CSBiology#30: Add amino acid tests (CSBiology#108)

* Add "teset_rangePpm" to testList "BioFSharp.Mass"

* Add testCase "formula" to testList "AminoAcids"

* Add "formulaModifiedAA" to testList "AminoAcids"

* Fix "formulaModifiedAA" testCase

* Add "isTerminator" to testList "AminoAcids"

* Add "isGap" to testList "AminoAcids"

* Add "setModification" to testList "AminoAcids"

* Clean up tests

* Change error message for test "setModification"

* Add "setModifications" to "AminoAcids" testList

* Add "getModifications" to "AminoAcids" testList

* Add testCase "getAminoAcidWithoutMod"

* Add test "tryGetModifications"

* Add test "tryGetModifications_withNone"

* Add test "isotopicLabelFunc"

* Add "isotopicLabelFunc_withUnmodifiedAAs"

* Add "charToParsedAminoAcidChar"

* Add test "aminoAcidSetStandard"

* Add test "aminoAcidSetProteinogenic"

* Add test "aminoAcidSetProteinogenicEucaryotes"

* Add test "aminoAcidSetAmbiguity"

* Add test "aminoAcidSetGapTer"

* Add test "aminoAcidSetPosCharged"

* Add test "aminoAcidSetNegCharged"

* Add test "aminoAcidSetPolarUncharged"

* Add test "aminoAcidSetHydrophobic"

* Add test "aminoAcidSetSpecialCases"

* Add test "isPolarUncharged"

* Add test "isModified_withUnmodAAs"

* Add test "isModified_withModAAs"

* Add test "getModifications_withUnmodAAs"

* Delete coverage.xml.637327725072680050L.exn

Seems like these are artifacts from your testing process, i cant reproduce these when starting the tests from your branch, so i would delete these and merge the PR afterwards

* Delete coverage.xml.637330276045185520L.exn

see previous commit

* Fix merge commit for aa tests

Co-authored-by: Kevin Schneider <[email protected]>
Co-authored-by: Kevin Schneider <[email protected]>

tests/BioFSharp.Tests.NetCore/BioFSharp/AminoAcidTests.fs

@@ -38,6 +38,21 @@ let allAAs = [
     AminoAcid.Glx; AminoAcid.Asx; AminoAcid.Gap; AminoAcid.Ter
 ]
 
+let allParsedAAs = [
+    StandardCodes AminoAcid.Ala; StandardCodes AminoAcid.Cys; StandardCodes AminoAcid.Asp
+    StandardCodes AminoAcid.Glu; StandardCodes AminoAcid.Phe; StandardCodes AminoAcid.Gly
+    StandardCodes AminoAcid.His; StandardCodes AminoAcid.Ile; StandardCodes AminoAcid.Lys
+    StandardCodes AminoAcid.Leu; StandardCodes AminoAcid.Met; StandardCodes AminoAcid.Asn
+    StandardCodes AminoAcid.Pyl; StandardCodes AminoAcid.Pro; StandardCodes AminoAcid.Gln
+    StandardCodes AminoAcid.Arg; StandardCodes AminoAcid.Ser; StandardCodes AminoAcid.Thr
+    StandardCodes AminoAcid.Sel; StandardCodes AminoAcid.Sel; StandardCodes AminoAcid.Val
+    StandardCodes AminoAcid.Trp; StandardCodes AminoAcid.Tyr; AmbiguityCodes AminoAcid.Xaa
+    AmbiguityCodes AminoAcid.Xle; AmbiguityCodes AminoAcid.Glx; AmbiguityCodes AminoAcid.Asx
+    GapTer AminoAcid.Gap; GapTer AminoAcid.Ter; NoAAChar '!'
+]
+
+let allModFormulas = (allFormulas |> List.map(fun f -> Formula.replaceElement f Elements.Table.N Elements.Table.Heavy.N15))
+
 let allSingleModAAs = allAAs |> List.map (fun aa -> AminoAcids.Mod (aa, [ModificationInfo.Table.N15]))
 let allDoubleModAAs = allAAs |> List.map (fun aa -> AminoAcids.Mod (aa, [ModificationInfo.Table.N15; ModificationInfo.Table.H2O]))
 
