-package lightning
-
-import (
- "bufio"
- "bytes"
- "context"
- "errors"
- "flag"
- "fmt"
- "io"
- "net/http"
- _ "net/http/pprof"
- "os"
- "path/filepath"
- "runtime"
- "sort"
- "strconv"
- "strings"
- "sync"
- "time"
-
- "git.arvados.org/arvados.git/sdk/go/arvados"
- "github.com/arvados/lightning/hgvs"
- "github.com/klauspost/pgzip"
- log "github.com/sirupsen/logrus"
-)
-
-type tvVariant struct {
- hgvs.Variant
- librefs map[tileLibRef]bool
-}
-
-type outputFormat struct {
- Filename string
- Head func(out io.Writer, cgs []CompactGenome)
- Print func(out io.Writer, seqname string, varslice []tvVariant)
- PadLeft bool
-}
-
-var (
- outputFormats = map[string]outputFormat{
- "hgvs-onehot": outputFormatHGVSOneHot,
- "hgvs": outputFormatHGVS,
- "pvcf": outputFormatPVCF,
- "vcf": outputFormatVCF,
- }
- outputFormatHGVS = outputFormat{Filename: "out.tsv", Head: headNone, Print: printHGVS}
- outputFormatHGVSOneHot = outputFormat{Filename: "out.tsv", Head: headNone, Print: printHGVSOneHot}
- outputFormatPVCF = outputFormat{Filename: "out.vcf", Head: headPVCF, Print: printPVCF, PadLeft: true}
- outputFormatVCF = outputFormat{Filename: "out.vcf", Head: headVCF, Print: printVCF, PadLeft: true}
- headNone = func(io.Writer, []CompactGenome) {}
-)
-
-type exporter struct {
- outputFormat outputFormat
- outputPerChrom bool
- compress bool
- maxTileSize int
-}
-
-func (cmd *exporter) 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)
- pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
- pprofdir := flags.String("pprof-dir", "", "write Go profile data to `directory` periodically")
- runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
- projectUUID := flags.String("project", "", "project `UUID` for output data")
- priority := flags.Int("priority", 500, "container request priority")
- refname := flags.String("ref", "", "reference genome `name`")
- inputDir := flags.String("input-dir", ".", "input `directory`")
- outputDir := flags.String("output-dir", ".", "output `directory`")
- outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs, pvcf, or vcf")
- outputBed := flags.String("output-bed", "", "also output bed `file`")
- flags.BoolVar(&cmd.outputPerChrom, "output-per-chromosome", true, "output one file per chromosome")
- flags.BoolVar(&cmd.compress, "z", false, "write gzip-compressed output files")
- labelsFilename := flags.String("output-labels", "", "also output genome labels csv `file`")
- flags.IntVar(&cmd.maxTileSize, "max-tile-size", 50000, "don't try to make annotations for tiles bigger than given `size`")
- err = flags.Parse(args)
- if err == flag.ErrHelp {
- err = nil
- return 0
- } else if err != nil {
- return 2
- }
- if flag.NArg() > 0 {
- err = fmt.Errorf("extra unparsed command line arguments: %q", flag.Args())
- return 2
- }
-
- if f, ok := outputFormats[*outputFormatStr]; !ok {
- err = fmt.Errorf("invalid output format %q", *outputFormatStr)
- return 2
- } else {
- cmd.outputFormat = f
- }
-
- if *pprof != "" {
- go func() {
- log.Println(http.ListenAndServe(*pprof, nil))
- }()
- }
- if *pprofdir != "" {
