1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
23 "git.arvados.org/arvados.git/sdk/go/arvados"
24 "github.com/arvados/lightning/hgvs"
25 "github.com/kshedden/gonpy"
26 log "github.com/sirupsen/logrus"
27 "golang.org/x/crypto/blake2b"
30 type sliceNumpy struct {
35 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
39 fmt.Fprintf(stderr, "%s\n", err)
42 flags := flag.NewFlagSet("", flag.ContinueOnError)
43 flags.SetOutput(stderr)
44 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
45 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
46 projectUUID := flags.String("project", "", "project `UUID` for output data")
47 priority := flags.Int("priority", 500, "container request priority")
48 inputDir := flags.String("input-dir", "./in", "input `directory`")
49 outputDir := flags.String("output-dir", "./out", "output `directory`")
50 ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
51 regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
52 expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
53 mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
54 flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
55 cmd.filter.Flags(flags)
56 err = flags.Parse(args)
57 if err == flag.ErrHelp {
60 } else if err != nil {
66 log.Println(http.ListenAndServe(*pprof, nil))
71 runner := arvadosContainerRunner{
72 Name: "lightning slice-numpy",
73 Client: arvados.NewClientFromEnv(),
74 ProjectUUID: *projectUUID,
81 err = runner.TranslatePaths(inputDir, regionsFilename)
85 runner.Args = []string{"slice-numpy", "-local=true",
87 "-input-dir=" + *inputDir,
88 "-output-dir=/mnt/output",
89 "-threads=" + fmt.Sprintf("%d", cmd.threads),
90 "-regions=" + *regionsFilename,
91 "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
92 "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
94 runner.Args = append(runner.Args, cmd.filter.Args()...)
96 output, err = runner.Run()
100 fmt.Fprintln(stdout, output)
104 infiles, err := allGobFiles(*inputDir)
108 if len(infiles) == 0 {
109 err = fmt.Errorf("no input files found in %s", *inputDir)
112 sort.Strings(infiles)
115 var refseq map[string][]tileLibRef
116 var reftiledata = make(map[tileLibRef][]byte, 11000000)
117 in0, err := open(infiles[0])
122 matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
124 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
129 DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
130 if len(ent.TagSet) > 0 {
131 taglen = len(ent.TagSet[0])
133 for _, cseq := range ent.CompactSequences {
134 if cseq.Name == *ref || *ref == "" {
135 refseq = cseq.TileSequences
138 for _, cg := range ent.CompactGenomes {
139 if matchGenome.MatchString(cg.Name) {
140 cgnames = append(cgnames, cg.Name)
143 for _, tv := range ent.TileVariants {
145 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
155 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
159 err = fmt.Errorf("tagset not found")
162 if len(cgnames) == 0 {
163 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
166 sort.Strings(cgnames)
169 labelsFilename := *outputDir + "/labels.csv"
170 log.Infof("writing labels to %s", labelsFilename)
172 f, err = os.Create(labelsFilename)
177 for i, name := range cgnames {
178 _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
180 err = fmt.Errorf("write %s: %w", labelsFilename, err)
186 err = fmt.Errorf("close %s: %w", labelsFilename, err)
191 log.Info("indexing reference tiles")
192 type reftileinfo struct {
193 variant tileVariantID
194 seqname string // chr1
195 pos int // distance from start of chr1 to start of tile
196 tiledata []byte // acgtggcaa...
198 reftile := map[tagID]*reftileinfo{}
199 for seqname, cseq := range refseq {
200 for _, libref := range cseq {
201 reftile[libref.Tag] = &reftileinfo{
203 variant: libref.Variant,
204 tiledata: reftiledata[libref],
209 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
210 log.Info("reconstructing reference sequences")
211 for seqname, cseq := range refseq {
212 seqname, cseq := seqname, cseq
213 throttleCPU.Go(func() error {
215 for _, libref := range cseq {
216 rt := reftile[libref.Tag]
218 if len(rt.tiledata) == 0 {
219 return fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
221 pos += len(rt.tiledata) - taglen
223 log.Printf("... %s done, len %d", seqname, pos)
227 err = throttleCPU.Wait()
233 if *regionsFilename != "" {
234 log.Printf("loading regions from %s", *regionsFilename)
235 mask, err = makeMask(*regionsFilename, *expandRegions)
239 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
240 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
241 for tag, rt := range reftile {
242 if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
246 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
249 var toMerge [][]int16
251 toMerge = make([][]int16, len(infiles))
254 throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
255 throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
256 log.Info("generating annotations and numpy matrix for each slice")
258 for infileIdx, infile := range infiles {
259 infileIdx, infile := infileIdx, infile
260 throttleMem.Go(func() error {
261 seq := make(map[tagID][]TileVariant, 50000)
262 cgs := make(map[string]CompactGenome, len(cgnames))
263 f, err := open(infile)
268 log.Infof("%04d: reading %s", infileIdx, infile)
269 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
270 for _, tv := range ent.TileVariants {
274 if mask != nil && reftile[tv.Tag] == nil {
280 variants := seq[tv.Tag]
281 if len(variants) == 0 {
282 variants = make([]TileVariant, 100)
284 for len(variants) <= int(tv.Variant) {
285 variants = append(variants, TileVariant{})
287 variants[int(tv.Variant)] = tv
288 seq[tv.Tag] = variants
290 for _, cg := range ent.CompactGenomes {
291 if matchGenome.MatchString(cg.Name) {
300 tagstart := cgs[cgnames[0]].StartTag
301 tagend := cgs[cgnames[0]].EndTag
305 log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
306 variantRemap := make([][]tileVariantID, tagend-tagstart)
307 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
308 for tag, variants := range seq {
309 tag, variants := tag, variants
310 throttleCPU.Acquire()
312 defer throttleCPU.Release()
313 count := make(map[[blake2b.Size256]byte]int, len(variants))
314 for _, cg := range cgs {
315 idx := int(tag-tagstart) * 2
316 if idx < len(cg.Variants) {
317 for allele := 0; allele < 2; allele++ {
318 v := cg.Variants[idx+allele]
319 if v > 0 && len(variants[v].Sequence) > 0 {
320 count[variants[v].Blake2b]++
325 // hash[i] will be the hash of
326 // the variant(s) that should
327 // be at rank i (0-based).
