[Protein Translation] add new practice exercise

config.json

@@ -601,6 +601,14 @@
         "practices": [],
         "prerequisites": [],
         "difficulty": 1
+      },
+      {
+        "slug": "protein-translation",
+        "name": "Protein Translation",
+        "uuid": "dc8bb817-1c79-476a-a666-bcad9455c66a",
+        "practices": [],
+        "prerequisites": [],
+        "difficulty": 2
       }
     ]
   },

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)

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

@@ -0,0 +1,19 @@
+{
+  "authors": [
+    "colinleach",
+    "jonmcalder"
+  ],
+  "files": {
+    "solution": [
+      "protein-translation.R"
+    ],
+    "test": [
+      "test_protein-translation.R"
+    ],
+    "example": [
+      ".meta/example.R"
+    ]
+  },
+  "blurb": "Translate RNA sequences into proteins.",
+  "source": "Tyler Long"
+}

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

@@ -0,0 +1,31 @@
+proteins <- function(bases) {
+  if (nchar(bases) == 0) return(NULL)
+
+  codons <- strsplit(bases, "(?<=.{3})", perl=TRUE)[[1]]
+
+  translation <- list(
+    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")
+
+  output <- c()
+
+  for (codon in codons) {
+    # All valid codons must be 3 characters
+    if (nchar(codon) != 3) stop("Invalid codon")
+
+    amino_acid <- translation[[codon]]
+
+    # Not all 3-letter sequences are valid codons
+    if (is.null(amino_acid)) stop("Invalid codon")
+
+    # Obey a STOP codon and return what we have so far
+    if (amino_acid == "STOP") break
+
+    output <- append(output, amino_acid)
+  }
+
+  output
+}

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

@@ -0,0 +1,100 @@
+# 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"

exercises/practice/protein-translation/protein-translation.R

@@ -0,0 +1,3 @@
+proteins <- function(bases) {
+
+}

exercises/practice/protein-translation/test_protein-translation.R

@@ -0,0 +1,125 @@
+source('./protein-translation.R')
+library(testthat)
+
+# test_that("Empty RNA sequence results in no proteins", {
+#   expect_equal(proteins(""), NULL)
+# })
+
+test_that("Methionine RNA sequence", {
+  expect_equal(proteins("AUG"), 'Methionine')
+})
+
+test_that("Phenylalanine RNA sequence 1", {
+  expect_equal(proteins("UUU"), 'Phenylalanine')
+})
+
+test_that("Phenylalanine RNA sequence 2", {
+  expect_equal(proteins("UUC"), 'Phenylalanine')
+})
+
+test_that("Leucine RNA sequence 1", {
+  expect_equal(proteins("UUA"), 'Leucine')
+})
+
+test_that("Leucine RNA sequence 2", {
+  expect_equal(proteins("UUG"), 'Leucine')
+})
+
+test_that("Serine RNA sequence 1", {
+  expect_equal(proteins("UCU"), 'Serine')
+})
+
+test_that("Serine RNA sequence 2", {
+  expect_equal(proteins("UCC"), 'Serine')
+})
+
+test_that("Serine RNA sequence 3", {
+  expect_equal(proteins("UCA"), 'Serine')
+})
+
+test_that("Serine RNA sequence 4", {
+  expect_equal(proteins("UCG"), 'Serine')
+})
+
+test_that("Tyrosine RNA sequence 1", {
+  expect_equal(proteins("UAU"), 'Tyrosine')
+})
+
+test_that("Tyrosine RNA sequence 2", {
+  expect_equal(proteins("UAC"), 'Tyrosine')
+})
+
+test_that("Cysteine RNA sequence 1", {
+  expect_equal(proteins("UGU"), 'Cysteine')
+})
+
+test_that("Cysteine RNA sequence 2", {
+  expect_equal(proteins("UGC"), 'Cysteine')
+})
+
+test_that("Tryptophan RNA sequence", {
+  expect_equal(proteins("UGG"), 'Tryptophan')
+})
+
+test_that("STOP codon RNA sequence 1", {
+  expect_equal(proteins("UAA"), c())
+})
+
+test_that("STOP codon RNA sequence 2", {
+  expect_equal(proteins("UAG"), c())
+})
+
+test_that("STOP codon RNA sequence 3", {
+  expect_equal(proteins("UGA"), c())
+})
+
+test_that("Sequence of two protein codons translates into proteins", {
+  expect_equal(proteins("UUUUUU"), c('Phenylalanine', 'Phenylalanine'))
+})
+
+test_that("Sequence of two different protein codons translates into proteins", {
+  expect_equal(proteins("UUAUUG"), c('Leucine', 'Leucine'))
+})
+
+test_that("Translate RNA strand into correct protein list", {
+  expect_equal(proteins("AUGUUUUGG"), 
+               c('Methionine', 'Phenylalanine', 'Tryptophan'))
+})
+
+test_that("Translation stops if STOP codon at beginning of sequence", {
+  expect_equal(proteins("UAGUGG"), c())
+})
+
+test_that("Translation stops if STOP codon at end of two-codon sequence", {
+  expect_equal(proteins("UGGUAG"), c('Tryptophan'))
+})
+
+test_that("Translation stops if STOP codon at end of three-codon sequence", {
+  expect_equal(proteins("AUGUUUUAA"), c('Methionine', 'Phenylalanine'))
+})
+
+test_that("Translation stops if STOP codon in middle of three-codon sequence", {
+  expect_equal(proteins("UGGUAGUGG"), c('Tryptophan'))
+})
+
+test_that("Translation stops if STOP codon in middle of six-codon sequence", {
+  expect_equal(proteins("UGGUGUUAUUAAUGGUUU"), 
+               c('Tryptophan', 'Cysteine', 'Tyrosine'))
+})
+
+test_that("Non-existing codon can't translate", {
+  expect_error(proteins("AAA"))
+})
+
+test_that("Unknown amino acids, not part of a codon, can't translate", {
+  expect_error(proteins("XYZ"))
+})
+
+test_that("Incomplete RNA sequence can't translate", {
+  expect_error(proteins("AUGU"))
+})
+
+test_that("Incomplete RNA sequence can translate if valid until a STOP codon", {
+  expect_equal(proteins("UUCUUCUAAUGGU"), c('Phenylalanine', 'Phenylalanine'))
+})
+