1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
29 "git.arvados.org/arvados.git/sdk/go/arvados"
30 "github.com/arvados/lightning/hgvs"
31 "github.com/james-bowman/nlp"
32 "github.com/kshedden/gonpy"
33 "github.com/sirupsen/logrus"
34 log "github.com/sirupsen/logrus"
35 "golang.org/x/crypto/blake2b"
36 "gonum.org/v1/gonum/mat"
39 const annotationMaxTileSpan = 100
41 type sliceNumpy struct {
44 chi2CaseControlColumn string
45 chi2CaseControlFile string
54 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
55 err := cmd.run(prog, args, stdin, stdout, stderr)
57 fmt.Fprintf(stderr, "%s\n", err)
62 func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) error {
63 flags := flag.NewFlagSet("", flag.ContinueOnError)
64 flags.SetOutput(stderr)
65 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
66 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
67 arvadosRAM := flags.Int("arvados-ram", 750000000000, "amount of memory to request for arvados container (`bytes`)")
68 arvadosVCPUs := flags.Int("arvados-vcpus", 96, "number of VCPUs to request for arvados container")
69 projectUUID := flags.String("project", "", "project `UUID` for output data")
70 priority := flags.Int("priority", 500, "container request priority")
71 inputDir := flags.String("input-dir", "./in", "input `directory`")
72 outputDir := flags.String("output-dir", "./out", "output `directory`")
73 ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
74 regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
75 expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
76 mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
77 hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
78 hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
79 onehotSingle := flags.Bool("single-onehot", false, "generate one-hot tile-based matrix")
80 onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix per input chunk")
81 onlyPCA := flags.Bool("pca", false, "generate pca matrix")
82 pcaComponents := flags.Int("pca-components", 4, "number of PCA components")
83 maxPCATiles := flags.Int("max-pca-tiles", 0, "maximum tiles to use as PCA input (filter, then drop every 2nd colum pair until below max)")
84 debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
85 flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads, and number of VCPUs to request for arvados container")
86 flags.StringVar(&cmd.chi2CaseControlFile, "chi2-case-control-file", "", "tsv file or directory indicating cases and controls for Χ² test (if directory, all .tsv files will be read)")
87 flags.StringVar(&cmd.chi2CaseControlColumn, "chi2-case-control-column", "", "name of case/control column in case-control files for Χ² test (value must be 0 for control, 1 for case)")
88 flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
89 flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
90 cmd.filter.Flags(flags)
91 err := flags.Parse(args)
92 if err == flag.ErrHelp {
94 } else if err != nil {
100 log.Println(http.ListenAndServe(*pprof, nil))
104 if cmd.chi2PValue != 1 && (cmd.chi2CaseControlFile == "" || cmd.chi2CaseControlColumn == "") {
105 return fmt.Errorf("cannot use provided -chi2-p-value=%f because -chi2-case-control-file= or -chi2-case-control-column= value is empty", cmd.chi2PValue)
108 cmd.debugTag = tagID(*debugTag)
111 runner := arvadosContainerRunner{
112 Name: "lightning slice-numpy",
113 Client: arvados.NewClientFromEnv(),
114 ProjectUUID: *projectUUID,
115 RAM: int64(*arvadosRAM),
116 VCPUs: *arvadosVCPUs,
121 err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CaseControlFile)
125 runner.Args = []string{"slice-numpy", "-local=true",
127 "-input-dir=" + *inputDir,
128 "-output-dir=/mnt/output",
129 "-threads=" + fmt.Sprintf("%d", cmd.threads),
130 "-regions=" + *regionsFilename,
131 "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
132 "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
133 "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
134 "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
135 "-single-onehot=" + fmt.Sprintf("%v", *onehotSingle),
136 "-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
137 "-pca=" + fmt.Sprintf("%v", *onlyPCA),
138 "-pca-components=" + fmt.Sprintf("%d", *pcaComponents),
139 "-max-pca-tiles=" + fmt.Sprintf("%d", *maxPCATiles),
140 "-chi2-case-control-file=" + cmd.chi2CaseControlFile,
141 "-chi2-case-control-column=" + cmd.chi2CaseControlColumn,
142 "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
143 "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
144 "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
146 runner.Args = append(runner.Args, cmd.filter.Args()...)