328 hash := make([][blake2b.Size256]byte, 0, len(count))
329 for b := range count {
330 hash = append(hash, b)
332 sort.Slice(hash, func(i, j int) bool {
333 bi, bj := &hash[i], &hash[j]
334 if ci, cj := count[*bi], count[*bj]; ci != cj {
337 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
340 // rank[b] will be the 1-based
341 // new variant number for
342 // variants whose hash is b.
343 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
344 for i, h := range hash {
345 rank[h] = tileVariantID(i + 1)
347 // remap[v] will be the new
348 // variant number for original
350 remap := make([]tileVariantID, len(variants))
351 for i, tv := range variants {
352 remap[i] = rank[tv.Blake2b]
354 variantRemap[tag-tagstart] = remap
359 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
360 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
361 annof, err := os.Create(annotationsFilename)
365 annow := bufio.NewWriterSize(annof, 1<<20)
367 for tag := tagstart; tag < tagend; tag++ {
368 rt, ok := reftile[tag]
373 // Excluded by specified
374 // regions, or reference does
375 // not use any variant of this
376 // tile. (TODO: log this?
377 // mention it in annotations?)
380 variants, ok := seq[tag]
385 reftilestr := strings.ToUpper(string(rt.tiledata))
386 remap := variantRemap[tag-tagstart]
387 done := make([]bool, len(variants))
388 for v, tv := range variants {
395 if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
398 if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
401 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
402 for _, diff := range diffs {
403 diff.Position += rt.pos
404 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)
418 log.Infof("%04d: preparing numpy", infileIdx)
419 throttleNumpyMem.Acquire()
422 out := make([]int16, rows*cols)
423 for row, name := range cgnames {
424 out := out[row*cols:]
426 for col, v := range cgs[name].Variants {
427 tag := tagstart + tagID(col/2)
428 if mask != nil && reftile[tag] == nil {
431 if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
432 out[outcol] = int16(variantRemap[tag-tagstart][v])
440 throttleNumpyMem.Release()
443 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
444 toMerge[infileIdx] = out
446 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
447 err = writeNumpyInt16(fnm, out, rows, cols)
452 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
456 if err = throttleMem.Wait(); err != nil {
460 log.Info("merging output matrix and annotations")
462 annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
463 annof, err := os.Create(annoFilename)
467 annow := bufio.NewWriterSize(annof, 1<<20)
471 for _, chunk := range toMerge {
472 cols += len(chunk) / rows
474 out := make([]int16, rows*cols)
476 for outIdx, chunk := range toMerge {
477 chunkcols := len(chunk) / rows
478 for row := 0; row < rows; row++ {
479 copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
481 toMerge[outIdx] = nil
483 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
484 log.Infof("reading %s", annotationsFilename)
485 buf, err := os.ReadFile(annotationsFilename)
489 err = os.Remove(annotationsFilename)
493 for _, line := range bytes.Split(buf, []byte{'\n'}) {
497 fields := bytes.SplitN(line, []byte{','}, 3)
498 incol, _ := strconv.Atoi(string(fields[1]))
499 fmt.Fprintf(annow, "%s,%d,%s\n", fields[0], incol+startcol/2, fields[2])
502 startcol += chunkcols
512 err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
520 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
521 output, err := os.Create(fnm)
526 bufw := bufio.NewWriterSize(output, 1<<26)
527 npw, err := gonpy.NewWriter(nopCloser{bufw})
531 log.WithFields(log.Fields{
535 }).Infof("writing numpy: %s", fnm)
536 npw.Shape = []int{rows, cols}
542 return output.Close()