1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
24 "git.arvados.org/arvados.git/sdk/go/arvados"
25 "github.com/arvados/lightning/hgvs"
26 "github.com/kshedden/gonpy"
27 log "github.com/sirupsen/logrus"
28 "golang.org/x/crypto/blake2b"
31 type sliceNumpy struct {
36 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
40 fmt.Fprintf(stderr, "%s\n", err)
43 flags := flag.NewFlagSet("", flag.ContinueOnError)
44 flags.SetOutput(stderr)
45 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
46 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
47 projectUUID := flags.String("project", "", "project `UUID` for output data")
48 priority := flags.Int("priority", 500, "container request priority")
49 inputDir := flags.String("input-dir", "./in", "input `directory`")
50 outputDir := flags.String("output-dir", "./out", "output `directory`")
51 ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
52 regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
53 expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
54 mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
55 flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
56 cmd.filter.Flags(flags)
57 err = flags.Parse(args)
58 if err == flag.ErrHelp {
61 } else if err != nil {
67 log.Println(http.ListenAndServe(*pprof, nil))
72 runner := arvadosContainerRunner{
73 Name: "lightning slice-numpy",
74 Client: arvados.NewClientFromEnv(),
75 ProjectUUID: *projectUUID,
82 err = runner.TranslatePaths(inputDir, regionsFilename)
86 runner.Args = []string{"slice-numpy", "-local=true",
88 "-input-dir=" + *inputDir,
89 "-output-dir=/mnt/output",
90 "-threads=" + fmt.Sprintf("%d", cmd.threads),
91 "-regions=" + *regionsFilename,
92 "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
93 "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
95 runner.Args = append(runner.Args, cmd.filter.Args()...)
97 output, err = runner.Run()
101 fmt.Fprintln(stdout, output)
105 infiles, err := allGobFiles(*inputDir)
109 if len(infiles) == 0 {
110 err = fmt.Errorf("no input files found in %s", *inputDir)
113 sort.Strings(infiles)
116 var refseq map[string][]tileLibRef
117 var reftiledata = make(map[tileLibRef][]byte, 11000000)
118 in0, err := open(infiles[0])
123 matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
125 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
130 DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
131 if len(ent.TagSet) > 0 {
132 taglen = len(ent.TagSet[0])
134 for _, cseq := range ent.CompactSequences {
135 if cseq.Name == *ref || *ref == "" {
136 refseq = cseq.TileSequences
139 for _, cg := range ent.CompactGenomes {
140 if matchGenome.MatchString(cg.Name) {
141 cgnames = append(cgnames, cg.Name)
144 for _, tv := range ent.TileVariants {
146 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
156 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
160 err = fmt.Errorf("tagset not found")
163 if len(cgnames) == 0 {
164 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
167 sort.Strings(cgnames)
170 labelsFilename := *outputDir + "/labels.csv"
171 log.Infof("writing labels to %s", labelsFilename)
173 f, err = os.Create(labelsFilename)
178 for i, name := range cgnames {
179 _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
181 err = fmt.Errorf("write %s: %w", labelsFilename, err)
187 err = fmt.Errorf("close %s: %w", labelsFilename, err)
192 log.Info("indexing reference tiles")
193 type reftileinfo struct {
194 variant tileVariantID
195 seqname string // chr1
196 pos int // distance from start of chromosome to starttag
197 tiledata []byte // acgtggcaa...
