-package lightning
-
-import (
- "bufio"
- "bytes"
- "context"
- "errors"
- "flag"
- "fmt"
- "io"
- "net/http"
- _ "net/http/pprof"
- "os"
- "path"
- "sort"
- "strings"
- "sync"
- "time"
-
- "git.arvados.org/arvados.git/sdk/go/arvados"
- "github.com/arvados/lightning/hgvs"
- log "github.com/sirupsen/logrus"
-)
-
-type outputFormat struct {
- Print func(out io.Writer, seqname string, varslice []hgvs.Variant)
- PadLeft bool
-}
-
-var (
- outputFormats = map[string]outputFormat{
- "hgvs-onehot": outputFormatHGVSOneHot,
- "hgvs": outputFormatHGVS,
- "vcf": outputFormatVCF,
- }
- outputFormatHGVS = outputFormat{Print: printHGVS}
- outputFormatHGVSOneHot = outputFormat{Print: printHGVSOneHot}
- outputFormatVCF = outputFormat{Print: printVCF, PadLeft: true}
-)
-
-type exporter struct {
- outputFormat outputFormat
- 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`")
- inputFilename := flags.String("i", "-", "input `file` (library)")
- outputFilename := flags.String("o", "-", "output `file`")
- outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs or vcf")
- outputBed := flags.String("output-bed", "", "also output bed `file`")
- 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 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 *outputFilename != "-" {
- err = errors.New("cannot specify output file in container mode: not implemented")
- return 1
- }
- runner := arvadosContainerRunner{
- Name: "lightning export",
- Client: arvados.NewClientFromEnv(),
- ProjectUUID: *projectUUID,
- RAM: 1600000000000,
- VCPUs: 64,
- Priority: *priority,
- }
- err = runner.TranslatePaths(inputFilename)
- 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",
- "-max-tile-size", fmt.Sprintf("%d", cmd.maxTileSize),
- "-i", *inputFilename,
- "-o", "/mnt/output/export.csv",
- }
- var output string
- output, err = runner.Run()
- if err != nil {
- return 1
- }
- fmt.Fprintln(stdout, output+"/export.csv")
- return 0
- }
-
- in, err := open(*inputFilename)
- if err != nil {
- return 1
- }
- defer in.Close()
- input, ok := in.(io.ReadSeeker)
- if !ok {
- err = fmt.Errorf("%s: %T cannot seek", *inputFilename, in)
- return 1
- }
-
- // Error out early if seeking doesn't work on the input file.
- _, err = input.Seek(0, io.SeekEnd)
- if err != nil {
- return 1
- }
- _, err = input.Seek(0, io.SeekStart)
- if err != nil {
- return 1
- }
-
- var cgs []CompactGenome
- tilelib := &tileLibrary{
- retainNoCalls: true,
- compactGenomes: map[string][]tileVariantID{},
- }
- err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), 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()
- _, outBasename := path.Split(*outputFilename)
- for i, name := range names {
- _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), outBasename)
- 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
- }
- }
-
- _, err = input.Seek(0, io.SeekStart)
- if err != nil {
- return 1
- }
-
- var output io.WriteCloser
- if *outputFilename == "-" {
- output = nopCloser{stdout}
- } else {
- output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0666)
- if err != nil {
- return 1
- }
- defer output.Close()
- }
- bufw := bufio.NewWriter(output)
-
- var bedout *os.File
- var bedbufw *bufio.Writer
- if *outputBed != "" {
- bedout, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
- if err != nil {
- return 1
- }
- defer bedout.Close()
- bedbufw = bufio.NewWriter(bedout)
- }
-
- err = cmd.export(bufw, bedout, input, strings.HasSuffix(*inputFilename, ".gz"), tilelib, refseq, cgs)
- if err != nil {
- return 1
- }
- err = bufw.Flush()
- if err != nil {
- return 1
- }
- err = output.Close()
- if err != nil {
- return 1
- }
- if bedout != nil {
- err = bedbufw.Flush()
- if err != nil {
- return 1
- }
- err = bedout.Close()
- if err != nil {
- return 1
- }
- }
- err = in.Close()
- if err != nil {
- return 1
- }
- return 0
-}
-
-func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, gz bool, tilelib *tileLibrary, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
- need := map[tileLibRef]bool{}
- var seqnames []string
- for seqname, librefs := range refseq {
- seqnames = append(seqnames, seqname)
- for _, libref := range librefs {
- if libref.Variant != 0 {
- need[libref] = true
- }
- }
- }
- sort.Strings(seqnames)
-
- for _, cg := range cgs {
- for i, variant := range cg.Variants {
