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keiravillekodekeiravillekode
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Add nucleotide-count exercise (#286)
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‎config.json

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"math"
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]
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},
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{
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"slug": "nucleotide-count",
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"name": "Nucleotide Count",
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"uuid": "4ce578b2-9cfb-498b-947f-79f97abeb224",
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"practices": [],
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"prerequisites": [],
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"difficulty": 2,
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"topics": []
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},
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{
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"slug": "eliuds-eggs",
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"name": "Eliud's Eggs",

‎exercises/practice/nucleotide-count/.docs/instructions.md

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# Instructions
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Each of us inherits from our biological parents a set of chemical instructions known as DNA that influence how our bodies are constructed.
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All known life depends on DNA!
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> Note: You do not need to understand anything about nucleotides or DNA to complete this exercise.
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DNA is a long chain of other chemicals and the most important are the four nucleotides, adenine, cytosine, guanine and thymine.
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A single DNA chain can contain billions of these four nucleotides and the order in which they occur is important!
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We call the order of these nucleotides in a bit of DNA a "DNA sequence".
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We represent a DNA sequence as an ordered collection of these four nucleotides and a common way to do that is with a string of characters such as "ATTACG" for a DNA sequence of 6 nucleotides.
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'A' for adenine, 'C' for cytosine, 'G' for guanine, and 'T' for thymine.
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Given a string representing a DNA sequence, count how many of each nucleotide is present.
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If the string contains characters that aren't A, C, G, or T then it is invalid and you should signal an error.
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For example:
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```text
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"GATTACA" -> 'A': 3, 'C': 1, 'G': 1, 'T': 2
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"INVALID" -> error
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```

‎exercises/practice/nucleotide-count/.meta/config.json

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{
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"authors": [
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"keiravillekode"
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],
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"files": {
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"solution": [
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"nucleotide-count.sml"
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],
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"test": [
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"test.sml"
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],
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"example": [
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".meta/example.sml"
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]
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},
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"blurb": "Given a DNA string, compute how many times each nucleotide occurs in the string.",
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"source": "The Calculating DNA Nucleotides_problem at Rosalind",
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"source_url": "https://rosalind.info/problems/dna/"
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}

‎exercises/practice/nucleotide-count/.meta/example.sml

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fun nucleotideCounts (strand: string): {a: int, c: int, g: int, t: int} =
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let
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fun recurse(a: int, c: int, g: int, t: int, nil) = {a = a, c = c, g = g, t = t}
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| recurse(a: int, c: int, g: int, t: int, hd :: tl) =
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case hd of
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#"A" => recurse(a + 1, c, g, t, tl)
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| #"C" => recurse(a, c + 1, g, t, tl)
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| #"G" => recurse(a, c, g + 1, t, tl)
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| #"T" => recurse(a, c, g, t + 1, tl)
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| _ => raise Fail "Invalid nucleotide in strand"
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in
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recurse (0, 0, 0, 0, explode strand)
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end

‎exercises/practice/nucleotide-count/.meta/tests.toml

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# This is an auto-generated file.
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#
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# Regenerating this file via `configlet sync` will:
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# - Recreate every `description` key/value pair
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# - Recreate every `reimplements` key/value pair, where they exist in problem-specifications
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# - Remove any `include = true` key/value pair (an omitted `include` key implies inclusion)
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# - Preserve any other key/value pair
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#
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# As user-added comments (using the # character) will be removed when this file
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# is regenerated, comments can be added via a `comment` key.
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[3e5c30a8-87e2-4845-a815-a49671ade970]
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description = "empty strand"
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[a0ea42a6-06d9-4ac6-828c-7ccaccf98fec]
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description = "can count one nucleotide in single-character input"
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[eca0d565-ed8c-43e7-9033-6cefbf5115b5]
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description = "strand with repeated nucleotide"
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[40a45eac-c83f-4740-901a-20b22d15a39f]
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description = "strand with multiple nucleotides"
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[b4c47851-ee9e-4b0a-be70-a86e343bd851]
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description = "strand with invalid nucleotides"

‎exercises/practice/nucleotide-count/nucleotide-count.sml

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fun nucleotideCounts (strand: string): {a: int, c: int, g: int, t: int} =
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raise Fail "'nucleotideCounts' is not implemented"

‎exercises/practice/nucleotide-count/test.sml

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(* version 1.0.0 *)
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use "testlib.sml";
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use "nucleotide-count.sml";
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infixr |>
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fun x |> f = f x
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val testsuite =
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describe "nucleotide-count" [
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test "empty strand"
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(fn _ => nucleotideCounts "" |> Expect.equalTo {a = 0, c = 0, g = 0, t = 0}),
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test "can count one nucleotide in single-character input"
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(fn _ => nucleotideCounts "G" |> Expect.equalTo {a = 0, c = 0, g = 1, t = 0}),
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test "strand with repeated nucleotide"
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(fn _ => nucleotideCounts "GGGGGGG" |> Expect.equalTo {a = 0, c = 0, g = 7, t = 0}),
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test "strand with multiple nucleotides"
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(fn _ => nucleotideCounts "AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC" |> Expect.equalTo {a = 20, c = 12, g = 17, t = 21}),
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test "strand with invalid nucleotides"
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(fn _ => (fn _ => nucleotideCounts "AGXXACT") |> Expect.error (Fail "Invalid nucleotide in strand"))
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]
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val _ = Test.run testsuite

