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Add protein-translation (#270)
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‎config.json

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"prerequisites": [],
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"difficulty": 2
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},
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{
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"slug": "protein-translation",
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"name": "Protein Translation",
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"uuid": "7ba9bb49-551d-47a9-9662-f66560d9d0c4",
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"practices": [],
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"prerequisites": [],
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"difficulty": 2
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},
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{
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"slug": "resistor-color",
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"name": "Resistor Color",

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

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# Instructions
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Translate RNA sequences into proteins.
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RNA can be broken into three nucleotide sequences called codons, and then translated to a polypeptide like so:
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RNA: `"AUGUUUUCU"` => translates to
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Codons: `"AUG", "UUU", "UCU"`
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=> which become a polypeptide with the following sequence =>
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Protein: `"Methionine", "Phenylalanine", "Serine"`
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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.
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If it works for one codon, the program should work for all of them.
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However, feel free to expand the list in the test suite to include them all.
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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.
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All subsequent codons after are ignored, like this:
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RNA: `"AUGUUUUCUUAAAUG"` =>
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Codons: `"AUG", "UUU", "UCU", "UAA", "AUG"` =>
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Protein: `"Methionine", "Phenylalanine", "Serine"`
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Note the stop codon `"UAA"` terminates the translation and the final methionine is not translated into the protein sequence.
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Below are the codons and resulting Amino Acids needed for the exercise.
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| Codon | Protein |
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| :----------------- | :------------ |
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| AUG | Methionine |
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| UUU, UUC | Phenylalanine |
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| UUA, UUG | Leucine |
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| UCU, UCC, UCA, UCG | Serine |
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| UAU, UAC | Tyrosine |
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| UGU, UGC | Cysteine |
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| UGG | Tryptophan |
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| UAA, UAG, UGA | STOP |
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Learn more about [protein translation on Wikipedia][protein-translation].
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[protein-translation]: https://en.wikipedia.org/wiki/Translation_(biology)

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

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{
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"authors": [
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"BNAndras"
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],
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"files": {
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"solution": [
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"source/protein_translation.d"
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],
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"test": [
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"source/protein_translation.d"
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],
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"example": [
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"example/protein_translation.d"
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]
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},
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"blurb": "Translate RNA sequences into proteins.",
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"source": "Tyler Long"
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}

