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bed.go
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bed.go
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// Copyright © 2016-2019 Wei Shen <shenwei356@gmail.com>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.
package cmd
import (
"fmt"
"os"
"runtime"
"strconv"
"strings"
"github.com/shenwei356/breader"
)
// BedFeature is the gff BedFeature struct
type BedFeature struct {
Chr string
Start int // 1based
End int // end included
Name *string
Strand *string
}
// Threads for bread.NewBufferedReader()
var Threads = runtime.NumCPU()
// ReadBedFeatures returns gtf BedFeatures of a file
func ReadBedFeatures(file string) ([]BedFeature, error) {
return ReadBedFilteredFeatures(file, []string{})
}
// ReadBedFilteredFeatures returns gtf BedFeatures of selected chrs from file
func ReadBedFilteredFeatures(file string, chrs []string) ([]BedFeature, error) {
if _, err := os.Stat(file); os.IsNotExist(err) {
return nil, err
}
chrsMap := make(map[string]struct{}, len(chrs))
for _, chr := range chrs {
chrsMap[chr] = struct{}{}
}
fn := func(line string) (interface{}, bool, error) {
line = strings.TrimRight(line, "\r\n")
if line == "" || line[0] == '#' || (len(line) > 7 && string(line[0:7]) == "browser") || (len(line) > 5 && string(line[0:5]) == "track") {
return nil, false, nil
}
items := strings.Split(line, "\t")
n := len(items)
if n < 3 {
return nil, false, nil
}
if len(chrs) > 0 { // selected chrs
if _, ok := chrsMap[items[0]]; !ok {
return nil, false, nil
}
}
start, err := strconv.Atoi(items[1])
if err != nil {
return nil, false, fmt.Errorf("%s: bad start: %s", items[0], items[1])
}
end, err := strconv.Atoi(items[2])
if err != nil {
return nil, false, fmt.Errorf("%s: bad end: %s", items[0], items[2])
}
if start >= end {
return nil, false, fmt.Errorf("%s: start (%d) must be <= end (%d)", items[0], start, end)
}
var name *string
if n >= 4 {
name = &items[3]
}
var strand *string
if n >= 6 {
if items[5] != "+" && items[5] != "-" {
return nil, false, fmt.Errorf("bad strand: %s", items[5])
}
strand = &items[5]
}
return BedFeature{items[0], start + 1, end, name, strand}, true, nil
}
reader, err := breader.NewBufferedReader(file, Threads, 100, fn)
if err != nil {
return nil, err
}
BedFeatures := []BedFeature{}
for chunk := range reader.Ch {
if chunk.Err != nil {
return nil, chunk.Err
}
for _, data := range chunk.Data {
BedFeatures = append(BedFeatures, data.(BedFeature))
}
}
return BedFeatures, nil
}