+++ /dev/null
-package main
-
-import (
- "bufio"
- "compress/gzip"
- "encoding/gob"
- "errors"
- "flag"
- "fmt"
- "io"
- "log"
- "net/http"
- _ "net/http/pprof"
- "os"
- "os/exec"
- "path/filepath"
- "regexp"
- "runtime"
- "sort"
- "strings"
- "sync"
- "sync/atomic"
- "time"
-
- "git.arvados.org/arvados.git/sdk/go/arvados"
-)
-
-type importer struct {
- tagLibraryFile string
- refFile string
- outputFile string
- projectUUID string
- runLocal bool
- encoder *gob.Encoder
-}
-
-func (cmd *importer) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
- var err error
- defer func() {
- if err != nil {
- fmt.Fprintf(stderr, "%s\n", err)
- }
- }()
- flags := flag.NewFlagSet("", flag.ContinueOnError)
- flags.SetOutput(stderr)
- flags.StringVar(&cmd.tagLibraryFile, "tag-library", "", "tag library fasta `file`")
- flags.StringVar(&cmd.refFile, "ref", "", "reference fasta `file`")
- flags.StringVar(&cmd.outputFile, "o", "", "output `file`")
- flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for output data")
- flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)")
- pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
- err = flags.Parse(args)
- if err == flag.ErrHelp {
- err = nil
- return 0
- } else if err != nil {
- return 2
- } else if cmd.tagLibraryFile == "" {
- fmt.Fprintln(os.Stderr, "cannot import without -tag-library argument")
- return 2
- } else if flags.NArg() == 0 {
- flags.Usage()
- return 2
- }
-
- if *pprof != "" {
- go func() {
- log.Println(http.ListenAndServe(*pprof, nil))
- }()
- }
-
- if !cmd.runLocal {
- runner := arvadosContainerRunner{
- Name: "lightning import",
- Client: arvados.NewClientFromEnv(),
- ProjectUUID: cmd.projectUUID,
- RAM: 30000000000,
- VCPUs: 16,
- }
- err = runner.TranslatePaths(&cmd.tagLibraryFile, &cmd.refFile, &cmd.outputFile)
- if err != nil {
- return 1
- }
- inputs := flags.Args()
- for i := range inputs {
- err = runner.TranslatePaths(&inputs[i])
- if err != nil {
- return 1
- }
- }
- if cmd.outputFile == "" {
- cmd.outputFile = "/mnt/output/library.gob"
- } else {
- // Not yet implemented, but this should write
- // the collection to an existing collection,
- // possibly even an in-place update.
- err = errors.New("cannot specify output file in container mode: not implemented")
- return 1
- }
- runner.Args = append([]string{"import", "-local=true", "-tag-library", cmd.tagLibraryFile, "-ref", cmd.refFile, "-o", cmd.outputFile}, inputs...)
