Added the Obesity disease to genetic analyses.

Changelog.md

@@ -6,6 +6,7 @@ Small and insignificant changes may not be included in this log.
 
 ## Unversioned Changes
 
+* Added the Obesity disease to genetic analyses. - *Simon Sarasova*
 * Implemented neural network prediction for polygenic diseases to replace old method. Added autism and homosexualness to genetic analyses. - *Simon Sarasova*
 * Increased the quantity of attributes that are extracted from the OpenSNP biobank data archive. - *Simon Sarasova*
 * Added numeric traits to genetic analyses. - *Simon Sarasova*

Contributors.md

@@ -9,4 +9,4 @@ Many other people have written code for modules which are imported by Seekia. Th
 
 Name | Date Of First Commit | Number Of Commits
 --- | --- | ---
-Simon Sarasova | June 13, 2023 | 278
+Simon Sarasova | June 13, 2023 | 279

internal/appUsers/appUsers.go

@@ -395,7 +395,8 @@ func initializeApplicationVariables()error{
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
 
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()
+	if (err != nil) { return err }
 
 	err = traits.InitializeTraitVariables()
 	if (err != nil) { return err }

internal/generate/generate_test.go

@@ -37,9 +37,13 @@ func TestGenerateParameters(t *testing.T){
 func TestGenerateProfiles(t *testing.T){
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
 
-	err := traits.InitializeTraitVariables()
+	err := polygenicDiseases.InitializePolygenicDiseaseVariables()
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
+
+	err = traits.InitializeTraitVariables()
 	if (err != nil) {
 		t.Fatalf("InitializeTraitVariables failed: " + err.Error())
 	}

internal/genetics/createCoupleGeneticAnalysis/createCoupleGeneticAnalysis_test.go

@@ -25,7 +25,11 @@ func TestCreateCoupleGeneticAnalysis_SingleGenomes(t *testing.T){
 	}
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()	
+
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()	
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
 
 	err = traits.InitializeTraitVariables()
 	if (err != nil) {
@@ -104,7 +108,11 @@ func TestCreateCoupleGeneticAnalysis_SingleAndMultipleGenomes(t *testing.T){
 	}
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()	
+
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()	
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
 
 	err = traits.InitializeTraitVariables()
 	if (err != nil) {
@@ -206,7 +214,11 @@ func TestCreateCoupleGeneticAnalysis_MultipleGenomes(t *testing.T){
 	}
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()	
+
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()	
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
 
 	err = traits.InitializeTraitVariables()
 	if (err != nil) {

internal/genetics/createPersonGeneticAnalysis/createPersonGeneticAnalysis_test.go

@@ -25,7 +25,11 @@ func TestCreatePersonGeneticAnalysis_SingleGenome(t *testing.T){
 	}
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
+
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()	
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
 
 	err = traits.InitializeTraitVariables()
 	if (err != nil) {
@@ -88,7 +92,11 @@ func TestCreatePersonGeneticAnalysis_MultipleGenomes(t *testing.T){
 	}
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
+
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()	
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
 
 	err = traits.InitializeTraitVariables()
 	if (err != nil) {

internal/genetics/geneticPrediction/geneticPrediction.go

@@ -804,7 +804,8 @@ func GetNumericOutcomeValueFromOutputLayer(attributeName string, outputLayer []f
 				return 54, 272, nil
 			}
 			case "Autism",
-				"Homosexualness":{
+				"Homosexualness",
+				"Obesity":{
 				return 0, 10, nil
 			}
 		}
@@ -860,6 +861,11 @@ func getNeuralNetworkLayerSizes(attributeName string)(int, int, int, int, error)
 			// There is 1 output neuron, representing a homosexualness value
 			return 12, 10, 5, 1, nil
 		}
+		case "Obesity":{
+			// There are 3000 input neurons
+			// There is 1 output neuron, representing an obesity value
+			return 3000, 3, 2, 1, nil
+		}
 	}
 
 	return 0, 0, 0, 0, errors.New("getNeuralNetworkLayerSizes called with unknown attributeName: " + attributeName)
@@ -931,7 +937,8 @@ func CreateGeneticPredictionTrainingData_OpenSNP(
 
 				return traitLociList, nil
 			}
-			case "Autism":{
+			case "Autism",
+				"Obesity":{
 
 				diseaseObject, err := polygenicDiseases.GetPolygenicDiseaseObject(attributeName)
 				if (err != nil) { return nil, err }
@@ -1106,6 +1113,21 @@ func CreateGeneticPredictionTrainingData_OpenSNP(
 
