-package main
+package lightning
import (
"bufio"
"net/http"
_ "net/http/pprof"
"os"
+ "path"
"sort"
"strings"
- "sync"
"time"
"git.arvados.org/arvados.git/sdk/go/arvados"
var (
outputFormats = map[string]outputFormat{
- "hgvs": outputFormatHGVS,
- "vcf": outputFormatVCF,
+ "hgvs-onehot": outputFormatHGVSOneHot,
+ "hgvs": outputFormatHGVS,
+ "vcf": outputFormatVCF,
}
- outputFormatHGVS = outputFormat{Print: printHGVS}
- outputFormatVCF = outputFormat{Print: printVCF, PadLeft: true}
+ outputFormatHGVS = outputFormat{Print: printHGVS}
+ outputFormatHGVSOneHot = outputFormat{Print: printHGVSOneHot}
+ outputFormatVCF = outputFormat{Print: printVCF, PadLeft: true}
)
type exporter struct {
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`")
- pick := flags.String("pick", "", "`name` of single genome to export")
+ labelsFilename := flags.String("output-labels", "", "also output genome labels csv `file`")
err = flags.Parse(args)
if err == flag.ErrHelp {
err = nil
Name: "lightning export",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
- RAM: 128000000000,
- VCPUs: 2,
+ RAM: 700000000000,
+ VCPUs: 32,
Priority: *priority,
}
err = runner.TranslatePaths(inputFilename)
}
*outputBed = "/mnt/output/" + *outputBed
}
- runner.Args = []string{"export", "-local=true", "-pick", *pick, "-ref", *refname, "-output-format", *outputFormatStr, "-output-bed", *outputBed, "-i", *inputFilename, "-o", "/mnt/output/export.csv"}
+ runner.Args = []string{"export", "-local=true",
+ "-ref", *refname,
+ "-output-format", *outputFormatStr,
+ "-output-bed", *outputBed,
+ "-output-labels", "/mnt/output/labels.csv",
+ "-i", *inputFilename,
+ "-o", "/mnt/output/export.csv",
+ }
var output string
output, err = runner.Run()
if err != nil {
return 0
}
- input, err := os.Open(*inputFilename)
+ in, err := open(*inputFilename)
if err != nil {
return 1
}
- defer input.Close()
+ 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)
return 1
}
- var mtx sync.Mutex
var cgs []CompactGenome
- tilelib := tileLibrary{
- includeNoCalls: true,
+ tilelib := &tileLibrary{
+ retainNoCalls: true,
+ compactGenomes: map[string][]tileVariantID{},
}
- err = tilelib.LoadGob(context.Background(), input, func(cg CompactGenome) {
- if *pick != "" && *pick != cg.Name {
- return
- }
- log.Debugf("export: pick %q", cg.Name)
- mtx.Lock()
- defer mtx.Unlock()
- cgs = append(cgs, cg)
- })
+ err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), nil)
if err != nil {
return 1
}
- sort.Slice(cgs, func(i, j int) bool { return cgs[i].Name < cgs[j].Name })
- log.Printf("export: pick %q => %d genomes", *pick, len(cgs))
refseq, ok := tilelib.refseqs[*refname]
if !ok {
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
bedbufw = bufio.NewWriter(bedout)
}
- err = cmd.export(bufw, bedout, input, tilelib.taglib.keylen, refseq, cgs)
+ err = cmd.export(bufw, bedout, input, strings.HasSuffix(*inputFilename, ".gz"), tilelib, refseq, cgs)
if err != nil {
return 1
}
return 1
}
}
- err = input.Close()
+ err = in.Close()
if err != nil {
return 1
}
return 0
}
-func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
+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 {
log.Infof("export: loading %d tile variants", len(need))
tileVariant := map[tileLibRef]TileVariant{}
- err := DecodeLibrary(librdr, func(ent *LibraryEntry) error {
+ err := DecodeLibrary(librdr, gz, func(ent *LibraryEntry) error {
for _, tv := range ent.TileVariants {
- libref := tileLibRef{Tag: tv.Tag, Variant: tv.Variant}
+ libref := tilelib.getRef(tv.Tag, tv.Sequence)
if need[libref] {
tileVariant[libref] = tv
