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))
314 count[blake2b.Sum256(rt.tiledata)] = 0
317 for _, cg := range cgs {
318 idx := int(tag-tagstart) * 2
319 if idx < len(cg.Variants) {
320 for allele := 0; allele < 2; allele++ {
321 v := cg.Variants[idx+allele]
322 if v > 0 && len(variants[v].Sequence) > 0 {
323 count[variants[v].Blake2b]++
328 // hash[i] will be the hash of
329 // the variant(s) that should
330 // be at rank i (0-based).
331 hash := make([][blake2b.Size256]byte, 0, len(count))
332 for b := range count {
333 hash = append(hash, b)
335 sort.Slice(hash, func(i, j int) bool {
336 bi, bj := &hash[i], &hash[j]
337 if ci, cj := count[*bi], count[*bj]; ci != cj {
340 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
343 // rank[b] will be the 1-based
344 // new variant number for
345 // variants whose hash is b.
346 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
347 for i, h := range hash {
348 rank[h] = tileVariantID(i + 1)
350 // remap[v] will be the new
351 // variant number for original
353 remap := make([]tileVariantID, len(variants))
354 for i, tv := range variants {
355 remap[i] = rank[tv.Blake2b]
357 variantRemap[tag-tagstart] = remap
359 rt.variant = rank[blake2b.Sum256(rt.tiledata)]
365 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
366 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
367 annof, err := os.Create(annotationsFilename)
371 annow := bufio.NewWriterSize(annof, 1<<20)
373 for tag := tagstart; tag < tagend; tag++ {
374 rt, ok := reftile[tag]
379 // Excluded by specified
380 // regions, or reference does
381 // not use any variant of this
382 // tile. (TODO: log this?
383 // mention it in annotations?)
386 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
388 reftilestr := strings.ToUpper(string(rt.tiledata))
389 remap := variantRemap[tag-tagstart]
390 done := make([]bool, len(variants))
391 for v, tv := range variants {
393 if v == rt.variant || done[v] {
398 if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
399 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
402 if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
403 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
406 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
407 for _, diff := range diffs {
408 diff.Position += rt.pos
409 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)
423 log.Infof("%04d: preparing numpy", infileIdx)
424 throttleNumpyMem.Acquire()
427 out := make([]int16, rows*cols)
428 for row, name := range cgnames {
429 out := out[row*cols:]
431 for col, v := range cgs[name].Variants {
432 tag := tagstart + tagID(col/2)
433 if mask != nil && reftile[tag] == nil {
436 if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
437 out[outcol] = int16(variantRemap[tag-tagstart][v])
445 throttleNumpyMem.Release()
448 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
449 toMerge[infileIdx] = out
451 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
452 err = writeNumpyInt16(fnm, out, rows, cols)
457 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
461 if err = throttleMem.Wait(); err != nil {
465 log.Info("merging output matrix and annotations")
467 annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
468 annof, err := os.Create(annoFilename)
472 annow := bufio.NewWriterSize(annof, 1<<20)
476 for _, chunk := range toMerge {
477 cols += len(chunk) / rows
479 out := make([]int16, rows*cols)
480 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
482 for outIdx, chunk := range toMerge {
483 chunkcols := len(chunk) / rows
484 for row := 0; row < rows; row++ {
485 copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
487 toMerge[outIdx] = nil
489 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
490 log.Infof("reading %s", annotationsFilename)
491 buf, err := os.ReadFile(annotationsFilename)
495 err = os.Remove(annotationsFilename)
499 for _, line := range bytes.Split(buf, []byte{'\n'}) {
503 fields := bytes.SplitN(line, []byte{','}, 9)
504 tag, _ := strconv.Atoi(string(fields[0]))
505 incol, _ := strconv.Atoi(string(fields[1]))
506 tileVariant, _ := strconv.Atoi(string(fields[2]))
507 hgvsID := string(fields[3])
508 seqname := string(fields[4])
509 pos, _ := strconv.Atoi(string(fields[5]))
512 // Null entry for un-diffable
517 // Null entry for ref tile
520 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
521 // The tile intersects one of
522 // the selected regions, but
523 // this particular HGVS
527 hgvsColPair := hgvsCols[hgvsID]
528 if hgvsColPair[0] == nil {
529 // values in new columns start
530 // out as -1 ("no data yet")
531 // or 0 ("=ref") here, may
532 // change to 1 ("hgvs variant
533 // present") below, either on
534 // this line or a future line.
535 hgvsColPair = [2][]int16{make([]int16, len(cgnames)), make([]int16, len(cgnames))}
536 rt, ok := reftile[tagID(tag)]
538 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
541 for ph := 0; ph < 2; ph++ {
542 for row := 0; row < rows; row++ {
543 v := chunk[row*chunkcols+incol*2+ph]
544 if tileVariantID(v) == rt.variant {
545 hgvsColPair[ph][row] = 0
547 hgvsColPair[ph][row] = -1
551 hgvsCols[hgvsID] = hgvsColPair
552 hgvsref := hgvs.Variant{
557 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, rt.variant, seqname, hgvsref.String(), seqname, pos, refseq, refseq, fields[8])
559 fmt.Fprintf(annow, "%d,%d,%d,%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, tileVariant, hgvsID, seqname, pos, refseq, fields[7], fields[8])
560 for ph := 0; ph < 2; ph++ {
561 for row := 0; row < rows; row++ {
562 v := chunk[row*chunkcols+incol*2+ph]
563 if int(v) == tileVariant {
564 hgvsColPair[ph][row] = 1
570 startcol += chunkcols
580 err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
586 cols = len(hgvsCols) * 2
587 log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
588 out = make([]int16, rows*cols)
589 hgvsIDs := make([]string, 0, len(hgvsCols))
590 for hgvsID := range hgvsCols {
591 hgvsIDs = append(hgvsIDs, hgvsID)
593 sort.Strings(hgvsIDs)
594 var hgvsLabels bytes.Buffer
595 for idx, hgvsID := range hgvsIDs {
596 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
597 for ph := 0; ph < 2; ph++ {
598 hgvscol := hgvsCols[hgvsID][ph]
599 for row, val := range hgvscol {
600 out[row*cols+idx*2+ph] = val
604 err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
609 fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
610 log.Printf("writing hgvs labels: %s", fnm)
611 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
619 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
620 output, err := os.Create(fnm)
625 bufw := bufio.NewWriterSize(output, 1<<26)
626 npw, err := gonpy.NewWriter(nopCloser{bufw})
630 log.WithFields(log.Fields{
634 }).Infof("writing numpy: %s", fnm)
635 npw.Shape = []int{rows, cols}
641 return output.Close()