 				outputLayer := []float32{outputValueFloat32}
 
+				return true, outputLayer, nil
+			}
+			case "Obesity":{
+
+				userObesityIsKnown := userPhenotypeDataObject.ObesityIsKnown
+				if (userObesityIsKnown == false){
+					return false, nil, nil
+				}
+
+				userObesity := userPhenotypeDataObject.Obesity
+
+				outputValueFloat32 := float32(userObesity)
+
+				outputLayer := []float32{outputValueFloat32}
+
 				return true, outputLayer, nil
 			}
 		}

internal/genetics/sampleAnalyses/sampleAnalyses_test.go

@@ -15,9 +15,13 @@ import "testing"
 func TestPersonSampleAnalyses(t *testing.T){
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
 
-	err := traits.InitializeTraitVariables()
+	err := polygenicDiseases.InitializePolygenicDiseaseVariables()	
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
+
+	err = traits.InitializeTraitVariables()
 	if (err != nil) {
 		t.Fatalf("InitializeTraitVariables failed: " + err.Error())
 	}
@@ -47,9 +51,13 @@ func TestPersonSampleAnalyses(t *testing.T){
 func TestCoupleSampleAnalyses(t *testing.T){
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
 
-	err := traits.InitializeTraitVariables()
+	err := polygenicDiseases.InitializePolygenicDiseaseVariables()	
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
+
+	err = traits.InitializeTraitVariables()
 	if (err != nil) {
 		t.Fatalf("InitializeTraitVariables failed: " + err.Error())
 	}

internal/network/serverRequest/serverRequest_test.go

@@ -1382,14 +1382,18 @@ func TestCreateAndReadRequest_BroadcastContent(t *testing.T){
 
 	// We initialize these variables so we can create fake profiles
 
-	err := traits.InitializeTraitVariables()
+	monogenicDiseases.InitializeMonogenicDiseaseVariables()
+
+	err := polygenicDiseases.InitializePolygenicDiseaseVariables()	
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
+
+	err = traits.InitializeTraitVariables()
 	if (err != nil) {
 		t.Fatalf("InitializeTraitVariables failed: " + err.Error())
 	}
 
-	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
-
 	err = profileFormat.InitializeProfileFormatVariables()
 	if (err != nil) {
 		t.Fatalf("Failed to initialize profile format variables: " + err.Error())

internal/network/serverResponse/serverResponse_test.go

@@ -326,14 +326,18 @@ func TestCreateAndReadResponse_GetProfilesInfo(t *testing.T){
 
 func TestCreateAndReadResponse_GetProfiles(t *testing.T){
 
-	err := traits.InitializeTraitVariables()
+	monogenicDiseases.InitializeMonogenicDiseaseVariables()
+
+	err := polygenicDiseases.InitializePolygenicDiseaseVariables()	
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
+
+	err = traits.InitializeTraitVariables()
 	if (err != nil) {
 		t.Fatalf("InitializeTraitVariables failed: " + err.Error())
 	}
 
-	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
-
 	err = profileFormat.InitializeProfileFormatVariables()
 	if (err != nil) {
 		t.Fatalf("Failed to initialize profile format variables: " + err.Error())

internal/profiles/attributeDisplay/attributeDisplay_test.go

@@ -19,7 +19,10 @@ func TestGetAttributeDisplayInfo(t *testing.T){
 		t.Fatalf("InitializeGlobalSettingsDatastore failed: " + err.Error())
 	}
 
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
 
 	err = traits.InitializeTraitVariables()
 	if (err != nil) {

internal/profiles/profileFormat/profileFormat_test.go

@@ -10,11 +10,15 @@ import "seekia/internal/helpers"
 import "testing"
 import "strings"
 
+
 func TestProfileFormat(t *testing.T){
 
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
+	err := polygenicDiseases.InitializePolygenicDiseaseVariables()
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
 
-	err := traits.InitializeTraitVariables()
+	err = traits.InitializeTraitVariables()
 	if (err != nil) {
 		t.Fatalf("InitializeTraitVariables failed: " + err.Error())
 	}
@@ -199,7 +203,10 @@ func TestProfileGeneticReferences(t *testing.T){
 		}
 	}
 
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()
+	if (err != nil) {
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
 
 	polygenicDiseaseObjectsList, err := polygenicDiseases.GetPolygenicDiseaseObjectsList()
 	if (err != nil) {

resources/geneticPredictionModels/geneticPredictionModels.go

@@ -27,6 +27,9 @@ var predictionModel_Autism []byte
 //go:embed predictionModels/HomosexualnessModel.gob
 var predictionModel_Homosexualness []byte
 
