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Add protein-translation exercise
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BNAndras committed Feb 6, 2024
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8 changes: 8 additions & 0 deletions config.json
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"practices": [],
"prerequisites": [],
"difficulty": 2
},
{
"slug": "protein-translation",
"name": "Protein Translation",
"uuid": "53835da9-e270-4fba-9fcd-b81050ebf764",
"practices": [],
"prerequisites": [],
"difficulty": 2
}
]
},
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45 changes: 45 additions & 0 deletions exercises/practice/protein-translation/.docs/instructions.md
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# 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)
18 changes: 18 additions & 0 deletions exercises/practice/protein-translation/.meta/config.json
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{
"authors": [
"BNAndras"
],
"files": {
"solution": [
"protein-translation.jl"
],
"test": [
"runtests.jl"
],
"example": [
".meta/example.jl"
]
},
"blurb": "Translate RNA sequences into proteins.",
"source": "Tyler Long"
}
35 changes: 35 additions & 0 deletions exercises/practice/protein-translation/.meta/example.jl
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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")
101 changes: 101 additions & 0 deletions exercises/practice/protein-translation/.meta/tests.toml
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# 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
3 changes: 3 additions & 0 deletions exercises/practice/protein-translation/protein-translation.jl
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function proteins(strand)

end
121 changes: 121 additions & 0 deletions exercises/practice/protein-translation/runtests.jl
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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

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