From cc9e01b869c9876de09b8db763effa2f366195ee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Pawe=C5=82=20Fertyk?= Date: Sun, 18 Feb 2024 17:59:19 +0100 Subject: [PATCH] Add protein-translation exercise --- config.json | 8 + .../protein-translation/.docs/instructions.md | 45 ++++++ .../protein-translation/.meta/config.json | 18 +++ .../protein-translation/.meta/example.gd | 30 ++++ .../protein-translation/.meta/tests.toml | 105 ++++++++++++ .../protein_translation.gd | 2 + .../protein_translation_test.gd | 150 ++++++++++++++++++ 7 files changed, 358 insertions(+) create mode 100644 exercises/practice/protein-translation/.docs/instructions.md create mode 100644 exercises/practice/protein-translation/.meta/config.json create mode 100644 exercises/practice/protein-translation/.meta/example.gd create mode 100644 exercises/practice/protein-translation/.meta/tests.toml create mode 100644 exercises/practice/protein-translation/protein_translation.gd create mode 100644 exercises/practice/protein-translation/protein_translation_test.gd diff --git a/config.json b/config.json index 9401d65..48e1dc2 100644 --- a/config.json +++ b/config.json @@ -139,6 +139,14 @@ "prerequisites": [], "difficulty": 2 }, + { + "slug": "protein-translation", + "name": "Protein Translation", + "uuid": "a93332b7-d630-4c58-b69f-3a01481774de", + "practices": [], + "prerequisites": [], + "difficulty": 2 + }, { "slug": "luhn", "name": "Luhn", diff --git a/exercises/practice/protein-translation/.docs/instructions.md b/exercises/practice/protein-translation/.docs/instructions.md new file mode 100644 index 0000000..7dc34d2 --- /dev/null +++ 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 new file mode 100644 index 0000000..0948b9e --- /dev/null +++ b/exercises/practice/protein-translation/.meta/config.json @@ -0,0 +1,18 @@ +{ + "authors": [ + "pfertyk" + ], + "files": { + "solution": [ + "protein_translation.gd" + ], + "test": [ + "protein_translation_test.gd" + ], + "example": [ + ".meta/example.gd" + ] + }, + "blurb": "Translate RNA sequences into proteins.", + "source": "Tyler Long" +} diff --git a/exercises/practice/protein-translation/.meta/example.gd b/exercises/practice/protein-translation/.meta/example.gd new file mode 100644 index 0000000..5fda85b --- /dev/null +++ b/exercises/practice/protein-translation/.meta/example.gd @@ -0,0 +1,30 @@ +const CODON_TO_PROTEINE = { + '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' +} + + +func proteins(strand): + var protein_list = [] + for i in range(0, len(strand), 3): + var codon = strand.substr(i, 3) + var proteine = CODON_TO_PROTEINE[codon] + if proteine == 'STOP': + break + protein_list.append(proteine) + return protein_list diff --git a/exercises/practice/protein-translation/.meta/tests.toml b/exercises/practice/protein-translation/.meta/tests.toml new file mode 100644 index 0000000..c083605 --- /dev/null +++ b/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" +include = false + +[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" +include = false + +[9d73899f-e68e-4291-b1e2-7bf87c00f024] +description = "Incomplete RNA sequence can't translate" +include = false + +[43945cf7-9968-402d-ab9f-b8a28750b050] +description = "Incomplete RNA sequence can translate if valid until a STOP codon" +include = false diff --git a/exercises/practice/protein-translation/protein_translation.gd b/exercises/practice/protein-translation/protein_translation.gd new file mode 100644 index 0000000..a6189d0 --- /dev/null +++ b/exercises/practice/protein-translation/protein_translation.gd @@ -0,0 +1,2 @@ +func proteins(strand): + pass diff --git a/exercises/practice/protein-translation/protein_translation_test.gd b/exercises/practice/protein-translation/protein_translation_test.gd new file mode 100644 index 0000000..15bdf5c --- /dev/null +++ b/exercises/practice/protein-translation/protein_translation_test.gd @@ -0,0 +1,150 @@ +func test_methionine_rna_sequence(solution_script): + var value = "AUG" + var expected = ["Methionine"] + return [solution_script.proteins(value), expected] + + +func test_phenylalanine_rna_sequence_1(solution_script): + var value = "UUU" + var expected = ["Phenylalanine"] + return [solution_script.proteins(value), expected] + + +func test_phenylalanine_rna_sequence_2(solution_script): + var value = "UUC" + var expected = ["Phenylalanine"] + return [solution_script.proteins(value), expected] + + +func test_leucine_rna_sequence_1(solution_script): + var value = "UUA" + var expected = ["Leucine"] + return [solution_script.proteins(value), expected] + + +func test_leucine_rna_sequence_2(solution_script): + var value = "UUG" + var expected = ["Leucine"] + return [solution_script.proteins(value), expected] + + +func test_serine_rna_sequence_1(solution_script): + var value = "UCU" + var expected = ["Serine"] + return [solution_script.proteins(value), expected] + + +func test_serine_rna_sequence_2(solution_script): + var value = "UCC" + var expected = ["Serine"] + return [solution_script.proteins(value), expected] + + +func test_serine_rna_sequence_3(solution_script): + var value = "UCA" + var expected = ["Serine"] + return [solution_script.proteins(value), expected] + + +func test_serine_rna_sequence_4(solution_script): + var value = "UCG" + var expected = ["Serine"] + return [solution_script.proteins(value), expected] + + +func test_tyrosine_rna_sequence_1(solution_script): + var value = "UAU" + var expected = ["Tyrosine"] + return [solution_script.proteins(value), expected] + + +func test_tyrosine_rna_sequence_2(solution_script): + var value = "UAC" + var expected = ["Tyrosine"] + return [solution_script.proteins(value), expected] + + +func test_cysteine_rna_sequence_1(solution_script): + var value = "UGU" + var expected = ["Cysteine"] + return [solution_script.proteins(value), expected] + + +func test_cysteine_rna_sequence_2(solution_script): + var value = "UGC" + var expected = ["Cysteine"] + return [solution_script.proteins(value), expected] + + +func test_tryptophan_rna_sequence(solution_script): + var value = "UGG" + var expected = ["Tryptophan"] + return [solution_script.proteins(value), expected] + + +func test_stop_codon_rna_sequence_1(solution_script): + var value = "UAA" + var expected = [] + return [solution_script.proteins(value), expected] + + +func test_stop_codon_rna_sequence_2(solution_script): + var value = "UAG" + var expected = [] + return [solution_script.proteins(value), expected] + + +func test_stop_codon_rna_sequence_3(solution_script): + var value = "UGA" + var expected = [] + return [solution_script.proteins(value), expected] + + +func test_sequence_of_two_protein_codons_translates_into_proteins(solution_script): + var value = "UUUUUU" + var expected = ["Phenylalanine", "Phenylalanine"] + return [solution_script.proteins(value), expected] + + +func test_sequence_of_two_different_protein_codons_translates_into_proteins(solution_script): + var value = "UUAUUG" + var expected = ["Leucine", "Leucine"] + return [solution_script.proteins(value), expected] + + +func test_translate_rna_strand_into_correct_protein_list(solution_script): + var value = "AUGUUUUGG" + var expected = ["Methionine", "Phenylalanine", "Tryptophan"] + return [solution_script.proteins(value), expected] + + +func test_translation_stops_if_stop_codon_at_beginning_of_sequence(solution_script): + var value = "UAGUGG" + var expected = [] + return [solution_script.proteins(value), expected] + + +func test_translation_stops_if_stop_codon_at_end_of_two_codon_sequence(solution_script): + var value = "UGGUAG" + var expected = ["Tryptophan"] + return [solution_script.proteins(value), expected] + + +func test_translation_stops_if_stop_codon_at_end_of_three_codon_sequence(solution_script): + var value = "AUGUUUUAA" + var expected = ["Methionine", "Phenylalanine"] + return [solution_script.proteins(value), expected] + + +func test_translation_stops_if_stop_codon_in_middle_of_three_codon_sequence(solution_script): + var value = "UGGUAGUGG" + var expected = ["Tryptophan"] + return [solution_script.proteins(value), expected] + + +func test_translation_stops_if_stop_codon_in_middle_of_six_codon_sequence(solution_script): + var value = "UGGUGUUAUUAAUGGUUU" + var expected = ["Tryptophan", "Cysteine", "Tyrosine"] + return [solution_script.proteins(value), expected] + +