148 output, err = runner.Run()
152 fmt.Fprintln(stdout, output)
156 infiles, err := allFiles(*inputDir, matchGobFile)
160 if len(infiles) == 0 {
161 err = fmt.Errorf("no input files found in %s", *inputDir)
164 sort.Strings(infiles)
166 var refseq map[string][]tileLibRef
167 var reftiledata = make(map[tileLibRef][]byte, 11000000)
168 in0, err := open(infiles[0])
173 matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
175 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
181 err = DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
182 if len(ent.TagSet) > 0 {
185 for _, cseq := range ent.CompactSequences {
186 if cseq.Name == *ref || *ref == "" {
187 refseq = cseq.TileSequences
190 for _, cg := range ent.CompactGenomes {
191 if matchGenome.MatchString(cg.Name) {
192 cmd.cgnames = append(cmd.cgnames, cg.Name)
195 for _, tv := range ent.TileVariants {
197 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
207 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
210 if len(tagset) == 0 {
211 err = fmt.Errorf("tagset not found")
215 taglib := &tagLibrary{}
216 err = taglib.setTags(tagset)
220 taglen := taglib.TagLen()
222 if len(cmd.cgnames) == 0 {
223 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
226 sort.Strings(cmd.cgnames)
227 err = cmd.useCaseControlFiles()
231 if len(cmd.cgnames) == 0 {
232 err = fmt.Errorf("fatal: 0 cases, 0 controls, nothing to do")
235 if cmd.filter.MinCoverage == 1 {
236 // In the generic formula below, floating point
237 // arithmetic can effectively push the coverage
238 // threshold above 1.0, which is impossible/useless.
239 // 1.0 needs to mean exactly 100% coverage.
240 cmd.minCoverage = len(cmd.cgnames)
242 cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
246 labelsFilename := *outputDir + "/samples.csv"
247 log.Infof("writing labels to %s", labelsFilename)
249 f, err = os.Create(labelsFilename)
254 for i, name := range cmd.cgnames {
256 if cmd.chi2Cases != nil && cmd.chi2Cases[i] {
259 _, err = fmt.Fprintf(f, "%d,%q,%d\n", i, trimFilenameForLabel(name), cc)
261 err = fmt.Errorf("write %s: %w", labelsFilename, err)
267 err = fmt.Errorf("close %s: %w", labelsFilename, err)
272 log.Info("indexing reference tiles")
273 type reftileinfo struct {
274 variant tileVariantID
275 seqname string // chr1
276 pos int // distance from start of chromosome to starttag
277 tiledata []byte // acgtggcaa...
