21 "git.arvados.org/arvados.git/sdk/go/arvados"
22 "github.com/arvados/lightning/hgvs"
23 log "github.com/sirupsen/logrus"
26 type outputFormat struct {
28 Print func(out io.Writer, seqname string, varslice []hgvs.Variant)
33 outputFormats = map[string]outputFormat{
34 "hgvs-onehot": outputFormatHGVSOneHot,
35 "hgvs": outputFormatHGVS,
36 "vcf": outputFormatVCF,
38 outputFormatHGVS = outputFormat{Filename: "out.csv", Print: printHGVS}
39 outputFormatHGVSOneHot = outputFormat{Filename: "out.csv", Print: printHGVSOneHot}
40 outputFormatVCF = outputFormat{Filename: "out.vcf", Print: printVCF, PadLeft: true}
43 type exporter struct {
44 outputFormat outputFormat
49 func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
53 fmt.Fprintf(stderr, "%s\n", err)
56 flags := flag.NewFlagSet("", flag.ContinueOnError)
57 flags.SetOutput(stderr)
58 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
59 pprofdir := flags.String("pprof-dir", "", "write Go profile data to `directory` periodically")
60 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
61 projectUUID := flags.String("project", "", "project `UUID` for output data")
62 priority := flags.Int("priority", 500, "container request priority")
63 refname := flags.String("ref", "", "reference genome `name`")
64 inputDir := flags.String("input-dir", ".", "input `directory`")
65 outputDir := flags.String("output-dir", ".", "output `directory`")
66 outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs or vcf")
67 outputBed := flags.String("output-bed", "", "also output bed `file`")
68 flags.BoolVar(&cmd.outputPerChrom, "output-per-chromosome", true, "output one file per chromosome")
69 labelsFilename := flags.String("output-labels", "", "also output genome labels csv `file`")
70 flags.IntVar(&cmd.maxTileSize, "max-tile-size", 50000, "don't try to make annotations for tiles bigger than given `size`")
71 err = flags.Parse(args)
72 if err == flag.ErrHelp {
75 } else if err != nil {
79 err = fmt.Errorf("extra unparsed command line arguments: %q", flag.Args())
83 if f, ok := outputFormats[*outputFormatStr]; !ok {
84 err = fmt.Errorf("invalid output format %q", *outputFormatStr)
92 log.Println(http.ListenAndServe(*pprof, nil))
96 go writeProfilesPeriodically(*pprofdir)
100 if *outputDir != "." {
101 err = errors.New("cannot specify output directory in container mode: not implemented")
104 runner := arvadosContainerRunner{
105 Name: "lightning export",
106 Client: arvados.NewClientFromEnv(),
107 ProjectUUID: *projectUUID,
113 err = runner.TranslatePaths(inputDir)
117 if *outputBed != "" {
118 if strings.Contains(*outputBed, "/") {
119 err = fmt.Errorf("cannot use -output-bed filename %q containing '/' char", *outputBed)
122 *outputBed = "/mnt/output/" + *outputBed
124 runner.Args = []string{"export", "-local=true",
126 "-pprof-dir", "/mnt/output",
128 "-output-format", *outputFormatStr,
129 "-output-bed", *outputBed,
130 "-output-labels", "/mnt/output/labels.csv",
131 "-output-per-chromosome=" + fmt.Sprintf("%v", cmd.outputPerChrom),
132 "-max-tile-size", fmt.Sprintf("%d", cmd.maxTileSize),
133 "-input-dir", *inputDir,
134 "-output-dir", "/mnt/output",
137 output, err = runner.Run()
141 fmt.Fprintln(stdout, output+"/export.csv")
145 var cgs []CompactGenome
146 tilelib := &tileLibrary{
148 retainTileSequences: true,
149 compactGenomes: map[string][]tileVariantID{},
151 err = tilelib.LoadDir(context.Background(), *inputDir, 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 for i, name := range names {
180 _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), cmd.outputFormat.Filename)
182 err = fmt.Errorf("write %s: %w", *labelsFilename, err)
188 err = fmt.Errorf("close %s: %w", *labelsFilename, err)
194 var bedbufw *bufio.Writer
195 if *outputBed != "" {
196 bedout, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
201 bedbufw = bufio.NewWriter(bedout)
204 err = cmd.export(*outputDir, bedout, tilelib, refseq, cgs)
209 err = bedbufw.Flush()
221 func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrary, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
222 var seqnames []string
223 var missing []tileLibRef
224 for seqname, librefs := range refseq {
225 seqnames = append(seqnames, seqname)
226 for _, libref := range librefs {
227 if libref.Variant != 0 && tilelib.TileVariantSequence(libref) == nil {
228 missing = append(missing, libref)
232 sort.Strings(seqnames)
234 if len(missing) > 0 {
235 if limit := 100; len(missing) > limit {
236 log.Warnf("first %d missing tiles: %v", limit, missing[:limit])
238 log.Warnf("missing tiles: %v", missing)
240 return fmt.Errorf("%d needed tiles are missing from library", len(missing))
243 outw := make([]io.WriteCloser, len(seqnames))
244 bedw := make([]io.WriteCloser, len(seqnames))
246 var merges sync.WaitGroup
247 merge := func(dst io.Writer, src []io.WriteCloser, label string) {
249 for i, seqname := range seqnames {
256 log.Infof("writing %s %s", seqname, label)
257 scanner := bufio.NewScanner(pr)
260 dst.Write(scanner.Bytes())
261 dst.Write([]byte{'\n'})
264 log.Infof("writing %s %s done", seqname, label)
268 if cmd.outputPerChrom {
269 for i, seqname := range seqnames {
270 f, err := os.OpenFile(filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename, ".", "."+seqname+".", 1)), os.O_CREATE|os.O_WRONLY, 0666)
275 log.Infof("writing %q", f.Name())
279 fnm := filepath.Join(outdir, cmd.outputFormat.Filename)
280 log.Infof("writing %q", fnm)
281 out, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY, 0666)
286 merge(out, outw, "output")
289 merge(bedout, bedw, "bed")
292 throttle := throttle{Max: runtime.NumCPU()}
293 log.Infof("assembling %d sequences in %d goroutines", len(seqnames), throttle.Max)
294 for seqidx, seqname := range seqnames {
295 seqidx, seqname := seqidx, seqname
300 defer throttle.Release()
305 outwb := bufio.NewWriter(outw)
307 cmd.exportSeq(outwb, bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tilelib, cgs)
315 // Align genome tiles to reference tiles, write diffs to outw, and (if
316 // bedw is not nil) write tile coverage to bedw.