- err = runner.Run()
- if err != nil {
- return 1
- }
- return 0
- }
-
- infiles, err := listInputFiles(flags.Args())
- if err != nil {
- return 1
- }
-
- tilelib, err := cmd.loadTileLibrary()
- if err != nil {
- return 1
- }
- go func() {
- for range time.Tick(10 * time.Second) {
- log.Printf("tilelib.Len() == %d", tilelib.Len())
- }
- }()
-
- var output io.WriteCloser
- if cmd.outputFile == "" {
- output = nopCloser{stdout}
- } else {
- output, err = os.OpenFile(cmd.outputFile, os.O_CREATE|os.O_WRONLY, 0777)
- if err != nil {
- return 1
- }
- defer output.Close()
- }
- bufw := bufio.NewWriter(output)
- cmd.encoder = gob.NewEncoder(bufw)
-
- err = cmd.tileInputs(tilelib, infiles)
- if err != nil {
- return 1
- }
- err = bufw.Flush()
- if err != nil {
- return 1
- }
- err = output.Close()
- if err != nil {
- return 1
- }
- return 0
-}
-
-func (cmd *importer) tileFasta(tilelib *tileLibrary, infile string) (tileSeq, error) {
- var input io.ReadCloser
- input, err := os.Open(infile)
- if err != nil {
- return nil, err
- }
- defer input.Close()
- if strings.HasSuffix(infile, ".gz") {
- input, err = gzip.NewReader(input)
- if err != nil {
- return nil, err
- }
- defer input.Close()
- }
- return tilelib.TileFasta(infile, input)
-}
-
-func (cmd *importer) loadTileLibrary() (*tileLibrary, error) {
- log.Printf("tag library %s load starting", cmd.tagLibraryFile)
- f, err := os.Open(cmd.tagLibraryFile)
- if err != nil {
- return nil, err
- }
- defer f.Close()
- var rdr io.ReadCloser = f
- if strings.HasSuffix(cmd.tagLibraryFile, ".gz") {
- rdr, err = gzip.NewReader(f)
- if err != nil {
- return nil, fmt.Errorf("%s: gzip: %s", cmd.tagLibraryFile, err)
- }
- defer rdr.Close()
- }
- var taglib tagLibrary
- err = taglib.Load(rdr)
- if err != nil {
- return nil, err
- }
- if taglib.Len() < 1 {
- return nil, fmt.Errorf("cannot tile: tag library is empty")
- }
- log.Printf("tag library %s load done", cmd.tagLibraryFile)
- return &tileLibrary{taglib: &taglib}, nil
-}
-
-func listInputFiles(paths []string) (files []string, err error) {
- for _, path := range paths {
- if fi, err := os.Stat(path); err != nil {
- return nil, fmt.Errorf("%s: stat failed: %s", path, err)
- } else if !fi.IsDir() {
- if !strings.HasSuffix(path, ".2.fasta") || strings.HasSuffix(path, ".2.fasta.gz") {
- files = append(files, path)
- }
- continue
- }
- d, err := os.Open(path)
- if err != nil {
- return nil, fmt.Errorf("%s: open failed: %s", path, err)
- }
- defer d.Close()
- names, err := d.Readdirnames(0)
- if err != nil {
- return nil, fmt.Errorf("%s: readdir failed: %s", path, err)
- }
- sort.Strings(names)
- for _, name := range names {
- if strings.HasSuffix(name, ".vcf") || strings.HasSuffix(name, ".vcf.gz") {
- files = append(files, filepath.Join(path, name))
- } else if strings.HasSuffix(name, ".1.fasta") || strings.HasSuffix(name, ".1.fasta.gz") {
- files = append(files, filepath.Join(path, name))
- }
- }
- d.Close()
- }
- for _, file := range files {
- if strings.HasSuffix(file, ".1.fasta") || strings.HasSuffix(file, ".1.fasta.gz") {
- continue
- } else if _, err := os.Stat(file + ".csi"); err == nil {
- continue
- } else if _, err = os.Stat(file + ".tbi"); err == nil {
- continue
- } else {
- return nil, fmt.Errorf("%s: cannot read without .tbi or .csi index file", file)
- }
- }
- return
-}
-
-func (cmd *importer) tileInputs(tilelib *tileLibrary, infiles []string) error {
- starttime := time.Now()
- errs := make(chan error, 1)
- todo := make(chan func() error, len(infiles)*2)
- var encodeJobs sync.WaitGroup
- for _, infile := range infiles {
- infile := infile
- var phases sync.WaitGroup
- phases.Add(2)
