19 "git.arvados.org/arvados.git/sdk/go/arvados"
20 "github.com/arvados/lightning/hgvs"
21 log "github.com/sirupsen/logrus"
24 type outputFormat struct {
25 Print func(out io.Writer, seqname string, varslice []hgvs.Variant)
30 outputFormats = map[string]outputFormat{
31 "hgvs-onehot": outputFormatHGVSOneHot,
32 "hgvs": outputFormatHGVS,
33 "vcf": outputFormatVCF,
35 outputFormatHGVS = outputFormat{Print: printHGVS}
36 outputFormatHGVSOneHot = outputFormat{Print: printHGVSOneHot}
37 outputFormatVCF = outputFormat{Print: printVCF, PadLeft: true}
40 type exporter struct {
41 outputFormat outputFormat
44 func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
48 fmt.Fprintf(stderr, "%s\n", err)
51 flags := flag.NewFlagSet("", flag.ContinueOnError)
52 flags.SetOutput(stderr)
53 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
54 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
55 projectUUID := flags.String("project", "", "project `UUID` for output data")
56 priority := flags.Int("priority", 500, "container request priority")
57 refname := flags.String("ref", "", "reference genome `name`")
58 inputFilename := flags.String("i", "-", "input `file` (library)")
59 outputFilename := flags.String("o", "-", "output `file`")
60 outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs or vcf")
61 outputBed := flags.String("output-bed", "", "also output bed `file`")
62 labelsFilename := flags.String("output-labels", "", "also output genome labels csv `file`")
63 err = flags.Parse(args)
64 if err == flag.ErrHelp {
67 } else if err != nil {
71 if f, ok := outputFormats[*outputFormatStr]; !ok {
72 err = fmt.Errorf("invalid output format %q", *outputFormatStr)
80 log.Println(http.ListenAndServe(*pprof, nil))
85 if *outputFilename != "-" {
86 err = errors.New("cannot specify output file in container mode: not implemented")
89 runner := arvadosContainerRunner{
90 Name: "lightning export",
91 Client: arvados.NewClientFromEnv(),
92 ProjectUUID: *projectUUID,
97 err = runner.TranslatePaths(inputFilename)
101 if *outputBed != "" {
102 if strings.Contains(*outputBed, "/") {
103 err = fmt.Errorf("cannot use -output-bed filename %q containing '/' char", *outputBed)
106 *outputBed = "/mnt/output/" + *outputBed
108 runner.Args = []string{"export", "-local=true",
110 "-output-format", *outputFormatStr,
111 "-output-bed", *outputBed,
112 "-output-labels", "/mnt/output/labels.csv",
113 "-i", *inputFilename,
114 "-o", "/mnt/output/export.csv",
117 output, err = runner.Run()
121 fmt.Fprintln(stdout, output+"/export.csv")
125 in, err := open(*inputFilename)
130 input, ok := in.(io.ReadSeeker)
132 err = fmt.Errorf("%s: %T cannot seek", *inputFilename, in)
136 // Error out early if seeking doesn't work on the input file.