@@ -114,4 +129,181 @@ let aminoAcidTests =
                 allMods
                 "AminoAcids.getModifications did not return correct Modifications for all modified AminoAcids"
         )
+
+        testCase "getModifications_withUnmodAAs" (fun () ->
+            let allEmptyLists = [for i in 1 .. 29 -> []]
+            Expect.equal
+                (allAAs |> List.map (fun aa -> AminoAcids.getModifications aa))
+                allEmptyLists
+                "AminoAcids.getModifications did not return correct empty list for all unmodified AminoAcids"
+        )
+        testCase "getAminoAcidWithoutMod" (fun () ->
+            Expect.equal    
+                (allSingleModAAs |> List.map (fun aa -> AminoAcids.getAminoAcidWithoutMod aa))
+                allAAs
+                "AminoAcids.getAminoAcidWithoutMod did not return correct AminoAcid for all AminoAcids"
+        )
+        testCase "tryGetModifications" (fun () ->
+            let allMods = [for i in 1 .. 29 -> Some [ModificationInfo.Table.N15]]
+            Expect.equal
+                (allSingleModAAs |> List.map (fun aa -> AminoAcids.tryGetModifications aa))
+                allMods
+                "AminoAcids.tryGetModifications did not return correct Modifications for all modified AminoAcids"
+        )
+        testCase "tryGetModifications_withNone" (fun () ->
+            Expect.equal
+                (allAAs |> List.map (fun aa -> AminoAcids.tryGetModifications aa))
+                [for i in 1 .. 29 -> None]
+                "AminoAcids.tryGetModifications did not return correct Modifications for all unmodified AminoAcids"
+        )
+        testCase "isotopicLabelFunc" (fun () ->
+            Expect.equal
+                (List.map2 (fun aa f -> AminoAcids.isotopicLabelFunc aa f) allSingleModAAs allFormulas)
+                allModFormulas
+                "AminoAcids.isotopicLabelFunc did not return correct function for all Modified AminoAcids"    
+        )
+        testCase "isotopicLabelFunc_withUnmodifiedAAs" (fun () ->
+            Expect.equal
+                (List.map2 (fun aa f -> AminoAcids.isotopicLabelFunc aa f) allAAs allFormulas)
+                allFormulas
+                "AminoAcids.isotopicLabelFunc did not return correct function for all unmodified AminoAcids"
+        )
+        testCase "charToParsedAminoAcidChar" (fun () -> // This function currently matches to Sel, not Sec. Will eventually need chane
+            let testParsedSymbols = List.append allSymbols ['!']
+            Expect.equal
+                (List.map (fun c -> AminoAcids.charToParsedAminoAcidChar c) testParsedSymbols)
+                allParsedAAs
+                "AminoAcids.charToParsedAminoAcidChar did not return correct AminoAcid from all AminoAcid chars"
+        )
+        testCase "aminoAcidSetStandard" (fun () ->
+            let testAASetStandard = set [
+                AminoAcid.Ala; AminoAcid.Cys; AminoAcid.Asp; AminoAcid.Glu
+                AminoAcid.Phe; AminoAcid.Gly; AminoAcid.His; AminoAcid.Ile
+                AminoAcid.Lys; AminoAcid.Leu; AminoAcid.Met; AminoAcid.Asn
+                AminoAcid.Pro; AminoAcid.Gln; AminoAcid.Arg; AminoAcid.Ser
+                AminoAcid.Thr; AminoAcid.Val; AminoAcid.Trp; AminoAcid.Tyr
+            ]
+            Expect.equal
+                AminoAcids.aminoAcidSetStandard
+                testAASetStandard
+                "AminoAcids.aminoAcidSetStandard did not return correct standard set of AminoAcids"
+        )
+        testCase "aminoAcidSetProteinogenic" (fun () ->
+            let testAASetProteinogenic = set [
+                AminoAcid.Ala; AminoAcid.Cys; AminoAcid.Asp; AminoAcid.Glu
+                AminoAcid.Phe; AminoAcid.Gly; AminoAcid.His; AminoAcid.Ile
+                AminoAcid.Lys; AminoAcid.Leu; AminoAcid.Met; AminoAcid.Asn
+                AminoAcid.Pro; AminoAcid.Gln; AminoAcid.Arg; AminoAcid.Ser
+                AminoAcid.Thr; AminoAcid.Val; AminoAcid.Trp; AminoAcid.Tyr
+                AminoAcid.Sel; AminoAcid.Sec; AminoAcid.Pyl
+            ]
+            Expect.equal
+                AminoAcids.aminoAcidSetProteinogenic
+                testAASetProteinogenic
+                "AminoAcids.aminoAcidSetProteinogenic did not return correct set of AminoAcids"
+        )
+        testCase "aminoAcidSetProteinogenicEucaryotes" (fun () ->
+            let testAASetProteinogenicEucaryotes = set [
+                AminoAcid.Ala; AminoAcid.Cys; AminoAcid.Asp; AminoAcid.Glu
+                AminoAcid.Phe; AminoAcid.Gly; AminoAcid.His; AminoAcid.Ile
+                AminoAcid.Lys; AminoAcid.Leu; AminoAcid.Met; AminoAcid.Asn
+                AminoAcid.Pro; AminoAcid.Gln; AminoAcid.Arg; AminoAcid.Ser