+//go:embed predictionModels/ObesityModel.gob
+var predictionModel_Obesity []byte
+
 
 //Outputs:
 //	-bool: Model exists
@@ -50,6 +53,9 @@ func GetGeneticPredictionModelBytes(traitName string)(bool, []byte){
 		case "Homosexualness":{
 			return true, predictionModel_Homosexualness
 		}
+		case "Obesity":{
+			return true, predictionModel_Obesity
+		}
 	}
 
 	return false, nil
@@ -87,6 +93,9 @@ var predictionAccuracy_Autism []byte
 //go:embed predictionModelAccuracies/HomosexualnessModelAccuracy.gob
 var predictionAccuracy_Homosexualness []byte
 
+//go:embed predictionModelAccuracies/ObesityModelAccuracy.gob
+var predictionAccuracy_Obesity []byte
+
 
 // The files returned by this function are .gob encoded geneticPrediction.NumericAttributePredictionAccuracyInfoMap objects
 func GetPredictionModelNumericAttributeAccuracyInfoBytes(attributeName string)([]byte, error){
@@ -101,6 +110,9 @@ func GetPredictionModelNumericAttributeAccuracyInfoBytes(attributeName string)([
 		case "Homosexualness":{
 			return predictionAccuracy_Homosexualness, nil
 		}
+		case "Obesity":{
+			return predictionAccuracy_Obesity, nil
+		}
 	}
 
 	return nil, errors.New("GetPredictionModelNumericAttributeAccuracyInfoBytes called with unknown attributeName: " + attributeName)

resources/geneticPredictionModels/geneticPredictionModels_test.go

@@ -9,7 +9,7 @@ import "seekia/internal/genetics/geneticPrediction"
 
 func TestGeneticPredictionModels(t *testing.T){
 
-	attributeNamesList := []string{"Eye Color", "Lactose Tolerance", "Height", "Autism"}
+	attributeNamesList := []string{"Eye Color", "Lactose Tolerance", "Height", "Autism", "Obesity"}
 
 	for _, attributeName := range attributeNamesList{
 
@@ -43,7 +43,7 @@ func TestGeneticPredictionModelAccuracies(t *testing.T){
 		}
 	}
 
-	numericAttributeNamesList := []string{"Height", "Autism", "Homosexualness"}
+	numericAttributeNamesList := []string{"Height", "Autism", "Homosexualness", "Obesity"}
 
 	for _, attributeName := range numericAttributeNamesList{
 

resources/geneticReferences/geneticReferences_test.go

@@ -185,7 +185,10 @@ func TestGeneticReferences(t *testing.T){
 		}
 	}
 
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()
+	if (err != nil){
+		t.Fatalf("InitializePolygenicDiseaseVariables failed: " + err.Error())
+	}
 
 	polygenicDiseaseObjectsList, err := polygenicDiseases.GetPolygenicDiseaseObjectsList()
 	if (err != nil) {

