Merge pull request #4 from CSBiology/developer

CSBiology#30: Add nucleotide tests (CSBiology#109)

tests/BioFSharp.Tests.NetCore/BioFSharp.Tests.NetCore.fsproj

@@ -10,6 +10,7 @@
     <Compile Include="Utils.fs" />
     <Compile Include="BioFSharp\AminoAcidTests.fs" />
     <Compile Include="BioFSharp\DigestionTests.fs" />
+    <Compile Include="BioFSharp\NucleotideTests.fs" />
     <Compile Include="BioFSharp\BioCollections.fs" />
     <Compile Include="BioFSharp\BioItemTests.fs" />
     <Compile Include="Main.fs" />

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 '!'
+]
+
+[<Tests>]
+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."
+        )
+    ]

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