- go writeProfilesPeriodically(*pprofdir)
- }
-
- if !*runlocal {
- if *outputDir != "." {
- err = errors.New("cannot specify output directory in container mode: not implemented")
- return 1
- }
- runner := arvadosContainerRunner{
- Name: "lightning export",
- Client: arvados.NewClientFromEnv(),
- ProjectUUID: *projectUUID,
- RAM: 700000000000,
- VCPUs: 96,
- Priority: *priority,
- APIAccess: true,
- }
- err = runner.TranslatePaths(inputDir)
- if err != nil {
- return 1
- }
- if *outputBed != "" {
- if strings.Contains(*outputBed, "/") {
- err = fmt.Errorf("cannot use -output-bed filename %q containing '/' char", *outputBed)
- return 1
- }
- *outputBed = "/mnt/output/" + *outputBed
- }
- runner.Args = []string{"export", "-local=true",
- "-pprof", ":6000",
- "-pprof-dir", "/mnt/output",
- "-ref", *refname,
- "-output-format", *outputFormatStr,
- "-output-bed", *outputBed,
- "-output-labels", "/mnt/output/labels.csv",
- "-output-per-chromosome=" + fmt.Sprintf("%v", cmd.outputPerChrom),
- "-max-tile-size", fmt.Sprintf("%d", cmd.maxTileSize),
- "-input-dir", *inputDir,
- "-output-dir", "/mnt/output",
- "-z=" + fmt.Sprintf("%v", cmd.compress),
- }
- var output string
- output, err = runner.Run()
- if err != nil {
- return 1
- }
- fmt.Fprintln(stdout, output)
- return 0
- }
-
- var cgs []CompactGenome
- tilelib := &tileLibrary{
- retainNoCalls: true,
- retainTileSequences: true,
- compactGenomes: map[string][]tileVariantID{},
- }
- err = tilelib.LoadDir(context.Background(), *inputDir, nil)
- if err != nil {
- return 1
- }
-
- refseq, ok := tilelib.refseqs[*refname]
- if !ok {
- err = fmt.Errorf("reference name %q not found in input; have %v", *refname, func() (names []string) {
- for name := range tilelib.refseqs {
- names = append(names, name)
- }
- return
- }())
- return 1
- }
-
- names := cgnames(tilelib)
- for _, name := range names {
- cgs = append(cgs, CompactGenome{Name: name, Variants: tilelib.compactGenomes[name]})
- }
- if *labelsFilename != "" {
- log.Infof("writing labels to %s", *labelsFilename)
- var f *os.File
- f, err = os.OpenFile(*labelsFilename, os.O_CREATE|os.O_WRONLY, 0777)
- if err != nil {
- return 1
- }
- defer f.Close()
- for i, name := range names {
- _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), cmd.outputFormat.Filename)
- if err != nil {
- err = fmt.Errorf("write %s: %w", *labelsFilename, err)
- return 1
- }
- }
- err = f.Close()
- if err != nil {
- err = fmt.Errorf("close %s: %w", *labelsFilename, err)
- return 1
- }
- }
-
- var bedout io.Writer
- var bedfile *os.File
- var bedbufw *bufio.Writer
- if *outputBed != "" {
- bedfile, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
- if err != nil {
- return 1
- }
- defer bedfile.Close()
- bedbufw = bufio.NewWriterSize(bedfile, 16*1024*1024)
- bedout = bedbufw
- }
-
- err = cmd.export(*outputDir, bedout, tilelib, refseq, cgs)
- if err != nil {
- return 1
- }
- if bedout != nil {
- err = bedbufw.Flush()
- if err != nil {
- return 1
- }
- err = bedfile.Close()
- if err != nil {
- return 1
- }
- }
- return 0
-}
-