resources/geneticReferences/polygenicDiseases/obesity.go

@@ -0,0 +1,83 @@
+package polygenicDiseases
+
+import "seekia/internal/helpers"
+
+import _ "embed"
+
+import "errors"
+import "encoding/gob"
+import "bytes"
+import "maps"
+
+
+//go:embed rsIDs/GiantObesityStudyLoci.gob
+var GiantObesityStudyLociFile []byte
+
+
+func getObesityDiseaseObject()(PolygenicDisease, error){
+
+	// Map Structure: rsID -> References Map
+	locusReferencesMap := make(map[int64]map[string]string)
+
+	referencesMap_List1 := make(map[string]string)
+	referencesMap_List1["GIANT consortium - Meta-analyses of Genome-Wide Association Studies - 2022 - Obesity"] = "https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files"
+
+	// These SNPs are taken from the meta-analyses of Genome-Wide Association Studies (GWAS) created by the GIANT consortium
+	//https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files
+
+	// Download link:
+	// https://portals.broadinstitute.org/collaboration/giant/images/0/09/PublicRelease.WHRadjBMI.C.All.Add.txt.gz
+
+	// SHA-256 Checksum:
+	// 2a863b0357037ae5c34853342052ed3c59735d6440da0fd15d1cab34b7d49daf
+
+	// See /utilities/extractGiantLoci/extractGiantLoci.go to see how they were extracted from the file
+
+	buffer := bytes.NewBuffer(GiantObesityStudyLociFile)
+	decoder := gob.NewDecoder(buffer)
+
+	var lociList_1 []int64
+
+	err := decoder.Decode(&lociList_1)
+	if (err != nil){ return PolygenicDisease{}, err }
+
+	for _, rsID := range lociList_1{
+		locusReferencesMap[rsID] = maps.Clone(referencesMap_List1)
+	}
+
+	obesityLociList := helpers.GetListOfMapKeys(locusReferencesMap)
+
+	referencesMap := make(map[string]string)
+	referencesMap["Obesity Genome-Wide Association Study (GWAS) created by the GIANT consortium"] = "https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files"
+
+	getAverageRiskProbabilitiesFunction := func(maleOrFemale string, inputAge int)(float64, error){
+
+		// Roughly 30% of people are obese.
+
+		if (maleOrFemale == "Male"){
+			return 0.30, nil
+		}
+
+		if (maleOrFemale != "Female"){
+			return 0, errors.New("Trying to get breast cancer risk probability for invalid maleOrFemale: " + maleOrFemale)
+		}
+
+		//TODO: Add different probabilities per age
+
+		return 0.30, nil
+	}
+
+	obesityObject := PolygenicDisease{
+		DiseaseName: "Obesity",
+		EffectedSex: "Both",
+		DiseaseDescription: "The condition of having an excessive amount of body fat.",
+		LocusReferencesMap: locusReferencesMap,
+		LociList: obesityLociList,
+		GetAverageRiskProbabilitiesFunction: getAverageRiskProbabilitiesFunction,
+		References: referencesMap,
+	}
+
+	return obesityObject, nil
+}
+
+

resources/geneticReferences/polygenicDiseases/polygenicDiseases.go

@@ -47,12 +47,15 @@ var polygenicDiseaseNamesList []string
 var polygenicDiseaseObjectsList []PolygenicDisease
 
 // This must be called once during application startup
-func InitializePolygenicDiseaseVariables(){
+func InitializePolygenicDiseaseVariables()error{
 
 	breastCancerObject := getBreastCancerDiseaseObject()
 	autismObject := getAutismDiseaseObject()
 
-	polygenicDiseaseObjectsList = []PolygenicDisease{breastCancerObject, autismObject}
+	obesityObject, err := getObesityDiseaseObject()
+	if (err != nil) { return err }
+
+	polygenicDiseaseObjectsList = []PolygenicDisease{breastCancerObject, autismObject, obesityObject}
 
 	polygenicDiseaseNamesList = make([]string, 0, len(polygenicDiseaseObjectsList))
 
@@ -62,6 +65,8 @@ func InitializePolygenicDiseaseVariables(){
 
 		polygenicDiseaseNamesList = append(polygenicDiseaseNamesList, diseaseName)
 	}
+
+	return nil
 }
 
 // Be aware that all of these functions are returning original objects/slices, not copies

resources/geneticReferences/polygenicDiseases/rsIDs/ReadMe.md

@@ -0,0 +1,2 @@
+### This folder contains files which are gob-encoded []int64
+### These int64s are rsIDs which influence various traits.

utilities/createGeneticModels/createGeneticModels.go

@@ -48,9 +48,13 @@ import "time"
 
 func main(){
 
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
+	err := polygenicDiseases.InitializePolygenicDiseaseVariables()
+	if (err != nil){
+		panic(err)
+		return
+	}
 
-	err := traits.InitializeTraitVariables()
+	err = traits.InitializeTraitVariables()
 	if (err != nil){
 		panic(err)
 		return
@@ -733,7 +737,7 @@ func setStartAndMonitorCreateTrainingDataPage(window fyne.Window, previousPage f
 			if (err != nil) { return false, false, err }
 
 			//TODO: Add more attributes
-			attributeNamesList := []string{"Eye Color", "Lactose Tolerance", "Height", "Autism", "Homosexualness"}
+			attributeNamesList := []string{"Eye Color", "Lactose Tolerance", "Height", "Autism", "Homosexualness", "Obesity"}
 
 			// We create the folders for each attribute's training data
 
@@ -1003,7 +1007,7 @@ func setTrainModelsPage(window fyne.Window, previousPage func()){
 	description3 := getLabelCentered("This will take a while.")
 	description4 := getLabelCentered("You must select a model to train.")
 