- if variant == 0 {
- continue
- }
- libref := tileLibRef{Tag: tagID(i / 2), Variant: variant}
- need[libref] = true
- }
- }
-
- log.Infof("export: loading %d tile variants", len(need))
- tileVariant := map[tileLibRef]TileVariant{}
- err := DecodeLibrary(librdr, gz, func(ent *LibraryEntry) error {
- for _, tv := range ent.TileVariants {
- libref := tilelib.getRef(tv.Tag, tv.Sequence)
- if need[libref] {
- tileVariant[libref] = tv
- }
- }
- return nil
- })
- if err != nil {
- return err
- }
-
- log.Infof("export: loaded %d tile variants", len(tileVariant))
- var missing []tileLibRef
- for libref := range need {
- if _, ok := tileVariant[libref]; !ok {
- missing = append(missing, libref)
- }
- }
- 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)
- }()
- }
- }
- merge(out, outw, "output")
- if bedout != nil {
- merge(bedout, bedw, "bed")
- }
-
- throttle := throttle{Max: 8}
- 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()
- }
- defer outw.Close()
- outwb := bufio.NewWriter(outw)
- defer outwb.Flush()
- cmd.exportSeq(outwb, bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tileVariant, cgs)
- }()
- }
-
- merges.Wait()
- return nil
-}
-
-// 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, tileVariant map[tileLibRef]TileVariant, cgs []CompactGenome) {
- refpos := 0
- variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
- for refstep, libref := range reftiles {
- reftile := tileVariant[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
- }
- genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
- if len(genometile.Sequence) == 0 {
- // Hash is known but sequence
- // is not, e.g., retainNoCalls
- // was false during import
- continue
- }
- if len(genometile.Sequence) > cmd.maxTileSize {
- continue
- }
- refSequence := reftile.Sequence
- // If needed, extend the reference
- // sequence up to the tag at the end
- // of the genometile sequence.
- refstepend := refstep + 1
- for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) && len(refSequence) <= cmd.maxTileSize {
- if &refSequence[0] == &reftile.Sequence[0] {
- refSequence = append([]byte(nil), refSequence...)
- }
- refSequence = append(refSequence, tileVariant[reftiles[refstepend]].Sequence...)
- refstepend++
- }
- // (TODO: handle no-calls)
- vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genometile.Sequence)), time.Second)
- for _, v := range vars {
- if cmd.outputFormat.PadLeft {
- v = v.PadLeft()
- }
- v.Position += refpos
- varslice := variantAt[v.Position]
- if varslice == nil {
- varslice = make([]hgvs.Variant, len(cgs)*2)
- variantAt[v.Position] = varslice
- }
- varslice[cgidx*2+phase] = v
- }
- }
- }
- refpos += len(reftile.Sequence) - taglen
-
- // Flush entries from variantAt that are behind
- // refpos. Flush all entries if this is the last
- // reftile of the path/chromosome.
- var flushpos []int
- 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] })
- for _, pos := range flushpos {
- varslice := variantAt[pos]
- delete(variantAt, pos)
- for i := range varslice {
- if varslice[i].Position == 0 {
- varslice[i].Position = pos
- }
- }
- cmd.outputFormat.Print(outw, seqname, varslice)
- }
- if bedw != nil && len(reftile.Sequence) > 0 {
- tilestart := refpos - len(reftile.Sequence) + 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 printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
- refs := map[string]map[string]int{}
- for _, v := range varslice {
- if v.Ref == "" && v.New == "" {
- continue
- }
- alts := refs[v.Ref]
- if alts == nil {
- alts = map[string]int{}
- refs[v.Ref] = alts
- }
- alts[v.New] = 0
- }
- for ref, alts := range refs {
- var altslice []string
- 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%s\t%s", 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 {
- 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 []hgvs.Variant) {
- 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 == var2 {
- 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 []hgvs.Variant) {
- vars := map[hgvs.Variant]bool{}
- for _, v := range varslice {
- if v.Ref != v.New {
- vars[v] = 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] == v || varslice[i+1] == v {
- out.Write([]byte("\t1"))
- } else {
- out.Write([]byte("\t0"))
- }
- }
- out.Write([]byte{'\n'})
- }
-}
projects / lightning.git / blobdiff