+                AminoAcid.Thr; AminoAcid.Val; AminoAcid.Trp; AminoAcid.Tyr
+                AminoAcid.Sel; AminoAcid.Sec;
+            ]
+            Expect.equal
+                AminoAcids.aminoAcidSetProteinogenicEucaryotes
+                testAASetProteinogenicEucaryotes
+                "AminoAcids.aminoAcidSetProteinogenicEucaryotes did not return correct set of AminoAcids"
+        )
+        testCase "aminoAcidSetAmbiguity" (fun () ->
+            let testAASetAmbiguity = set [
+                AminoAcid.Xaa; AminoAcid.Xle; AminoAcid.Glx; AminoAcid.Asx
+            ]
+            Expect.equal
+                AminoAcids.aminoAcidSetAmbiguity
+                testAASetAmbiguity
+                "AminoAcids.aminoAcidSetAmbiguity did not return the correct set of AminoAcids"
+        )
+        testCase "aminoAcidSetGapTer" (fun () ->
+            let testAASetGapTer = set [AminoAcid.Gap; AminoAcid.Ter]
+            Expect.equal
+                AminoAcids.aminoAcidSetGapTer
+                testAASetGapTer
+                "AminoAcids.aminoAcidSetGapTer did not return the correct set of AminoAcids"
+        )
+        testCase "aminoAcidSetPosCharged" (fun () ->
+            let testAAPosCharged = set [AminoAcid.Arg; AminoAcid.Lys; AminoAcid.His]
+            Expect.equal
+                AminoAcids.aminoAcidSetPosCharged
+                testAAPosCharged
+                "AminoAcids.aminoAcidSetPosCharged did not return the correct set of AminoAcids"
+        )
+        testCase "aminoAcidSetNegCharged" (fun () ->
+            let testAANegCharged = set [
+                AminoAcid.Asp; AminoAcid.Glu
+            ]
+            Expect.equal
+                AminoAcids.aminoAcidSetNegCharged
+                testAANegCharged
+                "AminoAcids.aminoAcidSetNegCharged did not return the correct set of AminoAcids"
+        )
+        testCase "aminoAcidSetPolarUncharged" (fun () ->
+            let testAASetPolarUncharged = set [
+                AminoAcid.Gln; AminoAcid.Asn; AminoAcid.Ser; AminoAcid.Thr
+            ]
+            Expect.equal
+                AminoAcids.aminoAcidSetPolarUncharged
+                testAASetPolarUncharged
+                "AminoAcids.aminoAcidSetPolarUncharged did not return the correct set of AminoAcids"
+        )
+        testCase "aminoAcidSetHydrophobic" (fun () ->
+            let testAASetHydrophobic = set [
+                AminoAcid.Ala; AminoAcid.Ile; AminoAcid.Leu; AminoAcid.Met
+                AminoAcid.Phe; AminoAcid.Trp; AminoAcid.Tyr; AminoAcid.Val
+            ]
+            Expect.equal
+                AminoAcids.aminoAcidSetHydrophobic
+                testAASetHydrophobic
+                "AminoAcids.aminoAcidSetHydrophobic did not return the correct set of AminoAcids"
+        )
+        testCase "aminoAcidSetSpecialCases" (fun () ->
+            let testAASetSpecialCases = set [
+                AminoAcid.Cys; AminoAcid.Sel; AminoAcid.Sec; AminoAcid.Gly
+                AminoAcid.Pro
+            ]
+            Expect.equal
+                AminoAcids.aminoAcidSetSpecialCases
+                testAASetSpecialCases
+                "AminoAcids.aminoAcidSetSpecialCases did not return the correct set of AminoAcids"
+        )
+        testCase "isPolarUncharged" (fun () ->
+            let testIsPolarUncharged = [
+                false; false; false; false
+                false; false; false; false
+                false; false; false; true
+                false; false; true;  false
+                true;  true;  false; false; false
+                false; false; false; false
+                false; false; false; false
+            ]
+            Expect.equal
+                (allAAs |> List.map (fun aa -> AminoAcids.isPolarUncharged aa))
+                testIsPolarUncharged
+                "AminoAcids.isPolarUncharged did not return correct boolean for each AminoAcid"
+        )
+        testCase "isModified_withUnmodAAs" (fun () ->
+            let testIsModifiedFalse = [for i in 1 .. 29 -> false]
+            Expect.equal
+                (allAAs |> List.map (fun aa -> AminoAcids.isModified aa))
+                testIsModifiedFalse
+                "AminoAcids.isModified did not return correct boolean for each unmodified AminoAcid"
+        )
+        testCase "isModified_withModAAs" (fun () ->
+            let testIsModifiedTrue = [for i in 1 .. 29 -> true]
+            Expect.equal
+                (allSingleModAAs |> List.map (fun aa -> AminoAcids.isModified aa))
+                testIsModifiedTrue
+                "AminoAcids.isModified did not return correct boolean for each modified AminoAcid"
+        )
     ]