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

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# This is an auto-generated file.
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#
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# Regenerating this file via `configlet sync` will:
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# - Recreate every `description` key/value pair
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# - Recreate every `reimplements` key/value pair, where they exist in problem-specifications
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# - Remove any `include = true` key/value pair (an omitted `include` key implies inclusion)
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# - Preserve any other key/value pair
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#
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# As user-added comments (using the # character) will be removed when this file
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# is regenerated, comments can be added via a `comment` key.
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[2c44f7bf-ba20-43f7-a3bf-f2219c0c3f98]
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description = "Empty RNA sequence results in no proteins"
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[96d3d44f-34a2-4db4-84cd-fff523e069be]
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description = "Methionine RNA sequence"
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[1b4c56d8-d69f-44eb-be0e-7b17546143d9]
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description = "Phenylalanine RNA sequence 1"
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[81b53646-bd57-4732-b2cb-6b1880e36d11]
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description = "Phenylalanine RNA sequence 2"
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[42f69d4f-19d2-4d2c-a8b0-f0ae9ee1b6b4]
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description = "Leucine RNA sequence 1"
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[ac5edadd-08ed-40a3-b2b9-d82bb50424c4]
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description = "Leucine RNA sequence 2"
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[8bc36e22-f984-44c3-9f6b-ee5d4e73f120]
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description = "Serine RNA sequence 1"
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[5c3fa5da-4268-44e5-9f4b-f016ccf90131]
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description = "Serine RNA sequence 2"
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[00579891-b594-42b4-96dc-7ff8bf519606]
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description = "Serine RNA sequence 3"
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[08c61c3b-fa34-4950-8c4a-133945570ef6]
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description = "Serine RNA sequence 4"
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[54e1e7d8-63c0-456d-91d2-062c72f8eef5]
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description = "Tyrosine RNA sequence 1"
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[47bcfba2-9d72-46ad-bbce-22f7666b7eb1]
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description = "Tyrosine RNA sequence 2"
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[3a691829-fe72-43a7-8c8e-1bd083163f72]
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description = "Cysteine RNA sequence 1"
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[1b6f8a26-ca2f-43b8-8262-3ee446021767]
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description = "Cysteine RNA sequence 2"
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[1e91c1eb-02c0-48a0-9e35-168ad0cb5f39]
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description = "Tryptophan RNA sequence"
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[e547af0b-aeab-49c7-9f13-801773a73557]
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description = "STOP codon RNA sequence 1"
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[67640947-ff02-4f23-a2ef-816f8a2ba72e]
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description = "STOP codon RNA sequence 2"
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[9c2ad527-ebc9-4ace-808b-2b6447cb54cb]
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description = "STOP codon RNA sequence 3"
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[f4d9d8ee-00a8-47bf-a1e3-1641d4428e54]
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description = "Sequence of two protein codons translates into proteins"
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[dd22eef3-b4f1-4ad6-bb0b-27093c090a9d]
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description = "Sequence of two different protein codons translates into proteins"
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[d0f295df-fb70-425c-946c-ec2ec185388e]
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description = "Translate RNA strand into correct protein list"
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[e30e8505-97ec-4e5f-a73e-5726a1faa1f4]
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description = "Translation stops if STOP codon at beginning of sequence"
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[5358a20b-6f4c-4893-bce4-f929001710f3]
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description = "Translation stops if STOP codon at end of two-codon sequence"
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[ba16703a-1a55-482f-bb07-b21eef5093a3]
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description = "Translation stops if STOP codon at end of three-codon sequence"
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[4089bb5a-d5b4-4e71-b79e-b8d1f14a2911]
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description = "Translation stops if STOP codon in middle of three-codon sequence"
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[2c2a2a60-401f-4a80-b977-e0715b23b93d]
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description = "Translation stops if STOP codon in middle of six-codon sequence"
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[f6f92714-769f-4187-9524-e353e8a41a80]
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description = "Sequence of two non-STOP codons does not translate to a STOP codon"
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[1e75ea2a-f907-4994-ae5c-118632a1cb0f]
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description = "Non-existing codon can't translate"
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include = false
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[9eac93f3-627a-4c90-8653-6d0a0595bc6f]
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description = "Unknown amino acids, not part of a codon, can't translate"
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reimplements = "1e75ea2a-f907-4994-ae5c-118632a1cb0f"
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[9d73899f-e68e-4291-b1e2-7bf87c00f024]
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description = "Incomplete RNA sequence can't translate"
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[43945cf7-9968-402d-ab9f-b8a28750b050]
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description = "Incomplete RNA sequence can translate if valid until a STOP codon"

‎exercises/practice/protein-translation/dub.sdl

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name "protein-translation"
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buildRequirements "disallowDeprecations"

‎exercises/practice/protein-translation/example/protein_translation.d

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module protein_translation;
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import std.algorithm;
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import std.range;
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import std.conv;
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immutable string[string] availableProteins = [
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"AUG": "Methionine",
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"UUU": "Phenylalanine",
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"UUC": "Phenylalanine",
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"UUA": "Leucine",
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"UUG": "Leucine",
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"UCU": "Serine",
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"UCC": "Serine",
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"UCA": "Serine",
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"UCG": "Serine",
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"UAU": "Tyrosine",
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"UAC": "Tyrosine",
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"UGU": "Cysteine",
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"UGC": "Cysteine",
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"UGG": "Tryptophan",
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"UAA": "STOP",
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"UAG": "STOP",
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"UGA": "STOP"
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];
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pure string[] proteins(immutable string strand)
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{
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string[] codons = strand.chunks(3).map!(chunk => chunk.array.to!string).array;
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string[] results = [];
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foreach (codon; codons) {
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if(codon!in availableProteins)
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throw new Exception("Invalid codon");
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string protein = availableProteins[codon];
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if (protein == "STOP")
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return results;
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results ~= protein;
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};
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return results;
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}
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‎exercises/practice/protein-translation/source/protein_translation.d

