Add Exercise: Protein Translation (#245)

* Add assert_equal for arrays of strings This is needed for e.g. the Protein-Translation exercise feautred in 48in24. * Add exercise: protein-translation * Remove tests with invalid codons --------- Co-authored-by: Joel <[email protected]>
exercism · Feb 15, 2024 · 9491982 · 9491982
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diff --git a/config.json b/config.json
@@ -477,6 +477,18 @@
         "practices": [],
         "prerequisites": [],
         "difficulty": 8
+      },
+      {
+        "slug": "protein-translation",
+        "name": "Protein Translation",
+        "uuid": "3d2ba0a1-2a2a-4e1f-89e8-c5add9ddceef",
+        "practices": [],
+        "prerequisites": [],
+        "difficulty": 5,
+        "topics": [
+          "lists",
+          "strings"
+        ]
       }
     ]
   }

diff --git a/exercises/practice/protein-translation/.docs/instructions.md b/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)
diff --git a/exercises/practice/protein-translation/.meta/config.json b/exercises/practice/protein-translation/.meta/config.json
@@ -0,0 +1,16 @@
+{
+  "authors": ["D3usXMachina"],
+  "files": {
+    "solution": [
+      "protein_translation.f90"
+    ],
+    "test": [
+      "protein_translation_test.f90"
+    ],
+    "example": [
+      ".meta/example.f90"
+    ]
+  },
+  "blurb": "Translate RNA sequences into proteins.",
+  "source": "Tyler Long"
+}
diff --git a/exercises/practice/protein-translation/.meta/example.f90 b/exercises/practice/protein-translation/.meta/example.f90
@@ -0,0 +1,63 @@
+module protein_translation
+  implicit none
+
+  character(len=13), parameter, private :: protein_names(7) = [&
+    "Methionine   ", &
+    "Phenylalanine", &
+    "Leucine      ", &
+    "Serine       ", &
+    "Tyrosine     ", &
+    "Cysteine     ", &
+    "Tryptophan   " &
+    ]
+
+contains
+
+  function proteins(rna) result(names)
+    character(len=*), intent(in) :: rna
+    integer, allocatable :: protein_ids(:)
+    character(len=13), allocatable :: names(:)
+    integer :: i, n_protein, max_n_proteins
+
+    max_n_proteins = len(rna)/3
+    allocate(protein_ids(0:max_n_proteins-1))
+
+    n_protein = 0
+    do i = 1, len(rna), 3
+      if (i + 2 > len(rna)) then
+        n_protein = 0
+        exit ! Invalid codon
+      end if
+      select case (rna(i:i+2))
+        case ("AUG") 
+          protein_ids(n_protein+1) = 1
+        case ("UUU", "UUC")
+          protein_ids(n_protein+1) = 2
+        case ("UUA", "UUG")
+          protein_ids(n_protein+1) = 3
+        case ("UCU", "UCC", "UCA", "UCG")
+          protein_ids(n_protein+1) = 4
+        case ("UAU", "UAC")
+          protein_ids(n_protein+1) = 5
+        case ("UGU", "UGC")
+          protein_ids(n_protein+1) = 6
+        case ("UGG")
+          protein_ids(n_protein+1) = 7
+        case ("UAA", "UAG", "UGA")
+          exit ! stop codon
+        case default
+          n_protein = 0
+          exit ! invalid codon
+      end select
+      n_protein = n_protein + 1
+    end do
+
+    allocate(names(n_protein))
+    do i = 1, n_protein
+      names(i) = protein_names(protein_ids(i))
+    end do
+
+  end function proteins
+
+end module protein_translation
+
diff --git a/exercises/practice/protein-translation/.meta/tests.toml b/exercises/practice/protein-translation/.meta/tests.toml
@@ -0,0 +1,88 @@
+# 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"
diff --git a/exercises/practice/protein-translation/CMakeLists.txt b/exercises/practice/protein-translation/CMakeLists.txt
@@ -0,0 +1,71 @@
+# Get the exercise name from the current directory
+get_filename_component(exercise ${CMAKE_CURRENT_SOURCE_DIR} NAME)
+
+# Basic CMake project
+cmake_minimum_required(VERSION 3.0.0)
+
+# Name the project after the exercise
+project(${exercise} Fortran)
+
+# set debug build default
+set(CMAKE_BUILD_TYPE Debug)
+
+# Get a source filename from the exercise name by replacing -'s with _'s
+string(REPLACE "-" "_" file ${exercise})
+
+# Activate Fortran compiler warnings
+if(CMAKE_Fortran_COMPILER_ID MATCHES "Intel") # Intel fortran
+  if(WIN32)
+    add_compile_options(/warn:all)
+  else()
+    add_compile_options(-warn all)
+  endif()
+endif()
+if(CMAKE_Fortran_COMPILER_ID MATCHES "GNU") # GFortran
+  add_compile_options(-std=f2008 -W -Wall -Wextra -pedantic -fbacktrace)
+endif()
+
+# Configure to run all the tests?
+if(${EXERCISM_RUN_ALL_TESTS})
+    add_definitions(-DEXERCISM_RUN_ALL_TESTS)
+    set(exercise_f90 ${file}_build_all.f90)
+else()
+    # if building in exercise folder add testlib
+    set(testlib_path ${CMAKE_CURRENT_SOURCE_DIR}/testlib)
+    if (NOT EXISTS ${testlib_path})
+      if (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../../../testlib) # in git repo locally?
+        file(COPY ${CMAKE_CURRENT_SOURCE_DIR}/../../../testlib DESTINATION  ${CMAKE_CURRENT_SOURCE_DIR} PATTERN *)
+      else() # get from git with http
+        message("Downloading testlib from https://raw.githubusercontent.com/exercism/fortran/master")
+        file(MAKE_DIRECTORY ${testlib_path} )
+        file(DOWNLOAD https://raw.githubusercontent.com/exercism/fortran/master/testlib/TesterMain.f90 ${testlib_path}/TesterMain.f90 SHOW_PROGRESS)
+        file(DOWNLOAD https://raw.githubusercontent.com/exercism/fortran/master/testlib/CMakeLists.txt ${testlib_path}/CMakeLists.txt SHOW_PROGRESS)
+      endif()
+    endif()
+    # add lib to build
+    add_subdirectory(testlib)
+    include_directories(testlib ${CMAKE_CURRENT_BINARY_DIR}/testlib)
+    if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/${file}.f90)
+        set(exercise_f90 ${file}.f90)
+    endif()
+endif()
+
+# Get test_files if exercise needs it
+file(GLOB test_files test_files/*.*)
+foreach(test_file ${test_files})
+    message("Copying ${test_file} to binary directory for example ${file}")
+    configure_file(${test_file} . COPYONLY)
+endforeach()
+
+# Build executable from sources and headers
+add_executable(${exercise} ${exercise_f90} ${file}_test.f90  )
+
+target_link_libraries(${exercise} TesterMain)
+
+include(CTest)
+
+add_test (${exercise}_test ${exercise} )
+
+# Run the tests on every build
+#add_custom_target(test_${exercise} ALL DEPENDS ${exercise} COMMAND ${exercise})
+
diff --git a/exercises/practice/protein-translation/protein_translation.f90 b/exercises/practice/protein-translation/protein_translation.f90
@@ -0,0 +1,14 @@
+module protein_translation
+  implicit none
+
+contains
+
+  function proteins(rna) result(names)
+    character(len=*), intent(in) :: rna
+    character(len=13), allocatable :: names(:)
+
+    names = [character(len=13) :: rna] ! Replace this line in your implementation
+  end function proteins
+
+end module protein_translation
+