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//Package bed is used to read bed features.
// ref: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
// ref: https://github.com/biogo/biogo/blob/master/io/featio/bed/bed.go
package bed
import (
"errors"
"fmt"
"os"
"reflect"
"regexp"
"runtime"
"strconv"
"strings"
"github.com/shenwei356/breader"
)
var (
// ErrBadBEDType error
ErrBadBEDType = errors.New("bad BED type")
// ErrBadBrowserLine error
ErrBadBrowserLine = errors.New("bad browser line")
)
// Feature is the interface of BED feature
type Feature interface {
Chr() string
Start() int
End() int
Len() int
Strand() *string
String() string
}
// BED3 struct
type BED3 struct {
Chrom string
ChromStart int
ChromEnd int
}
// Chr returns chromosome
func (b *BED3) Chr() string { return b.Chrom }
// Start returns start
func (b *BED3) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED3) End() int { return b.ChromEnd }
// Length returns length
func (b *BED3) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED3) Strand() *string { return nil }
// Name returns name
func (b *BED3) Name() string { return b.String() }
func (b *BED3) String() string {
return fmt.Sprintf("BED3 %s:[%d,%d)", b.Chrom, b.ChromStart, b.ChromEnd)
}
func parseBED3(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 3 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
return BED3{items[0], start, end}, true, nil
}
// BED4 struct
type BED4 struct {
Chrom string
ChromStart int
ChromEnd int
FeatName string
}
// Chr returns chromosome
func (b *BED4) Chr() string { return b.Chrom }
// Start returns start
func (b *BED4) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED4) End() int { return b.ChromEnd }
// Length returns length
func (b *BED4) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED4) Strand() *string { return nil }
// Name returns name
func (b *BED4) Name() string { return b.FeatName }
func (b *BED4) String() string {
return fmt.Sprintf("BED4 %s:[%d,%d) %s", b.Chrom, b.ChromStart, b.ChromEnd, b.FeatName)
}
func parseBED4(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 4 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
return BED4{items[0], start, end, items[3]}, true, nil
}
// BED5 struct
type BED5 struct {
Chrom string
ChromStart int
ChromEnd int
FeatName string
FeatScore int
}
// Chr returns chromosome
func (b *BED5) Chr() string { return b.Chrom }
// Start returns start
func (b *BED5) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED5) End() int { return b.ChromEnd }
// Length returns length
func (b *BED5) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED5) Strand() *string { return nil }
// Name returns name
func (b *BED5) Name() string { return b.FeatName }
func (b *BED5) String() string {
return fmt.Sprintf("BED5 %s:[%d,%d) %s (score: %d)", b.Chrom, b.ChromStart, b.ChromEnd, b.FeatName, b.FeatScore)
}
func parseBED5(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 5 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
score, err := strconv.Atoi(items[4])
if err != nil {
return nil, false, fmt.Errorf("bad score: %s", items[4])
}
return BED5{items[0], start, end, items[3], score}, true, nil
}
// BED6 struct
type BED6 struct {
Chrom string
ChromStart int
ChromEnd int
FeatName string
FeatScore int
FeatStrand *string
}
// Chr returns chromosome
func (b *BED6) Chr() string { return b.Chrom }
// Start returns start
func (b *BED6) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED6) End() int { return b.ChromEnd }
// Length returns length
func (b *BED6) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED6) Strand() *string { return b.FeatStrand }
// Name returns name
func (b *BED6) Name() string { return b.FeatName }
func (b *BED6) String() string {
return fmt.Sprintf("BED6 %s:[%d,%d)%s %s (score: %d)", b.Chrom, b.ChromStart, b.ChromEnd, *b.FeatStrand, b.FeatName, b.FeatScore)
}
func parseBED6(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 6 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
score, err := strconv.Atoi(items[4])