278 excluded bool // true if excluded by regions file
279 nexttag tagID // tagID of following tile (-1 for last tag of chromosome)
281 isdup := map[tagID]bool{}
282 reftile := map[tagID]*reftileinfo{}
283 for seqname, cseq := range refseq {
285 lastreftag := tagID(-1)
286 for _, libref := range cseq {
287 if cmd.filter.MaxTag >= 0 && libref.Tag > tagID(cmd.filter.MaxTag) {
290 tiledata := reftiledata[libref]
291 if len(tiledata) == 0 {
292 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
295 foundthistag := false
296 taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
297 if !foundthistag && tagid == libref.Tag {
301 if dupref, ok := reftile[tagid]; ok {
302 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique, also found inside %+v from %s @ %d", tileLibRef{Tag: tagid, Variant: dupref.variant}, dupref.seqname, dupref.pos, libref, seqname, pos+offset+1)
303 delete(reftile, tagid)
305 log.Printf("found tag %d at offset %d inside tile variant %+v on %s @ %d", tagid, offset, libref, seqname, pos+offset+1)
309 if isdup[libref.Tag] {
310 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
311 } else if reftile[libref.Tag] != nil {
312 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)
313 delete(reftile, libref.Tag)
314 log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
315 isdup[libref.Tag] = true
317 reftile[libref.Tag] = &reftileinfo{
319 variant: libref.Variant,
325 reftile[lastreftag].nexttag = libref.Tag
327 lastreftag = libref.Tag
329 pos += len(tiledata) - taglen
331 log.Printf("... %s done, len %d", seqname, pos+taglen)
335 if *regionsFilename != "" {
336 log.Printf("loading regions from %s", *regionsFilename)
337 mask, err = makeMask(*regionsFilename, *expandRegions)
341 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
342 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
343 for _, rt := range reftile {
344 if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
348 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
351 type hgvsColSet map[hgvs.Variant][2][]int8
352 encodeHGVS := throttle{Max: len(refseq)}
353 encodeHGVSTodo := map[string]chan hgvsColSet{}
354 tmpHGVSCols := map[string]*os.File{}
356 for seqname := range refseq {
358 f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
362 defer os.Remove(f.Name())
363 bufw := bufio.NewWriterSize(f, 1<<24)
364 enc := gob.NewEncoder(bufw)
365 tmpHGVSCols[seqname] = f
366 todo := make(chan hgvsColSet, 128)
367 encodeHGVSTodo[seqname] = todo
368 encodeHGVS.Go(func() error {
369 for colset := range todo {
370 err := enc.Encode(colset)
372 encodeHGVS.Report(err)
383 var toMerge [][]int16
384 if *mergeOutput || *hgvsSingle {
385 toMerge = make([][]int16, len(infiles))
387 var onehotIndirect [][2][]uint32 // [chunkIndex][axis][index]
388 var onehotChunkSize []uint32
389 var onehotXrefs [][]onehotXref
390 if *onehotSingle || *onlyPCA {
391 onehotIndirect = make([][2][]uint32, len(infiles))
392 onehotChunkSize = make([]uint32, len(infiles))
393 onehotXrefs = make([][]onehotXref, len(infiles))
395 chunkStartTag := make([]tagID, len(infiles))
397 throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
398 throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
399 log.Info("generating annotations and numpy matrix for each slice")
400 var errSkip = errors.New("skip infile")
402 for infileIdx, infile := range infiles {
403 infileIdx, infile := infileIdx, infile
404 throttleMem.Go(func() error {
405 seq := make(map[tagID][]TileVariant, 50000)
406 cgs := make(map[string]CompactGenome, len(cmd.cgnames))
407 f, err := open(infile)
412 log.Infof("%04d: reading %s", infileIdx, infile)
413 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
414 for _, tv := range ent.TileVariants {
419 // corresponding ref tile, if
420 // mask is in play (we can't
421 // determine coordinates for
423 if mask != nil && reftile[tv.Tag] == nil {
427 // corresponding ref tile is
428 // outside target regions --
429 // unless it's a potential