-func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrary, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
- var seqnames []string
- var missing []tileLibRef
- for seqname, librefs := range refseq {
- seqnames = append(seqnames, seqname)
- for _, libref := range librefs {
- if libref.Variant != 0 && tilelib.TileVariantSequence(libref) == nil {
- missing = append(missing, libref)
- }
- }
- }
- sort.Strings(seqnames)
-
- if len(missing) > 0 {
- if limit := 100; len(missing) > limit {
- log.Warnf("first %d missing tiles: %v", limit, missing[:limit])
- } else {
- log.Warnf("missing tiles: %v", missing)
- }
- return fmt.Errorf("%d needed tiles are missing from library", len(missing))
- }
-
- outw := make([]io.WriteCloser, len(seqnames))
- bedw := make([]io.WriteCloser, len(seqnames))
-
- var merges sync.WaitGroup
- merge := func(dst io.Writer, src []io.WriteCloser, label string) {
- var mtx sync.Mutex
- for i, seqname := range seqnames {
- pr, pw := io.Pipe()
- src[i] = pw
- merges.Add(1)
- seqname := seqname
- go func() {
- defer merges.Done()
- log.Infof("writing %s %s", seqname, label)
- scanner := bufio.NewScanner(pr)
- for scanner.Scan() {
- mtx.Lock()
- dst.Write(scanner.Bytes())
- dst.Write([]byte{'\n'})
- mtx.Unlock()
- }
- log.Infof("writing %s %s done", seqname, label)
- }()
- }
- }
- if cmd.outputPerChrom {
- for i, seqname := range seqnames {
- fnm := filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename, ".", "."+seqname+".", 1))
- if cmd.compress {
- fnm += ".gz"
- }
- f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666)
- if err != nil {
- return err
- }
- defer f.Close()
- log.Infof("writing %q", f.Name())
- outw[i] = f
- if cmd.compress {
- z := pgzip.NewWriter(f)
- defer z.Close()
- outw[i] = z
- }
- cmd.outputFormat.Head(outw[i], cgs)
- }
- } else {
- fnm := filepath.Join(outdir, cmd.outputFormat.Filename)
- if cmd.compress {
- fnm += ".gz"
- }
- f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666)
- if err != nil {
- return err
- }
- defer f.Close()
- log.Infof("writing %q", fnm)
- var out io.Writer = f
- if cmd.compress {
- z := pgzip.NewWriter(out)
- defer z.Close()
- out = z
- }
- cmd.outputFormat.Head(out, cgs)
- merge(out, outw, "output")
- }
- if bedout != nil {
- merge(bedout, bedw, "bed")
- }
-
- throttle := throttle{Max: runtime.NumCPU()}
- log.Infof("assembling %d sequences in %d goroutines", len(seqnames), throttle.Max)
- for seqidx, seqname := range seqnames {
- seqidx, seqname := seqidx, seqname
- outw := outw[seqidx]
- bedw := bedw[seqidx]
- throttle.Acquire()
- go func() {
- defer throttle.Release()
- if bedw != nil {
- defer bedw.Close()
- }
- outwb := bufio.NewWriterSize(outw, 8*1024*1024)
- cmd.exportSeq(outwb, bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tilelib, cgs)
- err := outwb.Flush()
- throttle.Report(err)
- err = outw.Close()
- throttle.Report(err)
- }()
- }
-
- merges.Wait()
- throttle.Wait()
- return throttle.Err()
-}
-
-// Align genome tiles to reference tiles, write diffs to outw, and (if
-// bedw is not nil) write tile coverage to bedw.
