From 668753ccea51cb04f8a8c1b76e8ae2bb209ec678 Mon Sep 17 00:00:00 2001
From: graemevissers <51211544+graemevissers@users.noreply.github.com>
Date: Wed, 26 Aug 2020 02:26:48 -0700
Subject: [PATCH] #30: Add nucleotide tests (#109)
* Add testCase "symbol"
* Add test "formula"
* Add test "isTerminator"
* Add test "isTerminator"
* Add test "isGap"
* Add test "name"
* Add NucleotideTests.fs to Main. Fix errors
* Add test "charToParsedNucleotideChar"
* Add test "complement"
* Add test "replaceTbyU"
* Add test "replaceUbyT"
---
.../BioFSharp.Tests.NetCore.fsproj | 1 +
.../BioFSharp/NucleotideTests.fs | 132 ++++++++++++++++++
tests/BioFSharp.Tests.NetCore/Main.fs | 2 +
3 files changed, 135 insertions(+)
create mode 100644 tests/BioFSharp.Tests.NetCore/BioFSharp/NucleotideTests.fs
diff --git a/tests/BioFSharp.Tests.NetCore/BioFSharp.Tests.NetCore.fsproj b/tests/BioFSharp.Tests.NetCore/BioFSharp.Tests.NetCore.fsproj
index 4269d670..ad1fc4f3 100644
--- a/tests/BioFSharp.Tests.NetCore/BioFSharp.Tests.NetCore.fsproj
+++ b/tests/BioFSharp.Tests.NetCore/BioFSharp.Tests.NetCore.fsproj
@@ -10,6 +10,7 @@
+
diff --git a/tests/BioFSharp.Tests.NetCore/BioFSharp/NucleotideTests.fs b/tests/BioFSharp.Tests.NetCore/BioFSharp/NucleotideTests.fs
new file mode 100644
index 00000000..94a71822
--- /dev/null
+++ b/tests/BioFSharp.Tests.NetCore/BioFSharp/NucleotideTests.fs
@@ -0,0 +1,132 @@
+module NucleotideTests
+
+open BioFSharp
+open Nucleotides
+open Formula
+open Expecto
+
+let allNucs = [
+ Nucleotide.A; Nucleotide.T; Nucleotide.G; Nucleotide.C; Nucleotide.U
+ Nucleotide.I; Nucleotide.Gap; Nucleotide.Ter; Nucleotide.R
+ Nucleotide.Y; Nucleotide.K; Nucleotide.M; Nucleotide.S
+ Nucleotide.W; Nucleotide.B; Nucleotide.D; Nucleotide.H
+ Nucleotide.V; Nucleotide.N
+]
+let allSymbols = ['A';'T';'G';'C';'U';'I';'-';'*';'R';'Y';'K';'M';'S';'W';'B';'D';'H';'V';'N']
+let allFormuals = [
+ Formula.Table.A; Formula.Table.T; Formula.Table.G; Formula.Table.C; Formula.Table.U
+ Formula.Table.I; Formula.emptyFormula; Formula.emptyFormula; Formula.emptyFormula
+ Formula.emptyFormula; Formula.emptyFormula; Formula.emptyFormula; Formula.emptyFormula
+ Formula.emptyFormula; Formula.emptyFormula; Formula.emptyFormula; Formula.emptyFormula
+ Formula.emptyFormula; Formula.emptyFormula
+]
+let allNames = [
+ "Adenine"; "Thymidine"; "Guanine"; "Cytosine"; "Uracil"
+ "Inosine"; "Gap" ; "Ter" ; "puRine" ; "pYrimidine"
+ "Keto" ; "aMino" ; "Strong base pair" ; "Weak base pair"
+ "not A" ; "not C" ; "not G" ; "not T/U" ; "Unspecified"
+]
+let allParsedNucChars = [
+ StandardCodes Nucleotide.A; Standard_DNAonly Nucleotide.T; StandardCodes Nucleotide.G
+ StandardCodes Nucleotide.C; Standard_RNAonly Nucleotide.U; Standard_RNAonly Nucleotide.I
+ GapTer Nucleotide.Gap; GapTer Nucleotide.Ter; AmbiguityCodes Nucleotide.R
+ AmbiguityCodes Nucleotide.Y; AmbiguityCodes Nucleotide.K; AmbiguityCodes Nucleotide.M
+ AmbiguityCodes Nucleotide.S; AmbiguityCodes Nucleotide.W; AmbiguityCodes Nucleotide.B
+ AmbiguityCodes Nucleotide.D; AmbiguityCodes Nucleotide.H; AmbiguityCodes Nucleotide.V
+ AmbiguityCodes Nucleotide.N; NoNucChar '!'
+]
+
+[]
+let nucleotideTests =
+ testList "Nucleotides" [
+ testCase "symbol" (fun() ->
+ let testSymbols = allNucs |> List.map(fun nuc -> Nucleotides.symbol nuc)
+ Expect.equal
+ testSymbols
+ allSymbols
+ "Nucleotides.symbol did not return the correct symbol for all Nucleotides."
