Add protein-translation exercise (#378)

config.json

@@ -465,6 +465,17 @@
           "math"
         ]
       },
+      {
+        "slug": "protein-translation",
+        "name": "Protein Translation",
+        "uuid": "3201c23c-e2eb-4e1a-8a44-b56acac572f5",
+        "practices": [],
+        "prerequisites": [],
+        "difficulty": 3,
+        "topics": [
+          "strings"
+        ]
+      },
       {
         "slug": "series",
         "name": "Series",

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 +1,18 @@
+{
+  "authors": [
+    "keiravillekode"
+  ],
+  "files": {
+    "solution": [
+      "protein-translation.el"
+    ],
+    "test": [
+      "protein-translation-test.el"
+    ],
+    "example": [
+      ".meta/example.el"
+    ]
+  },
+  "blurb": "Translate RNA sequences into proteins.",
+  "source": "Tyler Long"
+}

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

@@ -0,0 +1,44 @@
+;;; protein-translation.el --- Protein Translation (exercism)  -*- lexical-binding: t; -*-
+
+;;; Commentary:
+
+;;; Code:
+
+(require 'cl-lib)
+
+(defun translate (codon)
+  (pcase codon
+    ("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" nil)
+    ("UAG" nil)
+    ("UGA" nil)
+    (otherwise (error "Invalid codon"))))
+
+(defun proteins (strand)
+  (let* ((len (length strand))
+         (stop (- len (% len 3))))
+    (cl-labels
+      ((recur (index)
+        (if (= index stop)
+          (unless (= index len) (error "Invalid codon"))
+          (let* ((next (+ index 3))
+                 (protein (translate (substring strand index next))))
+            (when protein (cons protein (recur next)))))))
+      (recur 0))))
+
+(provide 'protein-translation)
+;;; protein-translation.el ends here
+

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

@@ -0,0 +1,102 @@
+# 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"
+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-test.el

@@ -0,0 +1,156 @@
+;;; protein-translation-test.el --- Tests for Protein Translation (exercism)  -*- lexical-binding: t; -*-
+
+;;; Commentary:
+
+;;; Code:
+
+
+(load-file "protein-translation.el")
+(declare-function proteins "protein-translation.el" (strand))
+
+
+(ert-deftest empty-rna-sequence-results-in-no-proteins ()
+  (should (equal '()
+            (proteins ""))))
+
+
+(ert-deftest methionine-rna-sequence ()
+  (should (equal '("Methionine")
+            (proteins "AUG"))))
+
+
+(ert-deftest phenylalanine-rna-sequence-1 ()
+  (should (equal '("Phenylalanine")
+            (proteins "UUU"))))
+
+
+(ert-deftest phenylalanine-rna-sequence-2 ()
+  (should (equal '("Phenylalanine")
+            (proteins "UUC"))))
+
+
+(ert-deftest leucine-rna-sequence-1 ()
+  (should (equal '("Leucine")
+            (proteins "UUA"))))
+
+
+(ert-deftest leucine-rna-sequence-2 ()
+  (should (equal '("Leucine")
+            (proteins "UUG"))))
+
+
+(ert-deftest serine-rna-sequence-1 ()
+  (should (equal '("Serine")
+            (proteins "UCU"))))
+
+
+(ert-deftest serine-rna-sequence-2 ()
+  (should (equal '("Serine")
+            (proteins "UCC"))))
+
+
+(ert-deftest serine-rna-sequence-3 ()
+  (should (equal '("Serine")
+            (proteins "UCA"))))
+
+
+(ert-deftest serine-rna-sequence-4 ()
+  (should (equal '("Serine")
+            (proteins "UCG"))))
+
+
+(ert-deftest tyrosine-rna-sequence-1 ()
+  (should (equal '("Tyrosine")
+            (proteins "UAU"))))
+
+
+(ert-deftest tyrosine-rna-sequence-2 ()
+  (should (equal '("Tyrosine")
+            (proteins "UAC"))))
+
+
+(ert-deftest cysteine-rna-sequence-1 ()
+  (should (equal '("Cysteine")
+            (proteins "UGU"))))
+
+
+(ert-deftest cysteine-rna-sequence-2 ()
+  (should (equal '("Cysteine")
+            (proteins "UGC"))))
+
+
+(ert-deftest tryptophan-rna-sequence ()
+  (should (equal '("Tryptophan")
+            (proteins "UGG"))))
+
+
+(ert-deftest stop-codon-rna-sequence-1 ()
+  (should (equal '()
+            (proteins "UAA"))))
+
+
+(ert-deftest stop-codon-rna-sequence-2 ()
+  (should (equal '()
+            (proteins "UAG"))))
+
+
+(ert-deftest stop-codon-rna-sequence-3 ()
+  (should (equal '()
+            (proteins "UGA"))))
+
+
+(ert-deftest sequence-of-two-protein-codons-translates-into-proteins ()
+  (should (equal '("Phenylalanine" "Phenylalanine")
+            (proteins "UUUUUU"))))
+
+
+(ert-deftest sequence-of-two-different-protein-codons-translates-into-proteins ()
+  (should (equal '("Leucine" "Leucine")
+            (proteins "UUAUUG"))))
+
+
+(ert-deftest translate-rna-strand-into-correct-protein-list ()
+  (should (equal '("Methionine" "Phenylalanine" "Tryptophan")
+            (proteins "AUGUUUUGG"))))
+
+
+(ert-deftest translation-stops-if-stop-codon-at-beginning-of-sequence ()
+  (should (equal '()
+            (proteins "UAGUGG"))))
+
+
+(ert-deftest translation-stops-if-stop-codon-at-end-of-two-codon-sequence ()
+  (should (equal '("Tryptophan")
+            (proteins "UGGUAG"))))
+
+
+(ert-deftest translation-stops-if-stop-codon-at-end-of-three-codon-sequence ()
+  (should (equal '("Methionine" "Phenylalanine")
+            (proteins "AUGUUUUAA"))))
+
+
+(ert-deftest translation-stops-if-stop-codon-in-middle-of-three-codon-sequence ()
+  (should (equal '("Tryptophan")
+            (proteins "UGGUAGUGG"))))
+
+
+(ert-deftest translation-stops-if-stop-codon-in-middle-of-six-codon-sequence ()
+  (should (equal '("Tryptophan" "Cysteine" "Tyrosine")
+            (proteins "UGGUGUUAUUAAUGGUUU"))))
+
+
+(ert-deftest unknown-amino-acids-not-part-of-a-codon-cant-translate ()
+  (should-error (proteins "XYZ")))
+
+
+(ert-deftest incomplete-rna-sequence-cant-translate ()
+  (should-error (proteins "AUGU")))
+
+
+(ert-deftest incomplete-rna-sequence-can-translate-if-valid-until-a-stop-codon ()
+  (should (equal '("Phenylalanine" "Phenylalanine")
+            (proteins "UUCUUCUAAUGGU"))))
+
+
+(provide 'protein-translation-test)
+;;; protein-translation-test.el ends here