431 if mask != nil && reftile[tv.Tag].excluded &&
432 (int(tv.Tag+1) >= len(tagset) ||
433 (bytes.HasSuffix(tv.Sequence, tagset[tv.Tag+1]) && reftile[tv.Tag+1] != nil && !reftile[tv.Tag+1].excluded)) {
436 if tv.Tag == cmd.debugTag {
437 log.Printf("infile %d %s tag %d variant %d hash %x", infileIdx, infile, tv.Tag, tv.Variant, tv.Blake2b[:3])
439 variants := seq[tv.Tag]
440 if len(variants) == 0 {
441 variants = make([]TileVariant, 100)
443 for len(variants) <= int(tv.Variant) {
444 variants = append(variants, TileVariant{})
446 variants[int(tv.Variant)] = tv
447 seq[tv.Tag] = variants
449 for _, cg := range ent.CompactGenomes {
450 if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
453 if !matchGenome.MatchString(cg.Name) {
456 // pad to full slice size
457 // to avoid out-of-bounds
459 if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
460 cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
468 } else if err != nil {
469 return fmt.Errorf("%04d: DecodeLibrary(%s): err", infileIdx, infile)
471 tagstart := cgs[cmd.cgnames[0]].StartTag
472 tagend := cgs[cmd.cgnames[0]].EndTag
473 chunkStartTag[infileIdx] = tagstart
477 log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
478 variantRemap := make([][]tileVariantID, tagend-tagstart)
479 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
480 for tag, variants := range seq {
481 tag, variants := tag, variants
482 throttleCPU.Go(func() error {
484 count := make(map[[blake2b.Size256]byte]int, len(variants))
488 count[blake2b.Sum256(rt.tiledata)] = 0
491 for cgname, cg := range cgs {
492 idx := int(tag-tagstart) * 2
493 for allele := 0; allele < 2; allele++ {
494 v := cg.Variants[idx+allele]
495 if v > 0 && len(variants[v].Sequence) > 0 {
496 count[variants[v].Blake2b]++
499 if v > 0 && tag == cmd.debugTag {
500 log.Printf("tag %d cg %s allele %d tv %d hash %x count is now %d", tag, cgname, allele, v, variants[v].Blake2b[:3], count[variants[v].Blake2b])
504 if alleleCoverage < cmd.minCoverage*2 {
505 idx := int(tag-tagstart) * 2
506 for _, cg := range cgs {
508 cg.Variants[idx+1] = 0
510 if tag == cmd.debugTag {
511 log.Printf("tag %d alleleCoverage %d < min %d, sample data wiped", tag, alleleCoverage, cmd.minCoverage*2)
516 // hash[i] will be the hash of
517 // the variant(s) that should
518 // be at rank i (0-based).
519 hash := make([][blake2b.Size256]byte, 0, len(count))
520 for b := range count {
521 hash = append(hash, b)
523 sort.Slice(hash, func(i, j int) bool {
524 bi, bj := &hash[i], &hash[j]
525 if ci, cj := count[*bi], count[*bj]; ci != cj {
528 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
531 // rank[b] will be the 1-based
532 // new variant number for
533 // variants whose hash is b.
534 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
535 for i, h := range hash {
536 rank[h] = tileVariantID(i + 1)
538 if tag == cmd.debugTag {
539 for h, r := range rank {
540 log.Printf("tag %d rank(%x) = %v", tag, h[:3], r)
543 // remap[v] will be the new
544 // variant number for original
546 remap := make([]tileVariantID, len(variants))
547 for i, tv := range variants {
548 remap[i] = rank[tv.Blake2b]
550 if tag == cmd.debugTag {
551 for in, out := range remap {
553 log.Printf("tag %d remap %d => %d", tag, in, out)
557 variantRemap[tag-tagstart] = remap
559 refrank := rank[blake2b.Sum256(rt.tiledata)]
560 if tag == cmd.debugTag {
561 log.Printf("tag %d reftile variant %d => %d", tag, rt.variant, refrank)
570 var onehotChunk [][]int8
571 var onehotXref []onehotXref
573 var annotationsFilename string
575 annotationsFilename = "/dev/null"
577 annotationsFilename = fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
578 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
580 annof, err := os.Create(annotationsFilename)
584 annow := bufio.NewWriterSize(annof, 1<<20)
586 for tag := tagstart; tag < tagend; tag++ {
588 if rt == nil && mask != nil {
589 // With no ref tile, we don't
590 // have coordinates to say
591 // this is in the desired
592 // regions -- so it's not.
