Add protein-translation

Author: glennj

config.json

@@ -338,6 +338,14 @@
         "prerequisites": [],
         "difficulty": 3
       },
+      {
+        "slug": "protein-translation",
+        "name": "Protein Translation",
+        "uuid": "951babbe-0acb-4ce8-a02a-6b2f2b8db216",
+        "practices": [],
+        "prerequisites": [],
+        "difficulty": 3
+      },
       {
         "slug": "proverb",
         "name": "Proverb",

exercises/practice/protein-translation/.busted

@@ -0,0 +1,5 @@
+return {
+  default = {
+    ROOT = { '.' }
+  }
+}

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

@@ -0,0 +1,38 @@
+# Instructions
+
+Your job is to translate RNA sequences into proteins.
+
+RNA strands are made up of three-nucleotide sequences called **codons**.
+Each codon translates to an **amino acid**.
+When joined together, those amino acids make a protein.
+
+In the real world, there are 64 codons, which in turn correspond to 20 amino acids.
+However, for this exercise, you’ll only use a few of the possible 64.
+They are listed below:
+
+| Codon              | Amino Acid    |
+| ------------------ | ------------- |
+| 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          |
+
+For example, the RNA string “AUGUUUUCU” has three codons: “AUG”, “UUU” and “UCU”.
+These map to Methionine, Phenylalanine, and Serine.
+
+## “STOP” Codons
+
+You’ll note from the table above that there are three **“STOP” codons**.
+If you encounter any of these codons, ignore the rest of the sequence — the protein is complete.
+
+For example, “AUGUUUUCUUAAAUG” contains a STOP codon (“UAA”).
+Once we reach that point, we stop processing.
+We therefore only consider the part before it (i.e. “AUGUUUUCU”), not any further codons after it (i.e. “AUG”).
+
+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 +1,18 @@
+{
+  "authors": [
+    "glennj"
+  ],
+  "files": {
+    "solution": [
+      "protein_translation.moon"
+    ],
+    "test": [
+      "protein_translation_spec.moon"
+    ],
+    "example": [
+      ".meta/example.moon"
+    ]
+  },
+  "blurb": "Translate RNA sequences into proteins.",
+  "source": "Tyler Long"
+}

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

@@ -0,0 +1,30 @@
+codon_map =
+  AUG: 'Methionine'
+  UUC: 'Phenylalanine'
+  UUU: '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'
+
+translate = (strand) ->
+  proteins = {}
+  while #strand > 0
+    codon, strand = strand\match '(...)(.*)'
+    switch codon_map[codon]
+      when nil then error 'Invalid codon'
+      when 'STOP' then break
+      else table.insert proteins, codon_map[codon]
+  proteins
+
+{ proteins: translate }

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

@@ -0,0 +1,21 @@
+string_list = (list) ->
+  "{#{table.concat [quote word for word in *list], ', '}}"
+
+{
+  module_imports: {'proteins'},
+
+  generate_test: (case, level) ->
+    local lines
+    if case.expected.error
+      lines = {
+        "f = -> proteins #{quote case.input.strand}",
+        "assert.has.errors f, #{quote case.expected.error}"
+      }
+    else
+      lines = {
+        "result = proteins #{quote case.input.strand}",
+        "expected = #{string_list case.expected}",
+        "assert.are.same expected, result"
+      }
+    table.concat [indent line, level for line in *lines], '\n'
+}

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

@@ -0,0 +1,105 @@
+# 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"
+
+[f6f92714-769f-4187-9524-e353e8a41a80]
+description = "Sequence of two non-STOP codons does not translate to a STOP codon"
+
+[1e75ea2a-f907-4994-ae5c-118632a1cb0f]
+description = "Non-existing codon can't translate"
+include = false
+
+[9eac93f3-627a-4c90-8653-6d0a0595bc6f]
+description = "Unknown amino acids, not part of a codon, can't translate"
+reimplements = "1e75ea2a-f907-4994-ae5c-118632a1cb0f"
+
+[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.moon

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

exercises/practice/protein-translation/protein_translation_spec.moon

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