‎exercises/practice/nucleotide-count/testlib.sml

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structure Expect =
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struct
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datatype expectation = Pass | Fail of string * string
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local
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fun failEq b a =
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Fail ("Expected: " ^ b, "Got: " ^ a)
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fun failExn b a =
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Fail ("Expected: " ^ b, "Raised: " ^ a)
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fun exnName (e: exn): string = General.exnName e
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in
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fun truthy a =
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if a
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then Pass
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else failEq "true" "false"
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fun falsy a =
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if a
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then failEq "false" "true"
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else Pass
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fun equalTo b a =
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if a = b
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then Pass
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else failEq (PolyML.makestring b) (PolyML.makestring a)
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fun nearTo delta b a =
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if Real.abs (a - b) <= delta * Real.abs a orelse
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Real.abs (a - b) <= delta * Real.abs b
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then Pass
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else failEq (Real.toString b ^ " +/- " ^ Real.toString delta) (Real.toString a)
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fun anyError f =
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(
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f ();
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failExn "an exception" "Nothing"
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) handle _ => Pass
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fun error e f =
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(
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f ();
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failExn (exnName e) "Nothing"
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) handle e' => if exnMessage e' = exnMessage e
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then Pass
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else failExn (exnMessage e) (exnMessage e')
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end
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end
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structure TermColor =
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struct
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datatype color = Red | Green | Yellow | Normal
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fun f Red = "\027[31m"
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| f Green = "\027[32m"
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| f Yellow = "\027[33m"
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| f Normal = "\027[0m"
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fun colorize color s = (f color) ^ s ^ (f Normal)
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val redit = colorize Red
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val greenit = colorize Green
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val yellowit = colorize Yellow
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end
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structure Test =
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struct
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datatype testnode = TestGroup of string * testnode list
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| Test of string * (unit -> Expect.expectation)
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local
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datatype evaluation = Success of string
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| Failure of string * string * string
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| Error of string * string
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fun indent n s = (implode (List.tabulate (n, fn _ => #" "))) ^ s
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fun fmt indentlvl ev =
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let
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val check = TermColor.greenit "\226\156\148 " (* ✔ *)
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val cross = TermColor.redit "\226\156\150 " (* ✖ *)
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val indentlvl = indentlvl * 2
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in
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case ev of
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Success descr => indent indentlvl (check ^ descr)
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| Failure (descr, exp, got) =>
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String.concatWith "\n" [indent indentlvl (cross ^ descr),
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indent (indentlvl + 2) exp,
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indent (indentlvl + 2) got]
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| Error (descr, reason) =>
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String.concatWith "\n" [indent indentlvl (cross ^ descr),
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indent (indentlvl + 2) (TermColor.redit reason)]
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end
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fun eval (TestGroup _) = raise Fail "Only a 'Test' can be evaluated"
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| eval (Test (descr, thunk)) =
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(
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case thunk () of
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Expect.Pass => ((1, 0, 0), Success descr)
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| Expect.Fail (s, s') => ((0, 1, 0), Failure (descr, s, s'))
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)
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handle e => ((0, 0, 1), Error (descr, "Unexpected error: " ^ exnMessage e))
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fun flatten depth testnode =
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let
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fun sum (x, y, z) (a, b, c) = (x + a, y + b, z + c)
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fun aux (t, (counter, acc)) =
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let
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val (counter', texts) = flatten (depth + 1) t
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in
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(sum counter' counter, texts :: acc)
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end
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in
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case testnode of
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TestGroup (descr, ts) =>
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let
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val (counter, texts) = foldr aux ((0, 0, 0), []) ts
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in
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(counter, (indent (depth * 2) descr) :: List.concat texts)
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end
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| Test _ =>
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let
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val (counter, evaluation) = eval testnode
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in
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(counter, [fmt depth evaluation])
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end
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end
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fun println s = print (s ^ "\n")
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in
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fun run suite =
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let
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val ((succeeded, failed, errored), texts) = flatten 0 suite
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val summary = String.concatWith ", " [
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TermColor.greenit ((Int.toString succeeded) ^ " passed"),
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TermColor.redit ((Int.toString failed) ^ " failed"),
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TermColor.redit ((Int.toString errored) ^ " errored"),
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(Int.toString (succeeded + failed + errored)) ^ " total"
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]
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val status = if failed = 0 andalso errored = 0
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then OS.Process.success
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else OS.Process.failure
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in
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List.app println texts;
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println "";
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println ("Tests: " ^ summary);
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OS.Process.exit status
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end
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end
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end
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fun describe description tests = Test.TestGroup (description, tests)
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fun test description thunk = Test.Test (description, thunk)

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