-	attributeNamesList := []string{"Eye Color", "Lactose Tolerance", "Height", "Autism", "Homosexualness"}
+	attributeNamesList := []string{"Eye Color", "Lactose Tolerance", "Height", "Autism", "Homosexualness", "Obesity"}
 
 	attributeNameSelector := widget.NewSelect(attributeNamesList, nil)
 
@@ -1269,7 +1273,8 @@ func setStartAndMonitorTrainModelPage(window fyne.Window, attributeName string,
 
 					case "Height",
 						"Autism",
-						"Homosexualness":{
+						"Homosexualness",
+						"Obesity":{
 						return true, nil
 					}
 					case "Lactose Tolerance",
@@ -1362,7 +1367,7 @@ func setTestModelsPage(window fyne.Window, previousPage func()){
 	description5 := getLabelCentered("The results will also be saved in the ModelAccuracies folder.")
 	description6 := getLabelCentered("You must select a model to test.")
 
-	attributeNamesList := []string{"Eye Color", "Lactose Tolerance", "Height", "Autism", "Homosexualness"}
+	attributeNamesList := []string{"Eye Color", "Lactose Tolerance", "Height", "Autism", "Homosexualness", "Obesity"}
 
 	attributeNameSelector := widget.NewSelect(attributeNamesList, nil)
 
@@ -1432,7 +1437,8 @@ func setStartAndMonitorTestModelPage(window fyne.Window, attributeName string, p
 
 			case "Height",
 				"Autism",
-				"Homosexualness":{
+				"Homosexualness",
+				"Obesity":{
 				return true, nil
 			}
 			case "Lactose Tolerance",
@@ -2341,6 +2347,9 @@ func getTrainingAndTestingDataFilepathLists(attributeName string)([]string, []st
 			case "Homosexualness":{
 				return 14500, nil
 			}
+			case "Obesity":{
+				return 24009, nil
+			}
 		}
 
 		return 0, errors.New("Unknown attributeName: " + attributeName)

utilities/createSampleGeneticAnalyses/createSampleGeneticAnalyses.go

@@ -31,7 +31,12 @@ func main(){
 	}
 
 	monogenicDiseases.InitializeMonogenicDiseaseVariables()
-	polygenicDiseases.InitializePolygenicDiseaseVariables()
+
+	err = polygenicDiseases.InitializePolygenicDiseaseVariables()
+	if (err != nil) {
+		log.Println("InitializePolygenicDiseaseVariables failed: " + err.Error())
+		return
+	}
 
 	err = traits.InitializeTraitVariables()
 	if (err != nil) {

utilities/extractGiantLoci/.gitignore

@@ -1,3 +1,5 @@
 GiantHeightStudy.txt
 GiantHeightStudyLoci.gob
+GiantObesityStudy.txt
+GiantObesityStudyLoci.gob
 NewLocusMetadata.gob

utilities/extractGiantLoci/extractGiantLoci.go

@@ -5,18 +5,28 @@
 // The files are a tab-delimeted file of rsIDs and their effect on a particular trait
 
 // The output file is a .gob encoded []int64 of the top 1000 most impactful loci on the trait.
-// These files are then saved into /resources/geneticReferences/traits/rsIDs
+// These files are then saved into the following folders:
+//		-Height -> /resources/geneticReferences/traits/rsIDs
+//		-Obesity -> /resources/geneticReferences/polygenicDiseases/rsIDs
 // The loci metadata for loci from these files is also imported into the locusMetadata package to enable them to be used in Seekia
 
 package main
 
-// Here is the file I used to extract causal rsIDs for height
-// Download link:
-// https://portals.broadinstitute.org/collaboration/giant/images/4/4e/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_ALL.gz
+// Here are the files I used to extract causal rsIDs
 
-//SHA-256 Checksum:
+// Trait: Height
+// Download Link:
+// https://portals.broadinstitute.org/collaboration/giant/images/4/4e/GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_ALL.gz
+// SHA-256 Checksum:
 // db18859724675f2f9ba86eff28cb4dacac0629c0b25c9806a6cf2eed6bb8b71e
 
+// Trait: Obesity (Waist-to-hip-ratio)
+// Download Link:
+// https://portals.broadinstitute.org/collaboration/giant/images/0/09/PublicRelease.WHRadjBMI.C.All.Add.txt.gz
+// SHA-256 Checksum:
+// 2a863b0357037ae5c34853342052ed3c59735d6440da0fd15d1cab34b7d49daf
+
+
 import "seekia/resources/geneticReferences/locusMetadata"
 import "seekia/resources/geneticReferences/modifyLocusMetadata"
 
