Parsing 23andMe genome data

genome.go

package main

import (
	"bufio"
	"bytes"
	"fmt"
	"io"
	"log"
	"os"
	"strconv"
)

// SNP or Single-nucleotide polymorphism
type SNP struct {
	RSID       string
	Chromosome string
	Position   int
	Genotype   string
}

type Genome []SNP

func checkErr(err error) {
	if err != nil {
		panic(err)
	}
}

func tsvLineToSNP(line []byte) (snp SNP, err error) {
	data := bytes.Split(line, []byte("\t"))
	if l := len(data); l != 4 {
		return SNP{}, fmt.Errorf("invalid len for SNP TSV, %d", l)
	}

	snp.Position, err = strconv.Atoi(string(data[2]))
	if err != nil {
		return SNP{}, fmt.Errorf("invalid position for SNP, %w", err)
	}

	snp.RSID = string(data[0])
	snp.Chromosome = string(data[1])
	snp.Genotype = string(data[3])

	return snp, nil
}

func readGenome(reader io.Reader) (genome Genome, err error) {
	scanner := bufio.NewScanner(reader)
	scanner.Split(bufio.ScanLines)

	for scanner.Scan() {
		snp, err := tsvLineToSNP(scanner.Bytes())
		if err != nil {
			return nil, fmt.Errorf("failed parsing tsv line, %w", err)
		}

		genome = append(genome, snp)
	}

	return genome, scanner.Err()
}

func main() {
	fp, err := os.Open("genome.txt")
	checkErr(err)
	defer fp.Close()

	genome, err := readGenome(fp)
	if err != nil {
    checkErr(err)
	}

	fmt.Println(len(genome))
}