137 _, err = input.Seek(0, io.SeekEnd)
141 _, err = input.Seek(0, io.SeekStart)
146 var cgs []CompactGenome
147 tilelib := &tileLibrary{
149 compactGenomes: map[string][]tileVariantID{},
151 err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), nil)
156 refseq, ok := tilelib.refseqs[*refname]
158 err = fmt.Errorf("reference name %q not found in input; have %v", *refname, func() (names []string) {
159 for name := range tilelib.refseqs {
160 names = append(names, name)
167 names := cgnames(tilelib)
168 for _, name := range names {
169 cgs = append(cgs, CompactGenome{Name: name, Variants: tilelib.compactGenomes[name]})
171 if *labelsFilename != "" {
172 log.Infof("writing labels to %s", *labelsFilename)
174 f, err = os.OpenFile(*labelsFilename, os.O_CREATE|os.O_WRONLY, 0777)
179 _, outBasename := path.Split(*outputFilename)
180 for i, name := range names {
181 _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), outBasename)
183 err = fmt.Errorf("write %s: %w", *labelsFilename, err)
189 err = fmt.Errorf("close %s: %w", *labelsFilename, err)
194 _, err = input.Seek(0, io.SeekStart)
199 var output io.WriteCloser
200 if *outputFilename == "-" {
201 output = nopCloser{stdout}
203 output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0666)
209 bufw := bufio.NewWriter(output)
212 var bedbufw *bufio.Writer
213 if *outputBed != "" {
214 bedout, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
219 bedbufw = bufio.NewWriter(bedout)
222 err = cmd.export(bufw, bedout, input, strings.HasSuffix(*inputFilename, ".gz"), tilelib, refseq, cgs)
235 err = bedbufw.Flush()
251 func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, gz bool, tilelib *tileLibrary, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
252 need := map[tileLibRef]bool{}
253 var seqnames []string
254 for seqname, librefs := range refseq {
255 seqnames = append(seqnames, seqname)
256 for _, libref := range librefs {
257 if libref.Variant != 0 {
262 sort.Strings(seqnames)
264 for _, cg := range cgs {
265 for i, variant := range cg.Variants {
269 libref := tileLibRef{Tag: tagID(i / 2), Variant: variant}
274 log.Infof("export: loading %d tile variants", len(need))
275 tileVariant := map[tileLibRef]TileVariant{}
276 err := DecodeLibrary(librdr, gz, func(ent *LibraryEntry) error {
277 for _, tv := range ent.TileVariants {
278 libref := tilelib.getRef(tv.Tag, tv.Sequence)
280 tileVariant[libref] = tv
289 log.Infof("export: loaded %d tile variants", len(tileVariant))
290 var missing []tileLibRef
291 for libref := range need {
292 if _, ok := tileVariant[libref]; !ok {
293 missing = append(missing, libref)
296 if len(missing) > 0 {
297 if limit := 100; len(missing) > limit {
298 log.Warnf("first %d missing tiles: %v", limit, missing[:limit])
300 log.Warnf("missing tiles: %v", missing)
302 return fmt.Errorf("%d needed tiles are missing from library", len(missing))
305 log.Infof("assembling %d sequences concurrently", len(seqnames))
306 throttle := throttle{Max: 8}
307 outbuf := make([]bytes.Buffer, len(seqnames))
308 bedbuf := make([]bytes.Buffer, len(seqnames))
309 for seqidx, seqname := range seqnames {
311 outbuf := &outbuf[seqidx]
312 bedbuf := &bedbuf[seqidx]
318 defer throttle.Release()
319 cmd.exportSeq(outbuf, bedbuf, tilelib.taglib.keylen, seqname, refseq[seqname], tileVariant, cgs)
320 log.Infof("assembled %q to outbuf %d bedbuf %d", seqname, outbuf.Len(), bedbuf.Len())
327 defer throttle.Release()
328 for i, seqname := range seqnames {
329 log.Infof("writing outbuf %s", seqname)
330 io.Copy(out, &outbuf[i])
336 defer throttle.Release()
337 for i, seqname := range seqnames {
338 log.Infof("writing bedbuf %s", seqname)
339 io.Copy(bedout, &bedbuf[i])
347 // Align genome tiles to reference tiles, write diffs to outw, and (if
348 // bedw is not nil) write tile coverage to bedw.
349 func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tileVariant map[tileLibRef]TileVariant, cgs []CompactGenome) {
351 variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
352 for refstep, libref := range reftiles {
353 reftile := tileVariant[libref]
354 tagcoverage := 0 // number of times the start tag was found in genomes -- max is len(cgs)*2
355 for cgidx, cg := range cgs {
356 for phase := 0; phase < 2; phase++ {
357 if len(cg.Variants) <= int(libref.Tag)*2+phase {
360 variant := cg.Variants[int(libref.Tag)*2+phase]
365 if variant == libref.Variant {
368 genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
369 if len(genometile.Sequence) == 0 {
370 // Hash is known but sequence
371 // is not, e.g., retainNoCalls
372 // was false during import
375 refSequence := reftile.Sequence
376 // If needed, extend the reference
377 // sequence up to the tag at the end
378 // of the genometile sequence.