+ )
+ testCase "formula" (fun() ->
+ let testFormulas = allNucs |> List.map(fun nuc -> Nucleotides.formula nuc)
+ Expect.equal
+ testFormulas
+ allFormuals
+ "Nucleotides.formula did not return the correct formula for all Nucleotides."
+ )
+ testCase "isTerminator" (fun() ->
+ let testBools = [
+ false; false; false; false; false; false; false; true; false
+ false; false; false; false; false; false; false; false; false
+ false
+ ]
+ Expect.equal
+ (allNucs |> List.map(fun nuc -> Nucleotides.isTerminator nuc))
+ testBools
+ "Nucleotides.isTerminator did not return the correct boolean for all Nucleotides."
+ )
+ testCase "isGap" (fun() ->
+ let testBools = [
+ false; false; false; false; false; false; true; false; false
+ false; false; false; false; false; false; false; false; false
+ false
+ ]
+ Expect.equal
+ (allNucs |> List.map(fun nuc -> Nucleotides.isGap nuc))
+ testBools
+ "Nucleotides.isGap did not return the correct boolean for all Nucleotides."
+ )
+ testCase "name" (fun() ->
+ let testNames = (allNucs |> List.map(fun nuc -> Nucleotides.name nuc))
+ Expect.equal
+ testNames
+ allNames
+ "Nucleotides.name did not return the correct name for all nucleotides."
+ )
+ testCase "charToParsedNucleotideChar" (fun() ->
+ let testSymbols = List.append allSymbols ['!']
+ let testParsedNucChars = (testSymbols |> List.map(fun nuc -> Nucleotides.charToParsedNucleotideChar nuc))
+ Expect.equal
+ testParsedNucChars
+ allParsedNucChars
+ "Nucleotides.charToParsedNucleotideChar did not return correct ParsedNucleotideChar for all Nucleotides."
+ )
+ testCase "complement" (fun () ->
+ let allComplementNucs = [
+ Nucleotide.T; Nucleotide.A; Nucleotide.C; Nucleotide.G; Nucleotide.A
+ Nucleotide.I; Nucleotide.Gap; Nucleotide.Ter; Nucleotide.Y; Nucleotide.R
+ Nucleotide.M; Nucleotide.K; Nucleotide.S; Nucleotide.W; Nucleotide.V
+ Nucleotide.H; Nucleotide.D; Nucleotide.B; Nucleotide.N
+ ]
+ let testComplementNucs = (allNucs |> List.map(fun nuc -> Nucleotides.complement nuc))
+ Expect.equal
+ testComplementNucs
+ allComplementNucs
+ "Nucleotides.complement did not return the correct complement Nucleotide for all Nucleotides."
+ )
+ testCase "replaceTbyU" (fun () ->
+ let allNucsReplaceTbyU = [
+ Nucleotide.A; Nucleotide.U; Nucleotide.G; Nucleotide.C; Nucleotide.U
+ Nucleotide.I; Nucleotide.Gap; Nucleotide.Ter; Nucleotide.R
+ Nucleotide.Y; Nucleotide.K; Nucleotide.M; Nucleotide.S; Nucleotide.W
+ Nucleotide.B; Nucleotide.D; Nucleotide.H; Nucleotide.V; Nucleotide.N
+ ]
+ let testNucsReplaceTbyU = (allNucs |> List.map(fun nuc -> Nucleotides.replaceTbyU nuc))
+ Expect.equal
+ testNucsReplaceTbyU
+ allNucsReplaceTbyU
+ "Nucleotides.replaceTbyU did not return the correct Nucleotide for all Nucleotides."
+ )
+ testCase "replaceUbyT" (fun () ->
+ let allNucsReplaceUbyT = [
+ Nucleotide.A; Nucleotide.T; Nucleotide.G; Nucleotide.C; Nucleotide.T
+ Nucleotide.I; Nucleotide.Gap; Nucleotide.Ter; Nucleotide.R
+ Nucleotide.Y; Nucleotide.K; Nucleotide.M; Nucleotide.S; Nucleotide.W
+ Nucleotide.B; Nucleotide.D; Nucleotide.H; Nucleotide.V; Nucleotide.N
+ ]
+ let testNucsReplaceUbyT = (allNucs |> List.map(fun nuc -> Nucleotides.replaceUbyT nuc))
+ Expect.equal
+ testNucsReplaceUbyT
+ allNucsReplaceUbyT
+ "Nucleotides.replaceUbyT did not return the correct Nucleotide for all Nucleotides."
+ )
+ ]
diff --git a/tests/BioFSharp.Tests.NetCore/Main.fs b/tests/BioFSharp.Tests.NetCore/Main.fs
index ec8403d9..9713bebd 100644
--- a/tests/BioFSharp.Tests.NetCore/Main.fs
+++ b/tests/BioFSharp.Tests.NetCore/Main.fs
@@ -20,4 +20,6 @@ let main argv =
Tests.runTestsWithCLIArgs [] argv AminoAcidTests.aminoAcidTests |> ignore
+ Tests.runTestsWithCLIArgs [] argv NucleotideTests.nucleotideTests |> ignore
+
0
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