199 isdup := map[tagID]bool{}
200 reftile := map[tagID]*reftileinfo{}
201 for seqname, cseq := range refseq {
203 for _, libref := range cseq {
204 tiledata := reftiledata[libref]
205 if len(tiledata) == 0 {
206 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
209 if isdup[libref.Tag] {
210 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
211 } else if reftile[libref.Tag] != nil {
212 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", tileLibRef{Tag: libref.Tag, Variant: reftile[libref.Tag].variant}, reftile[libref.Tag].seqname, reftile[libref.Tag].pos)
213 delete(reftile, libref.Tag)
214 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
215 isdup[libref.Tag] = true
217 reftile[libref.Tag] = &reftileinfo{
219 variant: libref.Variant,
224 pos += len(tiledata) - taglen
226 log.Printf("... %s done, len %d", seqname, pos+taglen)
230 if *regionsFilename != "" {
231 log.Printf("loading regions from %s", *regionsFilename)
232 mask, err = makeMask(*regionsFilename, *expandRegions)
236 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
237 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
238 for tag, rt := range reftile {
239 if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
243 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
246 var toMerge [][]int16
248 toMerge = make([][]int16, len(infiles))
251 throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
252 throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
253 log.Info("generating annotations and numpy matrix for each slice")
255 for infileIdx, infile := range infiles {
256 infileIdx, infile := infileIdx, infile
257 throttleMem.Go(func() error {
258 seq := make(map[tagID][]TileVariant, 50000)
259 cgs := make(map[string]CompactGenome, len(cgnames))
260 f, err := open(infile)
265 log.Infof("%04d: reading %s", infileIdx, infile)
266 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
267 for _, tv := range ent.TileVariants {
271 if mask != nil && reftile[tv.Tag] == nil {
277 variants := seq[tv.Tag]
278 if len(variants) == 0 {
279 variants = make([]TileVariant, 100)
281 for len(variants) <= int(tv.Variant) {
282 variants = append(variants, TileVariant{})
284 variants[int(tv.Variant)] = tv
285 seq[tv.Tag] = variants
287 for _, cg := range ent.CompactGenomes {
288 if matchGenome.MatchString(cg.Name) {
297 tagstart := cgs[cgnames[0]].StartTag
298 tagend := cgs[cgnames[0]].EndTag
302 log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
303 variantRemap := make([][]tileVariantID, tagend-tagstart)
304 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
305 for tag, variants := range seq {
306 tag, variants := tag, variants
307 throttleCPU.Acquire()
309 defer throttleCPU.Release()
310 count := make(map[[blake2b.Size256]byte]int, len(variants))
311 for _, cg := range cgs {
312 idx := int(tag-tagstart) * 2
313 if idx < len(cg.Variants) {
314 for allele := 0; allele < 2; allele++ {
315 v := cg.Variants[idx+allele]
316 if v > 0 && len(variants[v].Sequence) > 0 {
317 count[variants[v].Blake2b]++
322 // hash[i] will be the hash of
323 // the variant(s) that should
324 // be at rank i (0-based).
325 hash := make([][blake2b.Size256]byte, 0, len(count))
326 for b := range count {
327 hash = append(hash, b)
329 sort.Slice(hash, func(i, j int) bool {
330 bi, bj := &hash[i], &hash[j]
331 if ci, cj := count[*bi], count[*bj]; ci != cj {
334 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
337 // rank[b] will be the 1-based
338 // new variant number for
339 // variants whose hash is b.
340 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
341 for i, h := range hash {
342 rank[h] = tileVariantID(i + 1)
344 // remap[v] will be the new
345 // variant number for original
347 remap := make([]tileVariantID, len(variants))
348 for i, tv := range variants {
349 remap[i] = rank[tv.Blake2b]
351 variantRemap[tag-tagstart] = remap
356 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
357 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
358 annof, err := os.Create(annotationsFilename)
362 annow := bufio.NewWriterSize(annof, 1<<20)
364 for tag := tagstart; tag < tagend; tag++ {
365 rt, ok := reftile[tag]
370 // Excluded by specified
371 // regions, or reference does
372 // not use any variant of this
373 // tile. (TODO: log this?
374 // mention it in annotations?)