- variants := make([][]tileVariantID, 2)
- if strings.HasSuffix(infile, ".1.fasta") || strings.HasSuffix(infile, ".1.fasta.gz") {
- todo <- func() error {
- defer phases.Done()
- log.Printf("%s starting", infile)
- defer log.Printf("%s done", infile)
- tseqs, err := cmd.tileFasta(tilelib, infile)
- variants[0] = tseqs.Variants()
- return err
- }
- infile2 := regexp.MustCompile(`\.1\.fasta(\.gz)?$`).ReplaceAllString(infile, `.2.fasta$1`)
- todo <- func() error {
- defer phases.Done()
- log.Printf("%s starting", infile2)
- defer log.Printf("%s done", infile2)
- tseqs, err := cmd.tileFasta(tilelib, infile2)
- variants[1] = tseqs.Variants()
- return err
- }
- } else {
- for phase := 0; phase < 2; phase++ {
- phase := phase
- todo <- func() error {
- defer phases.Done()
- log.Printf("%s phase %d starting", infile, phase+1)
- defer log.Printf("%s phase %d done", infile, phase+1)
- tseqs, err := cmd.tileGVCF(tilelib, infile, phase)
- variants[phase] = tseqs.Variants()
- return err
- }
- }
- }
- encodeJobs.Add(1)
- go func() {
- defer encodeJobs.Done()
- phases.Wait()
- if len(errs) > 0 {
- return
- }
- ntags := len(variants[0])
- if ntags < len(variants[1]) {
- ntags = len(variants[1])
- }
- flat := make([]tileVariantID, ntags*2)
- for i := 0; i < ntags; i++ {
- flat[i*2] = variants[0][i]
- flat[i*2+1] = variants[1][i]
- }
- err := cmd.encoder.Encode(LibraryEntry{
- CompactGenomes: []CompactGenome{{Name: infile, Variants: flat}},
- })
- if err != nil {
- select {
- case errs <- err:
- default:
- }
- }
- }()
- }
- go close(todo)
- var tileJobs sync.WaitGroup
- running := int64(runtime.NumCPU())
- for i := 0; i < runtime.NumCPU(); i++ {
- tileJobs.Add(1)
- go func() {
- defer tileJobs.Done()
- defer atomic.AddInt64(&running, -1)
- for fn := range todo {
- if len(errs) > 0 {
- return
- }
- err := fn()
- if err != nil {
- select {
- case errs <- err:
- default:
- }
- }
- remain := len(todo) + int(atomic.LoadInt64(&running)) - 1
- ttl := time.Now().Sub(starttime) * time.Duration(remain) / time.Duration(cap(todo)-remain)
- eta := time.Now().Add(ttl)
- log.Printf("progress %d/%d, eta %v (%v)", cap(todo)-remain, cap(todo), eta, ttl)
- }
- }()
- }
- tileJobs.Wait()
- encodeJobs.Wait()
- go close(errs)
- return <-errs
-}
-
-func (cmd *importer) tileGVCF(tilelib *tileLibrary, infile string, phase int) (tileseq tileSeq, err error) {
- if cmd.refFile == "" {
- err = errors.New("cannot import vcf: reference data (-ref) not specified")
- return
- }
- args := []string{"bcftools", "consensus", "--fasta-ref", cmd.refFile, "-H", fmt.Sprint(phase + 1), infile}
- indexsuffix := ".tbi"
- if _, err := os.Stat(infile + ".csi"); err == nil {
- indexsuffix = ".csi"
- }
- if out, err := exec.Command("docker", "image", "ls", "-q", "lightning-runtime").Output(); err == nil && len(out) > 0 {
- args = append([]string{
- "docker", "run", "--rm",
- "--log-driver=none",
- "--volume=" + infile + ":" + infile + ":ro",
- "--volume=" + infile + indexsuffix + ":" + infile + indexsuffix + ":ro",
- "--volume=" + cmd.refFile + ":" + cmd.refFile + ":ro",
- "lightning-runtime",
- }, args...)
- }
- consensus := exec.Command(args[0], args[1:]...)
- consensus.Stderr = os.Stderr
- stdout, err := consensus.StdoutPipe()
- defer stdout.Close()
- if err != nil {
- return
- }
- err = consensus.Start()
- if err != nil {
- return
- }
- defer consensus.Wait()
- tileseq, err = tilelib.TileFasta(fmt.Sprintf("%s phase %d", infile, phase+1), stdout)
- if err != nil {
- return
- }
- err = stdout.Close()
- if err != nil {
- return
- }
- err = consensus.Wait()
- if err != nil {
- err = fmt.Errorf("%s phase %d: bcftools: %s", infile, phase, err)
- return
- }
- return
-}