593 // TODO: handle ref spanning
597 if rt != nil && rt.excluded {
598 // TODO: don't skip yet --
599 // first check for spanning
600 // tile variants that
601 // intersect non-excluded ref
605 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
608 remap := variantRemap[tag-tagstart]
609 maxv := tileVariantID(0)
610 for _, v := range remap {
615 if *onehotChunked || *onehotSingle || *onlyPCA {
616 onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart, seq)
617 if tag == cmd.debugTag {
618 log.WithFields(logrus.Fields{
621 }).Info("tv2homhet()")
623 onehotChunk = append(onehotChunk, onehot...)
624 onehotXref = append(onehotXref, xrefs...)
631 // Reference does not use any
632 // variant of this tile
634 // TODO: diff against the
635 // relevant portion of the
636 // ref's spanning tile
640 fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
642 reftilestr := strings.ToUpper(string(rt.tiledata))
644 done := make([]bool, maxv+1)
645 variantDiffs := make([][]hgvs.Variant, maxv+1)
646 for v, tv := range variants {
648 if v == 0 || v == rt.variant || done[v] {
653 if len(tv.Sequence) < taglen {
656 // if reftilestr doesn't end
657 // in the same tag as tv,
658 // extend reftilestr with
659 // following ref tiles until
660 // it does (up to an arbitrary
661 // sanity-check limit)
662 reftilestr := reftilestr
663 endtagstr := strings.ToUpper(string(tv.Sequence[len(tv.Sequence)-taglen:]))
664 for i, rt := 0, rt; i < annotationMaxTileSpan && !strings.HasSuffix(reftilestr, endtagstr) && rt.nexttag >= 0; i++ {
665 rt = reftile[rt.nexttag]
669 reftilestr += strings.ToUpper(string(rt.tiledata[taglen:]))
671 if mask != nil && !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(reftilestr)) {
674 if !strings.HasSuffix(reftilestr, endtagstr) {
675 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
678 if lendiff := len(reftilestr) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
679 fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
682 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
683 for i := range diffs {
684 diffs[i].Position += rt.pos
686 for _, diff := range diffs {
687 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)
690 variantDiffs[v] = diffs
694 // We can now determine, for each HGVS
695 // variant (diff) in this reftile
696 // region, whether a given genome
697 // phase/allele (1) has the variant, (0) has
698 // =ref or a different variant in that
699 // position, or (-1) is lacking
700 // coverage / couldn't be diffed.
701 hgvsCol := hgvsColSet{}
702 for _, diffs := range variantDiffs {
703 for _, diff := range diffs {
704 if _, ok := hgvsCol[diff]; ok {
707 hgvsCol[diff] = [2][]int8{
708 make([]int8, len(cmd.cgnames)),
709 make([]int8, len(cmd.cgnames)),
713 for row, name := range cmd.cgnames {
714 variants := cgs[name].Variants[(tag-tagstart)*2:]
715 for ph := 0; ph < 2; ph++ {
717 if int(v) >= len(remap) {
723 // hgvsCol[*][ph][row] is already 0
724 } else if len(variantDiffs[v]) == 0 {
725 // lacking coverage / couldn't be diffed
726 for _, col := range hgvsCol {
730 for _, diff := range variantDiffs[v] {
731 hgvsCol[diff][ph][row] = 1
736 for diff, colpair := range hgvsCol {
737 allele2homhet(colpair)
738 if !cmd.filterHGVScolpair(colpair) {
739 delete(hgvsCol, diff)
742 if len(hgvsCol) > 0 {
743 encodeHGVSTodo[rt.seqname] <- hgvsCol
758 // transpose onehotChunk[col][row] to numpy[row*ncols+col]
759 rows := len(cmd.cgnames)
760 cols := len(onehotChunk)
761 log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
762 throttleNumpyMem.Acquire()
763 out := onehotcols2int8(onehotChunk)
764 fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
765 err = writeNumpyInt8(fnm, out, rows, cols)
769 fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
770 err = writeNumpyInt32(fnm, onehotXref2int32(onehotXref), 4, len(onehotXref))
