seekia/internal/genetics/readBiobankData/openSNP.go

package readBiobankData

// file openSNP.go provides a datastructure and function to read data from the OpenSNP.org biobank.

import "seekia/internal/helpers"

import "encoding/csv"
import "os"
import "io"


type PhenotypeData_OpenSNP struct{

	UserID int


	EyeColorIsKnown bool

	// Either "Green", "Blue", "Hazel", or "Brown"
	EyeColor string


	LactoseToleranceIsKnown bool

	// true == Is lactose Tolerant
	LactoseTolerance bool


	HairColorIsKnown bool

	HairColor string


	HeightIsKnown bool

	// Height is expressed in centimeters
	Height float64
}

// This function reads the phenotypes_202308230100.csv file in the openSNP biobank data.
//
//Outputs:
//	-bool: Able to read file (file is well formed and not corrupt)
//	-[]PhenotypeData_OpenSNP
func ReadOpenSNPPhenotypesFile(fileObject *os.File)(bool, []PhenotypeData_OpenSNP){

	csvFileReader := csv.NewReader(fileObject)
	csvFileReader.LazyQuotes = true
	csvFileReader.Comma = ';'

	// First we read the first line (header line)

	_, err := csvFileReader.Read()
	if (err != nil){

		// File is corrupt
		return false, nil
	}

	// Now we iterate through each user's phenotype data

	//Map Structure: User ID -> Phenotype data object
	userPhenotypeDataMap := make(map[int]PhenotypeData_OpenSNP)

	for {

		userDataLineSlice, err := csvFileReader.Read()
		if (err != nil) {

			if (err == io.EOF){
				// We have reached the end of the file
				break
			}
			// File is corrupt
			return false, nil
		}

		userIDString := userDataLineSlice[0]

		userID, err := helpers.ConvertStringToInt(userIDString)
		if (err != nil){
			// File is corrupt
			return false, nil
		}

		_, exists := userPhenotypeDataMap[userID]
		if (exists == true){

			// This user has multiple entries
			// Each entry is identical except for the raw genome filename
			// We will continue

			continue
		}

		//Outputs:
		//	-bool: User eye color is known
		//	-string: User eye color
		getUserEyeColor := func()(bool, string){

			userEyeColorRaw := userDataLineSlice[5]

			switch userEyeColorRaw{

				case "-":{
					return false, ""
				}
				case "Brown",
					"brown",
					"Dark brown",
					"Brown/black",
					"Grey brown":{

					return true, "Brown"
				}
				case "Hazel",
					"hazel",
					"Brown-green",
					"brown-green",
					"Hazel/Light Brown",
					"Hazel (light brown, dark green, dark blue)",
					"Brown-amber",
					"Indeterminate brown-green with a subtle grey caste",
					"Hazel (brown/green)",
					"Green-hazel",
					"Amber - (yellow/ocre  brown)",
					"Hazel/light brown",
					"Green-brown",
					"green-brown",
					"Brown - brown and green in bright sunlight",
					"Hazel/yellow",
					"Brown-(green when external temperature rises)",
					"Ambar-green",
					"Olive-brown ringing burnt umber-brown",
					"Green with brown freckles",
					"Green-Hazel",
					"Ambar-Green",
					"Brown-Amber",
					"Hazel/Yellow",
					"Brown center starburst, amber and olive green, with dark gray outer ring":{

					return true, "Hazel"
				}
				case "Blue",
					"Blue-grey",
					"Blue grey",
					"Gray-blue",
					"Blue-grey with central heterochromia",
					"Dark blue",
					"blue",
					"Light blue-green",
					"blue-grey",
					"Dark Grayish-Blue Eyes (like a stone)":{

					return true, "Blue"
				}
				case "Green",
					"Green ",
					"green",
					"Green-gray",
					"Blue-green ",
					"Blue-green",
					"blue-green ",
					"Light-mixed green",
					"blue-green",
					"Blue with a yellow ring of flecks that make my eyes look green depending on the light or my  mood",
					"Light-mixed Green",
					"Blue-green heterochromia",
					"Blue-green-grey":{

					return true, "Green"
				}

				//TODO: Add grey as its own seperate color?
			}

			return false, ""
		}

		userEyeColorIsKnown, userEyeColor := getUserEyeColor()