if err != nil {
return nil, false, fmt.Errorf("bad score: %s", items[4])
}
var strand *string
if items[5] != "." {
strand = &items[5]
}
return BED6{items[0], start, end, items[3], score, strand}, true, nil
}
// BED12 struct
type BED12 struct {
Chrom string
ChromStart int
ChromEnd int
FeatName string
FeatScore int
FeatStrand *string
ThickStart int
ThickEnd int
RGB string
BlockCount int
BlockSizes []int
BlockStarts []int
}
// Chr returns chromosome
func (b *BED12) Chr() string { return b.Chrom }
// Start returns start
func (b *BED12) Start() int { return b.ChromStart }
// End returns end. (the site is not included)
func (b *BED12) End() int { return b.ChromEnd }
// Length returns length
func (b *BED12) Length() int { return b.ChromEnd - b.ChromStart }
// Strand returns strand
func (b *BED12) Strand() *string { return b.FeatStrand }
// Name returns name
func (b *BED12) Name() string { return b.FeatName }
func (b *BED12) String() string {
return fmt.Sprintf("BED12 %s:[%d,%d)%s %s (score: %d)", b.Chrom, b.ChromStart, b.ChromEnd, *b.FeatStrand, b.FeatName, b.FeatScore)
}
func parseBED12(line string) (interface{}, bool, error) {
if len(line) == 0 {
return nil, false, nil
}
items := strings.Split(strings.TrimRight(line, "\n"), "\t")
if len(items) < 12 {
return nil, false, ErrBadBEDType
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("bad start: %s", items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("bad end: %s", items[2])
}
score, err := strconv.Atoi(items[4])
if err != nil {
return nil, false, fmt.Errorf("bad score: %s", items[4])
}
var strand *string
if items[5] != "." {
strand = &items[5]
}
thickStart, err := strconv.Atoi(items[6])
if err != nil {
return nil, false, fmt.Errorf("bad thick start: %s", items[6])
}
thickEnd, err := strconv.Atoi(items[7])
if err != nil {
return nil, false, fmt.Errorf("bad thick end: %s", items[7])
}
blockCount, err := strconv.Atoi(items[9])
if err != nil {
return nil, false, fmt.Errorf("bad block count: %s", items[9])
}
blockSizes := []int{}
if blockCount > 0 {
items2 := strings.Split(items[10], ",")
for _, size := range items2[0:blockCount] {
s, err := strconv.Atoi(size)
if err != nil {
return nil, false, fmt.Errorf("bad block size: %s", size)
}
blockSizes = append(blockSizes, s)
}
}
blockStarts := []int{}
if blockCount > 0 {
items2 := strings.Split(items[11], ",")
for _, start := range items2[0:blockCount] {
s, err := strconv.Atoi(start)
if err != nil {
return nil, false, fmt.Errorf("bad block start: %s", start)
}
blockStarts = append(blockStarts, s)
}
}
return BED12{items[0], start, end, items[3], score, strand,
thickStart, thickEnd, items[8], blockCount, blockSizes, blockStarts}, true, nil
}
type meta struct {
name string
details map[string]string
}
// TrackItemRegexp is regular expression for parsing track items
var TrackItemRegexp = regexp.MustCompile(`(\w+)="?[^#]+?"?`)
// ReadFeatures returns bed data of a file, availabe type values are 3,4,5,6
func ReadFeatures(file string, n int) ([]Feature, map[string]map[string]string, error) {
if _, err := os.Stat(file); os.IsNotExist(err) {
return nil, nil, err
}
fn := func(line string) (interface{}, bool, error) {
if line[0] == '#' {
return nil, false, nil
}
if string(line[0:7]) == "browser" {
items := strings.Split(strings.TrimRight(line, "\n"), " ")
if len(items) < 3 {
return nil, false, ErrBadBrowserLine
}
details := make(map[string]string)
details[items[1]] = items[2]
return meta{"browser", details}, true, nil
}
if string(line[0:5]) == "track" {
details := make(map[string]string)
found := TrackItemRegexp.FindAllStringSubmatch(line, -1)
for _, sub := range found {
details[sub[0]] = sub[1]
}
return meta{"track", details}, true, nil
}
return nil, false, nil
}
reader, err := breader.NewBufferedReader(file, runtime.NumCPU(), 100, fn)
if err != nil {
return nil, nil, err
}
features := []Feature{}
for chunk := range reader.Ch {
if chunk.Err != nil {
return nil, nil, chunk.Err
}
for _, data := range chunk.Data {
fmt.Println(reflect.TypeOf(data).Kind())
}
}
return features, nil, nil
}
|