@@ -40,9 +50,14 @@ func main(){
 
 	extractGiantLoci := func()error{
 
-		fileBytes, err := os.ReadFile("./GiantHeightStudy.txt")	
-		if (err != nil) {
-			return errors.New("Could not open GiantHeightStudy.txt file: " + err.Error())
+//		heightOrObesity := "Height"
+		heightOrObesity := "Obesity"
+
+		filepath := "./Giant" + heightOrObesity + "Study.txt"
+
+		fileBytes, err := os.ReadFile(filepath)	
+		if (err != nil){
+			return errors.New("Could not open " + filepath + ": " + err.Error())
 		}
 
 		fileReader := bytes.NewReader(fileBytes)
@@ -51,11 +66,11 @@ func main(){
 
 		// We first read the header line
 
-		//These are the columns of the file:
+		//These are the columns of the Height file:
 
-		// COLUMN DESCRIPTION FOR FILE NAMED GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_*.gz
+		// Filename: GIANT_HEIGHT_YENGO_2022_GWAS_SUMMARY_STATS_*.gz
 		//	- SNPID
-		//		-represented as CHR:POS:REF:ALT)
+		//		-represented as CHR:POS:REF:ALT
 		//	- RSID
 		//		-RS NUMBER, WHEN AVAILABLE
 		//	- CHR
@@ -82,6 +97,22 @@ func main(){
 		//	- N
 		//		-Total sample size used in the GWAS analysis
 
+		// These are the columns of the Obesity (WHR) File:
+		// Filename: PublicRelease.WHRadjBMI.C.All.Add.txt.gz
+		//
+		//	-1. snpname - dbSNP rsID
+		//	-2. chr - chromosome
+		//	-3. pos - position
+		//	-4. markername - chr:pos
+		//	-5. ref - reference allele (hg19 + strand)
+		//	-6. alt - alternate allele (hg19 + strand)
+		//	-7. beta - beta
+		//	-8. se - standard error
+		//	-9. pvalue - P value
+		//	-10. n - sample size
+		//	-11. gmaf/eur_maf - alternate allele frequency in 1000 Genome Combined/European Ancestries
+		//	-12. exac_maf/exac_nfe_maf -alternate allele frequency in ExAC Combined/Non-Finnish European Ancestries
+
 		_, err = bufioReader.ReadString('\n')
 		if (err != nil) { return err }
 
@@ -91,7 +122,7 @@ func main(){
 			Effect float64
 		}
 
-		rsidsInfoMap := make(map[int64]LocusInfo)
+		lociInfoMap := make(map[int64]LocusInfo)
 
 		for {
 
@@ -102,58 +133,132 @@ func main(){
 					// We have reached the end of the file
 					break
 				}
+
 				// File is corrupt
 				return errors.New("Error reading file: " + err.Error())
 			}
 
 			lineElementsSlice := strings.Split(string(rsidInfoLine), "\t")
 
-			rsidString := lineElementsSlice[1]
-			rsidChromosomeString := lineElementsSlice[2]
-			rsidPositionString := lineElementsSlice[3]
-			rsidEffectString := lineElementsSlice[7]
+			//Outputs:
+			//	-bool: Locus information is available
+			//	-int64: Locus rsID
+			//	-int: Locus Chromosome
+			//	-int: Locus Position
+			//	-float64: Locus effect
+			//	-error
+			getLocusInfo := func()(bool, int64, int, int, float64, error){
 