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module protein_translation;
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pure string[] proteins(immutable string rna)
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{
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// implement this function
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}
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unittest
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{
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import std.exception : assertThrown;
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immutable int allTestsEnabled = 1;
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// Empty RNA sequence results in no proteins
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assert(proteins("") == []);
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static if (allTestsEnabled)
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{
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// Methionine RNA sequence
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assert(proteins("AUG") == ["Methionine"]);
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// Phenylalanine RNA sequence 1
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assert(proteins("UUU") == ["Phenylalanine"]);
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// Phenylalanine RNA sequence 2
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assert(proteins("UUC") == ["Phenylalanine"]);
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// Leucine RNA sequence 1
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assert(proteins("UUA") == ["Leucine"]);
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// Leucine RNA sequence 2
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assert(proteins("UUG") == ["Leucine"]);
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// Serine RNA sequence 1
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assert(proteins("UCU") == ["Serine"]);
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// Serine RNA sequence 2
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assert(proteins("UCC") == ["Serine"]);
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// Serine RNA sequence 3
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assert(proteins("UCA") == ["Serine"]);
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// Serine RNA sequence 4
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assert(proteins("UCG") == ["Serine"]);
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// Tyrosine RNA sequence 1
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assert(proteins("UAU") == ["Tyrosine"]);
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// Tyrosine RNA sequence 2
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assert(proteins("UAC") == ["Tyrosine"]);
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// Cysteine RNA sequence 1
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assert(proteins("UGU") == ["Cysteine"]);
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// Cysteine RNA sequence 2
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assert(proteins("UGC") == ["Cysteine"]);
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// Tryptophan RNA sequence
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assert(proteins("UGG") == ["Tryptophan"]);
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// STOP codon RNA sequence 1
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assert(proteins("UAA") == []);
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// STOP codon RNA sequence 2
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assert(proteins("UAG") == []);
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// STOP codon RNA sequence 3
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assert(proteins("UGA") == []);
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// Sequence of two protein codons translates into proteins
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assert(proteins("UUUUUU") == ["Phenylalanine", "Phenylalanine"]);
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// Sequence of two different protein codons translates into proteins
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assert(proteins("UUAUUG") == ["Leucine", "Leucine"]);
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// Translate RNA strand into correct protein list
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assert(proteins("AUGUUUUGG") == ["Methionine", "Phenylalanine", "Tryptophan"]);
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// Translation stops if STOP codon at beginning of sequence
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assert(proteins("UAGUGG") == []);
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// Translation stops if STOP codon at end of two-codon sequence
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assert(proteins("UGGUAG") == ["Tryptophan"]);
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// Translation stops if STOP codon at end of three-codon sequence
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assert(proteins("AUGUUUUAA") == ["Methionine", "Phenylalanine"]);
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// Translation stops if STOP codon in middle of three-codon sequence
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assert(proteins("UGGUAGUGG") == ["Tryptophan"]);
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// Translation stops if STOP codon in middle of six-codon sequence
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assert(proteins("UGGUGUUAUUAAUGGUUU") == ["Tryptophan", "Cysteine", "Tyrosine"]);
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// Sequence of two non-STOP codons does not translate to a STOP codon
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assert(proteins("AUGAUG") == ["Methionine", "Methionine"]);
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// Non-existing codon can't translate
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assertThrown(proteins("AAA"));
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// Unknown amino acids, not part of a codon, can't translate
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assertThrown(proteins("XYZ"));
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// Incomplete RNA sequence can't translate
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assertThrown(proteins("AUGU"));
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// Incomplete RNA sequence can translate if valid until a STOP codon
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assert(proteins("UUCUUCUAAUGGU") == ["Phenylalanine", "Phenylalanine"]);
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}
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}
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