		//Outputs:
		//	-bool: User lactose Tolerance is known
		//	-bool: User lactose Tolerance
		getUserLactoseTolerance := func()(bool, bool){

			userLactoseToleranceRaw := userDataLineSlice[6]

			switch userLactoseToleranceRaw{

				case "-":{
					return false, false
				}
				case "Yes",
					"Lactose-intolerant",
					"Lactose intolerant",
					"lactose-intolerant",
					" allergic to all forms of dairy ",
					" Allergic to all forms of dairy ",
					"Severe gi pain ",
					"severe GI pain ":{

					return true, false
				}
				case "No",
					"Lactose-tolerant",
					"Lactose tolerant",
					"lactose-tolerant",
					"lactose tolerant",
					"False":{
					return true, true 
				}
			}

			return false, false
		}

		userLactoseToleranceIsKnown, userLactoseTolerance := getUserLactoseTolerance()

		//Outputs:
		//	-bool: User hair color is known
		//	-string: Hair Color
		getUserHairColor := func()(bool, string){

			//userHairColorRaw := userDataLineSlice[11]

			//TODO

			return false, ""
		}

		userHairColorIsKnown, userHairColor := getUserHairColor()


		// Outputs:
		//	-bool: User height is known
		//	-int: User height (in centimeters)
		getUserHeight := func()(bool, float64){

			userHeightRaw := userDataLineSlice[13]					

			switch userHeightRaw{
				case "-":{
					return false, 0
				}
				case `4'0"`:{	
					return true, 121.92
				}
				case `4'1"`:{
					return true, 124.46
				}
				case `4'2"`:{
					return true, 127
				}
				case `4'3"`:{
					return true, 129.54
				}
				case `4'4"`:{
					return true, 132.08
				}
				case `4'5"`:{
					return true, 134.62
				}
				case `4'6"`:{
					return true, 137.16
				}
				case `4'7"`:{
					return true, 139.7
				}
				case `4'8"`:{
					return true, 142.24
				}
				case `4'9"`:{
					return true, 144.78
				}
				case `4'10"`:{
					return true, 147.32
				}
				case `4'11"`:{
					return true, 149.86
				}
				case `5'`:{
					return true, 152.4
				}
				case `5'1"`:{
					return true, 154.94
				}
				case `5'2"`:{
					return true, 157.48
				}
				case `5'3"`, `5'3''`, `160 cm`:{
					return true, 160
				}
				case `5'4"`:{
					return true, 162.56
				}
				case `5'5"`:{
					return true, 165.1
				}
				case `5'6"`:{
					return true, 167.64
				}
				case `168 cm`:{
					return true, 168
				}
				case `5'7"`:{
					return true, 170.18
				}
				case `5'8"`:{
					return true, 172.72
				}
				case `5'9"`:{
					return true, 175.26
				}
				case `5'10"`, `5'10''`:{
					return true, 177.8
				}
				case `179 cm`:{
					return true, 179
				}
				case `180cm`:{
					return true, 180
				}
				case `5'11"`:{
					return true, 180.34
				}
				case `6'`:{
					return true, 182.88
				}
				case `183 cm`:{
					return true, 183
				}
				case `6'1"`:{
					return true, 185.42
				}
				case `6'2"`:{
					return true, 187.96
				}
				case `6'3"`:{
					return true, 190.5
				}
				case `6'4"`:{
					return true, 193.04
				}
				case `6'5"`:{
					return true, 195.58
				}
				case `6'6"`:{
					return true, 198.12
				}
				case `6'7"`:{
					return true, 200.66
				}
				case `6'8"`:{
					return true, 203.2
				}
				case `6'9"`:{
					return true, 205.74
				}
				case `6'10"`:{
					return true, 208.28
				}
				case `6'11"`:{
					return true, 210.82
				}
				case `7'`:{
					return true, 213.36
				}

				//TODO: Add more responses
			}

			return false, 0
		}

		userHeightIsKnown, userHeight := getUserHeight()

		userPhenotypeDataObject := PhenotypeData_OpenSNP{
			UserID: userID,
			EyeColorIsKnown: userEyeColorIsKnown,
			EyeColor: userEyeColor,
			LactoseToleranceIsKnown: userLactoseToleranceIsKnown,
			LactoseTolerance: userLactoseTolerance,
			HairColorIsKnown: userHairColorIsKnown,
			HairColor: userHairColor,
			HeightIsKnown: userHeightIsKnown,
			Height: userHeight,
		}

		userPhenotypeDataMap[userID] = userPhenotypeDataObject
	}

	userPhenotypeDataList := helpers.GetListOfMapValues(userPhenotypeDataMap)

	return true, userPhenotypeDataList
}