}
return fmt.Errorf("%d needed tiles are missing from library", len(missing))
}
+ log.Infof("assembling %d sequences concurrently", len(seqnames))
+ throttle := throttle{Max: 8}
+ outbuf := make([]bytes.Buffer, len(seqnames))
+ bedbuf := make([]bytes.Buffer, len(seqnames))
+ for seqidx, seqname := range seqnames {
+ seqname := seqname
+ outbuf := &outbuf[seqidx]
+ bedbuf := &bedbuf[seqidx]
+ if bedout == nil {
+ bedbuf = nil
+ }
+ throttle.Acquire()
+ go func() {
+ defer throttle.Release()
+ cmd.exportSeq(outbuf, bedbuf, tilelib.taglib.keylen, seqname, refseq[seqname], tileVariant, cgs)
+ log.Infof("assembled %q to outbuf %d bedbuf %d", seqname, outbuf.Len(), bedbuf.Len())
+ }()
+ }
+ throttle.Wait()
+
+ throttle.Acquire()
+ go func() {
+ defer throttle.Release()
+ for i, seqname := range seqnames {
+ log.Infof("writing outbuf %s", seqname)
+ io.Copy(out, &outbuf[i])
+ }
+ }()
+ if bedout != nil {
+ throttle.Acquire()
+ go func() {
+ defer throttle.Release()
+ for i, seqname := range seqnames {
+ log.Infof("writing bedbuf %s", seqname)
+ io.Copy(bedout, &bedbuf[i])
+ }
+ }()
+ }
+ throttle.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
- for _, seqname := range seqnames {
- variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
- for refstep, libref := range refseq[seqname] {
- reftile := tileVariant[libref]
- coverage := int64(0) // number of ref bases that are called in genomes -- max is len(reftile.Sequence)*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
- }
- genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
- if variant == libref.Variant {
- continue
+ 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
+ }
+ 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:]) {
+ if &refSequence[0] == &reftile.Sequence[0] {
+ refSequence = append([]byte(nil), refSequence...)
}
- 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(refseq[seqname]) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) {
- if &refSequence[0] == &reftile.Sequence[0] {
- refSequence = append([]byte(nil), refSequence...)
- }
- refSequence = append(refSequence, tileVariant[refseq[seqname][refstepend]].Sequence...)
- refstepend++
+ 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()
}
- // (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
- log.Debugf("%s seq %s phase %d tag %d tile diff %s\n", cg.Name, seqname, phase, libref.Tag, v.String())
- varslice := variantAt[v.Position]
- if varslice == nil {
- varslice = make([]hgvs.Variant, len(cgs)*2)
- variantAt[v.Position] = varslice
- }
- varslice[cgidx*2+phase] = v
+ v.Position += refpos
+ varslice := variantAt[v.Position]
+ if varslice == nil {
+ varslice = make([]hgvs.Variant, len(cgs)*2)
+ variantAt[v.Position] = varslice
}
- coverage += int64(len(reftile.Sequence))
+ 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(refseq[seqname])-1
- for pos := range variantAt {
- if lastrefstep || pos <= refpos {
- flushpos = append(flushpos, pos)
- }
+ }
+ 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
- }
+ }
+ 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(out, seqname, varslice)
}
- if bedout != 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 * coverage / int64(len(reftile.Sequence)) / int64(len(cgs)) / 2
- fmt.Fprintf(bedout, "%s %d %d %d %d . %d %d\n",
- seqname, tilestart, tileend,
- libref.Tag,
- score,
- thickstart, thickend)
+ 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)
}
}
- return nil
}
func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
}
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