379 refstepend := refstep + 1
380 for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) {
381 if &refSequence[0] == &reftile.Sequence[0] {
382 refSequence = append([]byte(nil), refSequence...)
384 refSequence = append(refSequence, tileVariant[reftiles[refstepend]].Sequence...)
387 // (TODO: handle no-calls)
388 vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genometile.Sequence)), time.Second)
389 for _, v := range vars {
390 if cmd.outputFormat.PadLeft {
394 varslice := variantAt[v.Position]
396 varslice = make([]hgvs.Variant, len(cgs)*2)
397 variantAt[v.Position] = varslice
399 varslice[cgidx*2+phase] = v
403 refpos += len(reftile.Sequence) - taglen
405 // Flush entries from variantAt that are behind
406 // refpos. Flush all entries if this is the last
407 // reftile of the path/chromosome.
409 lastrefstep := refstep == len(reftiles)-1
410 for pos := range variantAt {
411 if lastrefstep || pos <= refpos {
412 flushpos = append(flushpos, pos)
415 sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
416 for _, pos := range flushpos {
417 varslice := variantAt[pos]
418 delete(variantAt, pos)
419 for i := range varslice {
420 if varslice[i].Position == 0 {
421 varslice[i].Position = pos
424 cmd.outputFormat.Print(outw, seqname, varslice)
426 if bedw != nil && len(reftile.Sequence) > 0 {
427 tilestart := refpos - len(reftile.Sequence) + taglen
432 thickstart := tilestart + taglen
438 // coverage score, 0 to 1000
441 score = 1000 * tagcoverage / len(cgs) / 2
444 fmt.Fprintf(bedw, "%s %d %d %d %d . %d %d\n",
445 seqname, tilestart, tileend,
448 thickstart, thickend)
453 func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
454 refs := map[string]map[string]int{}
455 for _, v := range varslice {
456 if v.Ref == "" && v.New == "" {
461 alts = map[string]int{}
466 for ref, alts := range refs {
467 var altslice []string
468 for alt := range alts {
469 altslice = append(altslice, alt)
471 sort.Strings(altslice)
472 for i, a := range altslice {
475 fmt.Fprintf(out, "%s\t%d\t%s\t%s", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
476 for i := 0; i < len(varslice); i += 2 {
477 v1, v2 := varslice[i], varslice[i+1]
478 a1, a2 := alts[v1.New], alts[v2.New]
485 fmt.Fprintf(out, "\t%d/%d", a1, a2)
487 out.Write([]byte{'\n'})
491 func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
492 for i := 0; i < len(varslice)/2; i++ {
494 out.Write([]byte{'\t'})
496 var1, var2 := varslice[i*2], varslice[i*2+1]
498 if var1.Ref == var1.New {
499 out.Write([]byte{'.'})
501 fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
504 fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
507 out.Write([]byte{'\n'})
510 func printHGVSOneHot(out io.Writer, seqname string, varslice []hgvs.Variant) {
511 vars := map[hgvs.Variant]bool{}
512 for _, v := range varslice {
518 // sort variants to ensure output is deterministic
519 sorted := make([]hgvs.Variant, 0, len(vars))
520 for v := range vars {
521 sorted = append(sorted, v)
523 sort.Slice(sorted, func(a, b int) bool { return hgvs.Less(sorted[a], sorted[b]) })
525 for _, v := range sorted {
526 fmt.Fprintf(out, "%s.%s", seqname, v.String())
527 for i := 0; i < len(varslice); i += 2 {
528 if varslice[i] == v || varslice[i+1] == v {
529 out.Write([]byte("\t1"))
531 out.Write([]byte("\t0"))
534 out.Write([]byte{'\n'})