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Add protein-translation (#139)
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‎config.json‎

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"prerequisites": [],
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"difficulty": 3
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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": "951babbe-0acb-4ce8-a02a-6b2f2b8db216",
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"practices": [],
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"prerequisites": [],
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"difficulty": 3
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},
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{
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"slug": "proverb",
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"name": "Proverb",

‎exercises/practice/protein-translation/.busted‎

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return {
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default = {
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ROOT = { '.' }
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}
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}

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

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# Instructions
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Your job is to translate RNA sequences into proteins.
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RNA strands are made up of three-nucleotide sequences called **codons**.
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Each codon translates to an **amino acid**.
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When joined together, those amino acids make a protein.
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In the real world, there are 64 codons, which in turn correspond to 20 amino acids.
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However, for this exercise, you’ll only use a few of the possible 64.
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They are listed below:
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| Codon | Amino Acid |
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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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For example, the RNA string “AUGUUUUCU” has three codons: “AUG”, “UUU” and “UCU”.
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These map to Methionine, Phenylalanine, and Serine.
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## “STOP” Codons
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You’ll note from the table above that there are three **“STOP” codons**.
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If you encounter any of these codons, ignore the rest of the sequence — the protein is complete.
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For example, “AUGUUUUCUUAAAUG” contains a STOP codon (“UAA”).
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Once we reach that point, we stop processing.
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We therefore only consider the part before it (i.e. “AUGUUUUCU”), not any further codons after it (i.e. “AUG”).
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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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"glennj"
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],
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"files": {
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"solution": [
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"protein_translation.moon"
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],
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"test": [
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"protein_translation_spec.moon"
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],
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"example": [
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".meta/example.moon"
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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/example.moon‎

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codon_map =
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AUG: 'Methionine'
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UUC: 'Phenylalanine'
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UUU: '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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translate = (strand) ->
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proteins = {}
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while #strand > 0
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codon, strand = strand\match '(...)(.*)'
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switch codon_map[codon]
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when nil then error 'Invalid codon'
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when 'STOP' then break
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else table.insert proteins, codon_map[codon]
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proteins
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{ proteins: translate }

‎exercises/practice/protein-translation/.meta/spec_generator.moon‎

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string_list = (list) ->
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"{#{table.concat [quote word for word in *list], ', '}}"
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{
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module_imports: {'proteins'},
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generate_test: (case, level) ->
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local lines
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if case.expected.error
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lines = {
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"f = -> proteins #{quote case.input.strand}",
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"assert.has.errors f, #{quote case.expected.error}"
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}
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else
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lines = {
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"result = proteins #{quote case.input.strand}",
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"expected = #{string_list case.expected}",
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"assert.are.same expected, result"
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}
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table.concat [indent line, level for line in *lines], '\n'
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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/protein_translation.moon‎

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{
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proteins: (strand) ->
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error 'Implement me'
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}