-			rsidWithoutPrefix, prefixFound := strings.CutPrefix(rsidString, "rs")
-			if (prefixFound == false){
-				// Some of the rsIDs are not formatted in the "rs123456" format
-				// We skip those
-				//log.Println("rs prefix not found in rsID: " + rsIDString)
+				if (heightOrObesity == "Height"){
+
+					rsidString := lineElementsSlice[1]
+					locusChromosomeString := lineElementsSlice[2]
+					locusPositionString := lineElementsSlice[3]
+					locusEffectString := lineElementsSlice[7]
+
+					rsidWithoutPrefix, prefixFound := strings.CutPrefix(rsidString, "rs")
+					if (prefixFound == false){
+						// Some of the rsIDs are not formatted in the "rs123456" format
+						// We skip those
+						// log.Println("rs prefix not found in rsID: " + rsidString)
+						return false, 0, 0, 0, 0, nil
+					}
+
+					rsID, err := helpers.ConvertStringToInt64(rsidWithoutPrefix)
+					if (err != nil){
+						return false, 0, 0, 0, 0, errors.New("RSID is invalid: " + err.Error())
+					}
+
+					locusChromosome, err := helpers.ConvertStringToInt(locusChromosomeString)
+					if (err != nil){
+						return false, 0, 0, 0, 0, errors.New("Locus Chromosome is invalid: " + err.Error())
+					}
+
+					locusPosition, err := helpers.ConvertStringToInt(locusPositionString)
+					if (err != nil){
+						return false, 0, 0, 0, 0, errors.New("Locus Position is invalid: " + err.Error())
+					}
+
+					locusEffectRaw, err := helpers.ConvertStringToFloat64(locusEffectString)
+					if (err != nil) {
+						if (locusEffectString == ""){
+							// The database has at least 1 entry with no effect provided
+							return false, 0, 0, 0, 0, nil
+						}
+						return false, 0, 0, 0, 0, errors.New("RSID effect is invalid: " + err.Error())
+					}
+
+					return true, rsID, locusChromosome, locusPosition, locusEffectRaw, nil
+				}
+
+				rsidString := lineElementsSlice[0]
+				locusChromosomeString := lineElementsSlice[1]
+				locusPositionString := lineElementsSlice[2]
+				locusEffectString := lineElementsSlice[6]
+
+				if (rsidString == "-" || rsidString == ""){
+					return false, 0, 0, 0, 0, nil
+				}
+
+				rsidWithoutPrefix, prefixFound := strings.CutPrefix(rsidString, "rs")
+				if (prefixFound == false){
+					return false, 0, 0, 0, 0, errors.New("Obesity GWAS file contains invalid rsID: " + rsidString)
+				}
+
+				rsID, err := helpers.ConvertStringToInt64(rsidWithoutPrefix)
+				if (err != nil){
+					return false, 0, 0, 0, 0, errors.New("RSID is invalid: " + err.Error())
+				}
+
+				locusChromosome, err := helpers.ConvertStringToInt(locusChromosomeString)
+				if (err != nil){
+
+					if (locusChromosomeString == "X"){
+						// TODO: Add the ability to read these chromosomes
+						return false, 0, 0, 0, 0, nil
+					}
+
+					return false, 0, 0, 0, 0, errors.New("Locus Chromosome is invalid: " + err.Error())
+				}
+
+				locusPosition, err := helpers.ConvertStringToInt(locusPositionString)
+				if (err != nil){
+					
+					hasSuffix := strings.HasSuffix(locusPositionString, "+08")
+					if (hasSuffix == true){
+						// This is an invalid entry in the file
+						return false, 0, 0, 0, 0, nil
+					}
+					return false, 0, 0, 0, 0, errors.New("Locus Position is invalid: " + err.Error())
+				}
+
+				locusEffectRaw, err := helpers.ConvertStringToFloat64(locusEffectString)
+				if (err != nil) {
+					return false, 0, 0, 0, 0, errors.New("RSID effect is invalid: " + err.Error())
+				}
+
+				return true, rsID, locusChromosome, locusPosition, locusEffectRaw, nil
+			}
+
+			locusInfoExists, locusRSID, locusChromosome, locusPosition, locusEffectRaw, err := getLocusInfo()
+			if (err != nil) { return err }
+			if (locusInfoExists == false){
 				continue
 			}
 
-			rsID, err := helpers.ConvertStringToInt64(rsidWithoutPrefix)
-			if (err != nil){
-				return errors.New("RSID is invalid: " + err.Error())
-			}
-
-			rsidChromosome, err := helpers.ConvertStringToInt(rsidChromosomeString)
-			if (err != nil){ return err }
-
-			rsidPosition, err := helpers.ConvertStringToInt(rsidPositionString)
-			if (err != nil){ return err }
-
-			rsidEffectRaw, err := helpers.ConvertStringToFloat64(rsidEffectString)
-			if (err != nil) {
-				if (rsidEffectString == ""){
-					// The database has at least 1 entry with no effect provided
-					continue
-				}
-				return err
-			}
-
 			// Effect can be negative, we make it positive
-			rsidEffect := math.Abs(rsidEffectRaw)
+			locusEffect := math.Abs(locusEffectRaw)
 
-			existingLocusValue, exists := rsidsInfoMap[rsID]
+			existingLocusValue, exists := lociInfoMap[locusRSID]
 			if (exists == false){
 
 				newLocusInfo := LocusInfo{
-					Chromosome: rsidChromosome,
-					Position: rsidPosition,
-					Effect: rsidEffect,
+					Chromosome: locusChromosome,
+					Position: locusPosition,
+					Effect: locusEffect,
 				}
 