-func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tilelib *tileLibrary, cgs []CompactGenome) {
- t0 := time.Now()
- progressbar := time.NewTicker(time.Minute)
- defer progressbar.Stop()
- var outmtx sync.Mutex
- defer outmtx.Lock()
- refpos := 0
- variantAt := map[int][]tvVariant{} // variantAt[chromOffset][genomeIndex*2+phase]
- for refstep, libref := range reftiles {
- select {
- case <-progressbar.C:
- var eta interface{}
- if refstep > 0 {
- fin := t0.Add(time.Duration(float64(time.Now().Sub(t0)) * float64(len(reftiles)) / float64(refstep)))
- eta = fmt.Sprintf("%v (%v)", fin.Format(time.RFC3339), fin.Sub(time.Now()))
- } else {
- eta = "N/A"
- }
- log.Printf("exportSeq: %s: refstep %d of %d, %.0f/s, ETA %v", seqname, refstep, len(reftiles), float64(refstep)/time.Now().Sub(t0).Seconds(), eta)
- default:
- }
- diffs := map[tileLibRef][]hgvs.Variant{}
- refseq := tilelib.TileVariantSequence(libref)
- tagcoverage := 0 // number of times the start tag was found in genomes -- max is len(cgs)*2
- for cgidx, cg := range cgs {
- for phase := 0; phase < 2; phase++ {
- if len(cg.Variants) <= int(libref.Tag)*2+phase {
- continue
- }
- variant := cg.Variants[int(libref.Tag)*2+phase]
- if variant == 0 {
- continue
- }
- tagcoverage++
- if variant == libref.Variant {
- continue
- }
- glibref := tileLibRef{Tag: libref.Tag, Variant: variant}
- vars, ok := diffs[glibref]
- if !ok {
- genomeseq := tilelib.TileVariantSequence(glibref)
- if len(genomeseq) == 0 {
- // Hash is known but sequence
- // is not, e.g., retainNoCalls
- // was false during import
- continue
- }
- if len(genomeseq) > cmd.maxTileSize {
- continue
- }
- refSequence := refseq
- // If needed, extend the
- // reference sequence up to
- // the tag at the end of the
- // genomeseq sequence.
- refstepend := refstep + 1
- for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genomeseq[len(genomeseq)-taglen:]) && len(refSequence) <= cmd.maxTileSize {
- if &refSequence[0] == &refseq[0] {
- refSequence = append([]byte(nil), refSequence...)
- }
- refSequence = append(refSequence, tilelib.TileVariantSequence(reftiles[refstepend])...)
- refstepend++
- }
- // (TODO: handle no-calls)
- if len(refSequence) <= cmd.maxTileSize {
- refstr := strings.ToUpper(string(refSequence))
- genomestr := strings.ToUpper(string(genomeseq))
- vars, _ = hgvs.Diff(refstr, genomestr, time.Second)
- }
- diffs[glibref] = vars
- }
- for _, v := range vars {
- if cmd.outputFormat.PadLeft {
- v = v.PadLeft()
- }
- v.Position += refpos
- varslice := variantAt[v.Position]
- if varslice == nil {
- varslice = make([]tvVariant, len(cgs)*2)
- variantAt[v.Position] = varslice
- }
- varslice[cgidx*2+phase].Variant = v
- if varslice[cgidx*2+phase].librefs == nil {
- varslice[cgidx*2+phase].librefs = map[tileLibRef]bool{glibref: true}
- } else {
- varslice[cgidx*2+phase].librefs[glibref] = true
- }
- }
- }
- }
- refpos += len(refseq) - taglen
-
- // Flush entries from variantAt that are behind
- // refpos. Flush all entries if this is the last
- // reftile of the path/chromosome.
- flushpos := make([]int, 0, len(variantAt))
- lastrefstep := refstep == len(reftiles)-1
- for pos := range variantAt {
- if lastrefstep || pos <= refpos {
- flushpos = append(flushpos, pos)
- }
- }
- sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
- flushvariants := make([][]tvVariant, len(flushpos))
- for i, pos := range flushpos {
- varslice := variantAt[pos]
- delete(variantAt, pos)
- for i := range varslice {
- if varslice[i].Position == 0 {
- varslice[i].Position = pos
- }
- }
- flushvariants[i] = varslice
- }
- outmtx.Lock()
- go func() {
- defer outmtx.Unlock()
- for _, varslice := range flushvariants {
- cmd.outputFormat.Print(outw, seqname, varslice)
- }
- }()
- if bedw != nil && len(refseq) > 0 {
