cytobandManager.go

package data

import (
	"bytes"
	"compress/gzip"
	"encoding/json"
	"io"
	"io/ioutil"
	"net/http"
	"strconv"
	"strings"

	"github.com/gorilla/mux"
	"github.com/nimezhu/genomedb"
	"github.com/nimezhu/netio"
)

type Band struct {
	Chr   string `json:"chr"`
	Start int    `json:"start"`
	End   int    `json:"end"`
	Id    string `json:"id"`
	Value string `json:"value"`
}
type CytoBand struct {
	data map[string][]Band
}
type CytoBandManager struct {
	prefix string
	data   map[string]*CytoBand
}

func NewCytoBandManager(id string) *CytoBandManager {
	m := &CytoBandManager{id, make(map[string]*CytoBand)}
	return m
}
func InitCytoBandManager(id string) *CytoBandManager {
	m := &CytoBandManager{id, make(map[string]*CytoBand)}
	files, _ := genomedb.AssetDir("cytoBand")
	for _, v := range files {
		a := strings.Split(v, ".")
		m.Add(a[0])
	}
	return m
}

func parseCytoBand(txt string) (CytoBand, error) {
	lines := strings.Split(txt, "\n")
	cytoband := CytoBand{}
	m := make(map[string][]Band)
	for _, line := range lines {
		t := strings.Split(line, "\t")
		if len(t) >= 5 {
			_, ok := m[t[0]]
			if !ok {
				m[t[0]] = make([]Band, 0, 100)
			}
			start, _ := strconv.Atoi(t[1])
			end, _ := strconv.Atoi(t[2])
			m[t[0]] = append(m[t[0]], Band{t[0], start, end, t[3], t[4]})
		}
	}
	cytoband.data = m
	return cytoband, nil
}
func (m *CytoBandManager) AddURI(uri string, key string) error {
	var f io.Reader
	var err error
	if v, ok := genomedb.Asset("cytoBand/" + key + ".cytoBand.txt.gz"); ok == nil {
		f = bytes.NewReader(v)
	} else {
		f, err = netio.NewReadSeeker(uri)
		if err != nil {
			return err
		}
	}

	z, err := gzip.NewReader(f)
	if err != nil {
		return err
	}
	txt, err := ioutil.ReadAll(z)
	if err != nil {
		return err
	}
	//log.Println("TODO....", string(txt))
	cytoband, err := parseCytoBand(string(txt))
	if err != nil {
		return err
	}
	m.data[key] = &cytoband
	return nil
}
func generateUrl(genome string) string {
	uri := "http://hgdownload.cse.ucsc.edu/goldenPath/" + genome + "/database/cytoBand.txt.gz"
	return uri
}
func (m *CytoBandManager) Add(genome string) error {
	return m.AddURI(generateUrl(genome), genome)
}

func (m *CytoBandManager) Del(genome string) error {
	delete(m.data, genome)
	return nil
}
func (m *CytoBandManager) List() []string {
	keys := []string{}
	for k, _ := range m.data {
		keys = append(keys, k)
	}
	return keys
}

func (m *CytoBandManager) Get(genome string) (string, bool) {
	if _, ok := m.data[genome]; ok {
		return generateUrl(genome), true
	}
	return "", false
}
func (m *CytoBandManager) Move(key1 string, key2 string) bool {
	v, ok := m.data[key1]
	if ok {
		m.data[key2] = v
		delete(m.data, key1)
	}
	return ok
}
func (m *CytoBandManager) ServeTo(router *mux.Router) {
	router.HandleFunc("/"+m.prefix+"/{id}/list", func(w http.ResponseWriter, r *http.Request) {
		params := mux.Vars(r)
		id := params["id"]
		if d, ok := m.data[id]; ok {
			l := make([]string, 0, 100)
			for k, _ := range d.data {
				l = append(l, k)
			}
			j, _ := json.Marshal(l)
			w.Write(j)
		}
	})
	router.HandleFunc("/"+m.prefix+"/{id}/get/{chr}", func(w http.ResponseWriter, r *http.Request) {
		params := mux.Vars(r)
		id := params["id"]
		chr := params["chr"]
		if d, ok := m.data[id]; ok {
			if d2, ok2 := d.data[chr]; ok2 {
				j, _ := json.Marshal(d2)
				w.Write(j)
			}
		}
	})
}