317 func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tilelib *tileLibrary, cgs []CompactGenome) {
319 variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
320 for refstep, libref := range reftiles {
321 refseq := tilelib.TileVariantSequence(libref)
322 tagcoverage := 0 // number of times the start tag was found in genomes -- max is len(cgs)*2
323 for cgidx, cg := range cgs {
324 for phase := 0; phase < 2; phase++ {
325 if len(cg.Variants) <= int(libref.Tag)*2+phase {
328 variant := cg.Variants[int(libref.Tag)*2+phase]
333 if variant == libref.Variant {
336 genomeseq := tilelib.TileVariantSequence(tileLibRef{Tag: libref.Tag, Variant: variant})
337 if len(genomeseq) == 0 {
338 // Hash is known but sequence
339 // is not, e.g., retainNoCalls
340 // was false during import
343 if len(genomeseq) > cmd.maxTileSize {
346 refSequence := refseq
347 // If needed, extend the reference
348 // sequence up to the tag at the end
349 // of the genomeseq sequence.
350 refstepend := refstep + 1
351 for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genomeseq[len(genomeseq)-taglen:]) && len(refSequence) <= cmd.maxTileSize {
352 if &refSequence[0] == &refseq[0] {
353 refSequence = append([]byte(nil), refSequence...)
355 refSequence = append(refSequence, tilelib.TileVariantSequence(reftiles[refstepend])...)
358 // (TODO: handle no-calls)
359 vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genomeseq)), time.Second)
360 for _, v := range vars {
361 if cmd.outputFormat.PadLeft {
365 varslice := variantAt[v.Position]
367 varslice = make([]hgvs.Variant, len(cgs)*2)
368 variantAt[v.Position] = varslice
370 varslice[cgidx*2+phase] = v
374 refpos += len(refseq) - taglen
376 // Flush entries from variantAt that are behind
377 // refpos. Flush all entries if this is the last
378 // reftile of the path/chromosome.
380 lastrefstep := refstep == len(reftiles)-1
381 for pos := range variantAt {
382 if lastrefstep || pos <= refpos {
383 flushpos = append(flushpos, pos)
386 sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
387 for _, pos := range flushpos {
388 varslice := variantAt[pos]
389 delete(variantAt, pos)
390 for i := range varslice {
391 if varslice[i].Position == 0 {
392 varslice[i].Position = pos
395 cmd.outputFormat.Print(outw, seqname, varslice)
397 if bedw != nil && len(refseq) > 0 {
398 tilestart := refpos - len(refseq) + taglen
403 thickstart := tilestart + taglen
409 // coverage score, 0 to 1000
412 score = 1000 * tagcoverage / len(cgs) / 2
415 fmt.Fprintf(bedw, "%s %d %d %d %d . %d %d\n",
416 seqname, tilestart, tileend,
419 thickstart, thickend)
424 func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
425 refs := map[string]map[string]int{}
426 for _, v := range varslice {
427 if v.Ref == "" && v.New == "" {
432 alts = map[string]int{}
437 for ref, alts := range refs {
438 var altslice []string
439 for alt := range alts {
440 altslice = append(altslice, alt)
442 sort.Strings(altslice)
443 for i, a := range altslice {
446 fmt.Fprintf(out, "%s\t%d\t%s\t%s", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
447 for i := 0; i < len(varslice); i += 2 {
448 v1, v2 := varslice[i], varslice[i+1]
449 a1, a2 := alts[v1.New], alts[v2.New]
456 fmt.Fprintf(out, "\t%d/%d", a1, a2)
458 out.Write([]byte{'\n'})
462 func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
463 for i := 0; i < len(varslice)/2; i++ {
465 out.Write([]byte{'\t'})
467 var1, var2 := varslice[i*2], varslice[i*2+1]
469 if var1.Ref == var1.New {
470 out.Write([]byte{'.'})
472 fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
475 fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
478 out.Write([]byte{'\n'})
481 func printHGVSOneHot(out io.Writer, seqname string, varslice []hgvs.Variant) {
482 vars := map[hgvs.Variant]bool{}
483 for _, v := range varslice {
489 // sort variants to ensure output is deterministic
490 sorted := make([]hgvs.Variant, 0, len(vars))
491 for v := range vars {
492 sorted = append(sorted, v)
494 sort.Slice(sorted, func(a, b int) bool { return hgvs.Less(sorted[a], sorted[b]) })
496 for _, v := range sorted {
497 fmt.Fprintf(out, "%s.%s", seqname, v.String())
498 for i := 0; i < len(varslice); i += 2 {
499 if varslice[i] == v || varslice[i+1] == v {
500 out.Write([]byte("\t1"))
502 out.Write([]byte("\t0"))
505 out.Write([]byte{'\n'})