-				rsidsInfoMap[rsID] = newLocusInfo
+				lociInfoMap[locusRSID] = newLocusInfo
 			} else {
 
 				// We see if the effect of this allele is greater
@@ -165,24 +270,24 @@ func main(){
 				existingPosition := existingLocusValue.Position
 				existingEffect := existingLocusValue.Effect
 
-				if (existingChromosome != rsidChromosome){
+				if (existingChromosome != locusChromosome){
 					return errors.New("GIANT gwas contains two rsIDs with conflicting chromosomes.")
 				}
-				if (existingPosition != rsidPosition){
+				if (existingPosition != locusPosition){
 					return errors.New("GIANT gwas contains two rsIDs with conflicting positions.")
 				}				
-				if (existingEffect < rsidEffect){
+				if (existingEffect < locusEffect){
 
 					// We update the value with the new effect
-					existingLocusValue.Effect = rsidEffect
-					rsidsInfoMap[rsID] = existingLocusValue
+					existingLocusValue.Effect = locusEffect
+					lociInfoMap[locusRSID] = existingLocusValue
 				}
 			}
 		}
 
 		// We find the top 10,000 rsIDs with the greatest effect
 
-		rsidsList := helpers.GetListOfMapKeys(rsidsInfoMap)
+		rsidsList := helpers.GetListOfMapKeys(lociInfoMap)
 
 		compareFunction := func(rsid1 int64, rsid2 int64)int{
 
@@ -190,14 +295,14 @@ func main(){
 				panic("Identical rsIDs found during sort.")
 			}
 
-			rsid1Info, exists := rsidsInfoMap[rsid1]
+			rsid1Info, exists := lociInfoMap[rsid1]
 			if (exists == false){
-				panic("rsid1 is missing from rsidsInfoMap.")
+				panic("rsid1 is missing from lociInfoMap.")
 			}
 
-			rsid2Info, exists := rsidsInfoMap[rsid2]
+			rsid2Info, exists := lociInfoMap[rsid2]
 			if (exists == false){
-				panic("rsid2 is missing from rsidsInfoMap.")
+				panic("rsid2 is missing from lociInfoMap.")
 			}
 
 			rsid1Effect := rsid1Info.Effect
@@ -225,17 +330,16 @@ func main(){
 
 		for _, rsID := range mostImpactfulLoci{
 
-			locusInfo, exists := rsidsInfoMap[rsID]
+			locusInfo, exists := lociInfoMap[rsID]
 			if (exists == false){
-				return errors.New("rsidsInfoMap missing rsID.")
+				return errors.New("lociInfoMap missing rsID.")
 			}
 
 			locusChromosome := locusInfo.Chromosome
 			locusPosition := locusInfo.Position
 
-			locusReferencesMap := map[string]string{
-				"Height Genome-Wide Association Study (GWAS) created by the GIANT consortium": "https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files",
-			}
+			locusReferencesMap := make(map[string]string)
+			locusReferencesMap[heightOrObesity + " Genome-Wide Association Study (GWAS) created by the GIANT consortium"] = "https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files"
 
 			newLocusMetadata := locusMetadata.LocusMetadata{
 				RSIDsList: []int64{rsID},
@@ -251,12 +355,16 @@ func main(){
 			locusMetadatasToAddList = append(locusMetadatasToAddList, newLocusMetadata)
 		}
 
+		// We add the locus metadatas
+
 		_, newLocusMetadataFileBytes, err := modifyLocusMetadata.AddLocusMetadata(locusMetadatasToAddList)
 		if (err != nil) { return err }
 
 		err = localFilesystem.CreateOrOverwriteFile(newLocusMetadataFileBytes, "./", "NewLocusMetadata.gob")
 		if (err != nil){ return err }
 
+		// We create the rsIDs list file
+
 		buffer := new(bytes.Buffer)
 
 		gobEncoder := gob.NewEncoder(buffer)
@@ -266,7 +374,9 @@ func main(){
 
 		encodedBytes := buffer.Bytes()
 
-		err = localFilesystem.CreateOrOverwriteFile(encodedBytes, "./", "GiantHeightStudyLoci.gob")
+		filename := "Giant" + heightOrObesity + "StudyLoci.gob"
+
+		err = localFilesystem.CreateOrOverwriteFile(encodedBytes, "./", filename)
 		if (err != nil){ return err }
 
 		return nil