378 reftilestr := strings.ToUpper(string(rt.tiledata))
379 remap := variantRemap[tag-tagstart]
380 done := make([]bool, len(variants))
381 for v, tv := range variants {
388 if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
389 fmt.Fprintf(annow, "%d,%d,%d,.,%s,%d,.,,\n", tag, outcol, v, rt.seqname, rt.pos)
392 if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
393 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
396 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
397 for _, diff := range diffs {
398 diff.Position += rt.pos
399 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, outcol, v, rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New, diff.Left)
413 log.Infof("%04d: preparing numpy", infileIdx)
414 throttleNumpyMem.Acquire()
417 out := make([]int16, rows*cols)
418 for row, name := range cgnames {
419 out := out[row*cols:]
421 for col, v := range cgs[name].Variants {
422 tag := tagstart + tagID(col/2)
423 if mask != nil && reftile[tag] == nil {
426 if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
427 out[outcol] = int16(variantRemap[tag-tagstart][v])
435 throttleNumpyMem.Release()
438 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
439 toMerge[infileIdx] = out
441 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
442 err = writeNumpyInt16(fnm, out, rows, cols)
447 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
451 if err = throttleMem.Wait(); err != nil {
455 log.Info("merging output matrix and annotations")
457 annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
458 annof, err := os.Create(annoFilename)
462 annow := bufio.NewWriterSize(annof, 1<<20)
466 for _, chunk := range toMerge {
467 cols += len(chunk) / rows
469 out := make([]int16, rows*cols)
470 hgvs := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
472 for outIdx, chunk := range toMerge {
473 chunkcols := len(chunk) / rows
474 for row := 0; row < rows; row++ {
475 copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
477 toMerge[outIdx] = nil
479 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
480 log.Infof("reading %s", annotationsFilename)
481 buf, err := os.ReadFile(annotationsFilename)
485 err = os.Remove(annotationsFilename)
489 for _, line := range bytes.Split(buf, []byte{'\n'}) {
493 fields := bytes.SplitN(line, []byte{','}, 8)
494 incol, _ := strconv.Atoi(string(fields[1]))
495 tileVariant, _ := strconv.Atoi(string(fields[2]))
496 hgvsID := string(fields[3])
497 seqname := string(fields[4])
498 pos, _ := strconv.Atoi(string(fields[5]))
500 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
501 // The tile intersects one of
502 // the selected regions, but
503 // this particular HGVS
507 fmt.Fprintf(annow, "%s,%d,%d,%s,%s,%d,%s,%s\n", fields[0], incol+startcol/2, tileVariant, hgvsID, seqname, pos, refseq, fields[7])
508 hgvscols := hgvs[hgvsID]
509 if hgvscols[0] == nil {
510 hgvscols = [2][]int16{make([]int16, len(cgnames)), make([]int16, len(cgnames))}
511 hgvs[hgvsID] = hgvscols
513 for ph := 0; ph < 2; ph++ {
514 for row := 0; row < rows; row++ {
515 v := chunk[row*chunkcols+incol*2+ph]
516 if int(v) == tileVariant {
517 if len(hgvsID) == 0 {
518 // we have the tile variant sequence, but the diff against ref didn't work out (see lendiff above)
519 hgvscols[ph][row] = -2
521 hgvscols[ph][row] = 1
524 hgvscols[ph][row] = -1
530 startcol += chunkcols
540 err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
547 log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
548 out = make([]int16, rows*cols)
549 hgvsIDs := make([]string, 0, len(hgvs))
550 for hgvsID := range hgvs {
551 hgvsIDs = append(hgvsIDs, hgvsID)
553 sort.Strings(hgvsIDs)
554 var hgvsLabels bytes.Buffer
555 for idx, hgvsID := range hgvsIDs {
556 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
557 for ph := 0; ph < 2; ph++ {
558 hgvscol := hgvs[hgvsID][ph]
559 for row, val := range hgvscol {
560 out[row*cols+idx*2+ph] = val
564 err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
569 fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
570 log.Printf("writing hgvs labels: %s", fnm)
571 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
579 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
580 output, err := os.Create(fnm)
585 bufw := bufio.NewWriterSize(output, 1<<26)
586 npw, err := gonpy.NewWriter(nopCloser{bufw})
590 log.WithFields(log.Fields{
594 }).Infof("writing numpy: %s", fnm)
595 npw.Shape = []int{rows, cols}
601 return output.Close()