‎exercises/practice/protein-translation/protein_translation_spec.moon‎

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import proteins from require 'protein_translation'
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describe 'protein-translation', ->
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it 'Empty RNA sequence results in no proteins', ->
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result = proteins ''
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expected = {}
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assert.are.same expected, result
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pending 'Methionine RNA sequence', ->
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result = proteins 'AUG'
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expected = {'Methionine'}
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assert.are.same expected, result
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pending 'Phenylalanine RNA sequence 1', ->
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result = proteins 'UUU'
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expected = {'Phenylalanine'}
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assert.are.same expected, result
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pending 'Phenylalanine RNA sequence 2', ->
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result = proteins 'UUC'
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expected = {'Phenylalanine'}
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assert.are.same expected, result
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pending 'Leucine RNA sequence 1', ->
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result = proteins 'UUA'
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expected = {'Leucine'}
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assert.are.same expected, result
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pending 'Leucine RNA sequence 2', ->
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result = proteins 'UUG'
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expected = {'Leucine'}
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assert.are.same expected, result
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pending 'Serine RNA sequence 1', ->
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result = proteins 'UCU'
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expected = {'Serine'}
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assert.are.same expected, result
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pending 'Serine RNA sequence 2', ->
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result = proteins 'UCC'
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expected = {'Serine'}
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assert.are.same expected, result
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pending 'Serine RNA sequence 3', ->
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result = proteins 'UCA'
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expected = {'Serine'}
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assert.are.same expected, result
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pending 'Serine RNA sequence 4', ->
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result = proteins 'UCG'
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expected = {'Serine'}
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assert.are.same expected, result
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pending 'Tyrosine RNA sequence 1', ->
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result = proteins 'UAU'
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expected = {'Tyrosine'}
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assert.are.same expected, result
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pending 'Tyrosine RNA sequence 2', ->
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result = proteins 'UAC'
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expected = {'Tyrosine'}
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assert.are.same expected, result
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pending 'Cysteine RNA sequence 1', ->
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result = proteins 'UGU'
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expected = {'Cysteine'}
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assert.are.same expected, result
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pending 'Cysteine RNA sequence 2', ->
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result = proteins 'UGC'
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expected = {'Cysteine'}
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assert.are.same expected, result
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pending 'Tryptophan RNA sequence', ->
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result = proteins 'UGG'
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expected = {'Tryptophan'}
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assert.are.same expected, result
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pending 'STOP codon RNA sequence 1', ->
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result = proteins 'UAA'
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expected = {}
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assert.are.same expected, result
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pending 'STOP codon RNA sequence 2', ->
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result = proteins 'UAG'
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expected = {}
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assert.are.same expected, result
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pending 'STOP codon RNA sequence 3', ->
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result = proteins 'UGA'
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expected = {}
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assert.are.same expected, result
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pending 'Sequence of two protein codons translates into proteins', ->
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result = proteins 'UUUUUU'
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expected = {'Phenylalanine', 'Phenylalanine'}
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assert.are.same expected, result
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pending 'Sequence of two different protein codons translates into proteins', ->
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result = proteins 'UUAUUG'
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expected = {'Leucine', 'Leucine'}
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assert.are.same expected, result
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pending 'Translate RNA strand into correct protein list', ->
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result = proteins 'AUGUUUUGG'
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expected = {'Methionine', 'Phenylalanine', 'Tryptophan'}
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assert.are.same expected, result
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pending 'Translation stops if STOP codon at beginning of sequence', ->
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result = proteins 'UAGUGG'
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expected = {}
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assert.are.same expected, result
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pending 'Translation stops if STOP codon at end of two-codon sequence', ->
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result = proteins 'UGGUAG'
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expected = {'Tryptophan'}
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assert.are.same expected, result
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pending 'Translation stops if STOP codon at end of three-codon sequence', ->
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result = proteins 'AUGUUUUAA'
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expected = {'Methionine', 'Phenylalanine'}
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assert.are.same expected, result
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pending 'Translation stops if STOP codon in middle of three-codon sequence', ->
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result = proteins 'UGGUAGUGG'
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expected = {'Tryptophan'}
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assert.are.same expected, result
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pending 'Translation stops if STOP codon in middle of six-codon sequence', ->
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result = proteins 'UGGUGUUAUUAAUGGUUU'
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expected = {'Tryptophan', 'Cysteine', 'Tyrosine'}
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assert.are.same expected, result
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pending 'Sequence of two non-STOP codons does not translate to a STOP codon', ->
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result = proteins 'AUGAUG'
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expected = {'Methionine', 'Methionine'}
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assert.are.same expected, result
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pending "Unknown amino acids, not part of a codon, can't translate", ->
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f = -> proteins 'XYZ'
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assert.has.errors f, 'Invalid codon'
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pending "Incomplete RNA sequence can't translate", ->
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f = -> proteins 'AUGU'
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assert.has.errors f, 'Invalid codon'
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pending 'Incomplete RNA sequence can translate if valid until a STOP codon', ->
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result = proteins 'UUCUUCUAAUGGU'
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expected = {'Phenylalanine', 'Phenylalanine'}
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assert.are.same expected, result

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