part of a codon, can't translate" begin + @test_throws DomainError proteins("XYZ") + end + + @testset "Incomplete RNA sequence can't translate" begin + @test_throws DomainError proteins("AUGU") + end +end