seekia/resources/geneticReferences/traits/eyeColor.go

package traits

import "seekia/internal/helpers"

import "maps"

func getEyeColorTraitObject()Trait{

	// Map Structure: rsID -> References Map
	locusReferencesMap := make(map[int64]map[string]string)

	referencesMap_List1 := make(map[string]string)
	referencesMap_List1["SNPedia.com - Eye Color"] = "https://www.snpedia.com/index.php/Eye_color"

	// These SNPs are taken from https://www.snpedia.com/index.php/Eye_color

	lociList_1 := []int64{
		2733832,
		1800401,
		1800407,
		1800414,
		12913823,
		4911442,
		6058017,
		4911414,
		4778241,
		12593929,
		7183877,
		3935591,
		7170852,
		2238289,
		3940272,
		8028689,
		2240203,
		11631797,
		916977,
		3768056,
		728405,
		2835621,
		892839,
		9782955,
		12452184,
		10209564,
		1325127,
		7277820,
		1105879,
		7219915,
		12913832,
		2070959,
		2835630,
		9894429,
		1393350,
		2252893,
		1003719,
		3794604,
		7174027,
		989869,
		4778138,
		12906280,
	}

	for _, rsID := range lociList_1{

		locusReferencesMap[rsID] = maps.Clone(referencesMap_List1)
	}

	referencesMap_List2 := make(map[string]string)
	referencesMap_List2["Genome-wide association studies of pigmentation and skin cancer: a review and meta-analysis"] = "https://pubmed.ncbi.nlm.nih.gov/20546537/"

	// These SNPs are taken from https://pubmed.ncbi.nlm.nih.gov/20546537/

	lociList_2 := []int64{
		12203592,
		1408799,
		1126809,
		12896399,
		7495174,
		1667394,
	}

	for _, rsID := range lociList_2{

		locusReferencesMap[rsID] = maps.Clone(referencesMap_List2)
	}


	referencesMap_List3 := make(map[string]string)
	referencesMap_List3["Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color."] = "https://pubmed.ncbi.nlm.nih.gov/33692100/"

	// These SNPs are taken from https://pubmed.ncbi.nlm.nih.gov/33692100/

	lociList_3 := []int64{
		6693258,
		351385,
		2385028,
		13016869,
		112747614,
		121908120,
		12614022,
		74409360,
		3912104,
		116359091,
		4521336,
		141318671,
		6828137,
		62330021,
		16891982,
		348613,
		72777200,
		11957757,
		//12203592, (is a duplicate, was also found in the other study)
		6910861,
		341147,
		2854746,
		6944702,
		6997494,
		12543326,
		147068120,
		13297008,
		12552712,
		12335410,
		72928978,
		//1126809, (is a duplicate, was also found in the other study)
		9971729,
		790464,
		2095645,
		9301973,
		138777265,
		17184180,
		4778218,
		1129038,
		1426654,
		4790309,
		3809761,
		6420484,
		73488486,
		2748901,
		2835660,
		622330,
		35051352,

		// TODO: Add these loci once we can handle X Chromosome loci.
		// 78542430,
		// 5957354,
	}

	for _, rsID := range lociList_3{
		locusReferencesMap[rsID] = maps.Clone(referencesMap_List3)
	}

	eyeColorLociList := helpers.GetListOfMapKeys(locusReferencesMap)

	referencesMap := make(map[string]string)
	referencesMap["SNPedia.com - Eye Color"] = "https://www.snpedia.com/index.php/Eye_color"
	referencesMap["Genome-wide association studies of pigmentation and skin cancer: a review and meta-analysis"] = "https://pubmed.ncbi.nlm.nih.gov/20546537/"
	referencesMap["Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color."] = "https://pubmed.ncbi.nlm.nih.gov/33692100/"

	eyeColorObject := Trait{
		TraitName: "Eye Color",
		TraitDescription: "The color of a person's eyes.",
		DiscreteOrNumeric: "Discrete",
		LocusReferencesMap: locusReferencesMap,
		LociList: eyeColorLociList,
		LociList_Rules: []int64{},
		RulesList: []TraitRule{},
		OutcomesList: []string{"Blue", "Green", "Hazel", "Brown"},
		ReferencesMap: referencesMap,
	}

	return eyeColorObject
}