/
vcf-freq.go
97 lines (81 loc) · 1.84 KB
/
vcf-freq.go
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package main
import (
"bufio"
"errors"
"fmt"
"github.com/codegangsta/cli"
"github.com/knmkr/go-vcf-tools/lib"
"io"
"os"
"regexp"
"strconv"
"strings"
)
func doFreq(c *cli.Context) {
reader := bufio.NewReaderSize(os.Stdin, 128*1024)
line, err := lib.Readln(reader)
for err == nil {
if strings.HasPrefix(line, "##") {
// pass
} else if strings.HasPrefix(line, "#CHROM") {
fmt.Println("#CHROM\tPOS\tID\tAllele\tFreq")
break
} else {
err = errors.New("Invalid VCF header")
break
}
line, err = lib.Readln(reader)
}
if err != nil && err != io.EOF {
panic(err)
}
pattern := regexp.MustCompile(`[|/]`)
line, err = lib.Readln(reader)
for err == nil {
records := strings.Split(line, "\t")
chrom := records[0]
pos := records[1]
id := records[2]
ref := records[3]
alt := strings.Split(records[4], ",")
format := strings.Split(records[8], ":")
gts := records[9:]
alleles := []string{}
alleles = append(alleles, ref)
alleles = append(alleles, alt...)
var count []int
for i := 0; i < len(alleles); i++ {
count = append(count, 0)
}
for i := range gts {
gt := strings.Split(gts[i], ":")
for j := range gt {
if format[j] == "GT" {
gt_idxs := pattern.Split(gt[j], -1)
for i := range gt_idxs {
gt_idx, _ := strconv.Atoi(gt_idxs[i])
count[gt_idx] += 1
}
}
}
}
total := float64(sum(count)) // TODO: decimal?
freqs := []string{}
for i := range count {
freqs = append(freqs, fmt.Sprintf("%.4f", float64(count[i])/total)) // TODO:
}
result := []string{chrom, pos, id, strings.Join(alleles, ","), strings.Join(freqs, ",")}
fmt.Println(strings.Join(result, "\t"))
line, err = lib.Readln(reader)
}
if err != nil && err != io.EOF {
panic(err)
}
}
func sum(vals []int) int {
var result int
for i := range vals {
result += vals[i]
}
return result
}