- tilestart := refpos - len(refseq) + taglen
- tileend := refpos
- if !lastrefstep {
- tileend += taglen
- }
- thickstart := tilestart + taglen
- if refstep == 0 {
- thickstart = 0
- }
- thickend := refpos
-
- // coverage score, 0 to 1000
- score := 1000
- if len(cgs) > 0 {
- score = 1000 * tagcoverage / len(cgs) / 2
- }
-
- fmt.Fprintf(bedw, "%s %d %d %d %d . %d %d\n",
- seqname, tilestart, tileend,
- libref.Tag,
- score,
- thickstart, thickend)
- }
- }
-}
-
-func bucketVarsliceByRef(varslice []tvVariant) map[string]map[string]int {
- byref := map[string]map[string]int{}
- for _, v := range varslice {
- if v.Ref == "" && v.New == "" {
- continue
- }
- alts := byref[v.Ref]
- if alts == nil {
- alts = map[string]int{}
- byref[v.Ref] = alts
- }
- alts[v.New]++
- }
- return byref
-}
-
-func headVCF(out io.Writer, cgs []CompactGenome) {
- fmt.Fprint(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
-}
-
-func printVCF(out io.Writer, seqname string, varslice []tvVariant) {
- for ref, alts := range bucketVarsliceByRef(varslice) {
- altslice := make([]string, 0, len(alts))
- for alt := range alts {
- altslice = append(altslice, alt)
- }
- sort.Strings(altslice)
-
- info := "AC="
- for i, a := range altslice {
- if i > 0 {
- info += ","
- }
- info += strconv.Itoa(alts[a])
- }
- fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t%s\n", seqname, varslice[0].Position, ref, strings.Join(altslice, ","), info)
- }
-}
-
-func headPVCF(out io.Writer, cgs []CompactGenome) {
- fmt.Fprintln(out, `##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">`)
- fmt.Fprintf(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT")
- for _, cg := range cgs {
- fmt.Fprintf(out, "\t%s", cg.Name)
- }
- fmt.Fprintf(out, "\n")
-}
-
-func printPVCF(out io.Writer, seqname string, varslice []tvVariant) {
- for ref, alts := range bucketVarsliceByRef(varslice) {
- altslice := make([]string, 0, len(alts))
- for alt := range alts {
- altslice = append(altslice, alt)
- }
- sort.Strings(altslice)
- for i, a := range altslice {
- alts[a] = i + 1
- }
- fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t.\tGT", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
- for i := 0; i < len(varslice); i += 2 {
- v1, v2 := varslice[i], varslice[i+1]
- a1, a2 := alts[v1.New], alts[v2.New]
- if v1.Ref != ref {
- // variant on allele 0 belongs on a
- // different output line -- same
- // chr,pos but different "ref" length
- a1 = 0
- }
- if v2.Ref != ref {
- a2 = 0
- }
- fmt.Fprintf(out, "\t%d/%d", a1, a2)
- }
- out.Write([]byte{'\n'})
- }
-}
-
-func printHGVS(out io.Writer, seqname string, varslice []tvVariant) {
- for i := 0; i < len(varslice)/2; i++ {
- if i > 0 {
- out.Write([]byte{'\t'})
- }
- var1, var2 := varslice[i*2], varslice[i*2+1]
- if var1.Variant == var2.Variant {
- if var1.Ref == var1.New {
- out.Write([]byte{'.'})
- } else {
- fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
- }
- } else {
- fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
- }
- }
- out.Write([]byte{'\n'})
-}
-
-func printHGVSOneHot(out io.Writer, seqname string, varslice []tvVariant) {
- vars := map[hgvs.Variant]bool{}
- for _, v := range varslice {
- if v.Ref != v.New {
- vars[v.Variant] = true
- }
- }
-
- // sort variants to ensure output is deterministic
- sorted := make([]hgvs.Variant, 0, len(vars))
- for v := range vars {
- sorted = append(sorted, v)
- }
- sort.Slice(sorted, func(a, b int) bool { return hgvs.Less(sorted[a], sorted[b]) })
-
- for _, v := range sorted {
- fmt.Fprintf(out, "%s.%s", seqname, v.String())
- for i := 0; i < len(varslice); i += 2 {
- if varslice[i].Variant == v || varslice[i+1].Variant == v {
- out.Write([]byte("\t1"))
- } else {
- out.Write([]byte("\t0"))
- }
- }
- out.Write([]byte{'\n'})
- }
-}
projects / lightning.git / blobdiff