775 throttleNumpyMem.Release()
777 if *onehotSingle || *onlyPCA {
778 onehotIndirect[infileIdx] = onehotChunk2Indirect(onehotChunk)
779 onehotChunkSize[infileIdx] = uint32(len(onehotChunk))
780 onehotXrefs[infileIdx] = onehotXref
781 n := len(onehotIndirect[infileIdx][0])
782 log.Infof("%04d: keeping onehot coordinates in memory (n=%d, mem=%d)", infileIdx, n, n*8*2)
784 if !(*onehotSingle || *onehotChunked || *onlyPCA) || *mergeOutput || *hgvsSingle {
785 log.Infof("%04d: preparing numpy (rows=%d, cols=%d)", infileIdx, len(cmd.cgnames), 2*outcol)
786 throttleNumpyMem.Acquire()
787 rows := len(cmd.cgnames)
789 out := make([]int16, rows*cols)
790 for row, name := range cmd.cgnames {
792 for col, v := range cgs[name].Variants {
793 tag := tagstart + tagID(col/2)
794 if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
797 if rt := reftile[tag]; rt == nil || rt.excluded {
801 out[outidx] = 0 // tag not found / spanning tile
802 } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
803 out[outidx] = int16(variantRemap[tag-tagstart][v])
805 out[outidx] = -1 // low quality tile variant
807 if tag == cmd.debugTag {
808 log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
816 throttleNumpyMem.Release()
817 if *mergeOutput || *hgvsSingle {
818 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
819 toMerge[infileIdx] = out
821 if !*mergeOutput && !*onehotChunked && !*onehotSingle {
822 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
823 err = writeNumpyInt16(fnm, out, rows, cols)
830 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
834 if err = throttleMem.Wait(); err != nil {
839 log.Info("flushing hgvsCols temp files")
840 for seqname := range refseq {
841 close(encodeHGVSTodo[seqname])
843 err = encodeHGVS.Wait()
847 for seqname := range refseq {
848 log.Infof("%s: reading hgvsCols from temp file", seqname)
849 f := tmpHGVSCols[seqname]
850 _, err = f.Seek(0, io.SeekStart)
854 var hgvsCols hgvsColSet
855 dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
857 err = dec.Decode(&hgvsCols)
862 log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
863 variants := make([]hgvs.Variant, 0, len(hgvsCols))
864 for v := range hgvsCols {
865 variants = append(variants, v)
867 sort.Slice(variants, func(i, j int) bool {
868 vi, vj := &variants[i], &variants[j]
869 if vi.Position != vj.Position {
870 return vi.Position < vj.Position
871 } else if vi.Ref != vj.Ref {
872 return vi.Ref < vj.Ref
874 return vi.New < vj.New
877 rows := len(cmd.cgnames)
878 cols := len(variants) * 2
879 log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
880 out := make([]int8, rows*cols)
881 for varIdx, variant := range variants {
882 hgvsCols := hgvsCols[variant]
883 for row := range cmd.cgnames {
884 for ph := 0; ph < 2; ph++ {
885 out[row*cols+varIdx+ph] = hgvsCols[ph][row]
889 err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
895 fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
896 log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
897 var hgvsLabels bytes.Buffer
898 for varIdx, variant := range variants {
899 fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
901 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
908 if *mergeOutput || *hgvsSingle {
909 var annow *bufio.Writer
912 annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
913 annof, err = os.Create(annoFilename)
917 annow = bufio.NewWriterSize(annof, 1<<20)
920 rows := len(cmd.cgnames)
922 for _, chunk := range toMerge {
923 cols += len(chunk) / rows
925 log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
928 out = make([]int16, rows*cols)
930 hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
932 for outIdx, chunk := range toMerge {
933 chunkcols := len(chunk) / rows
935 for row := 0; row < rows; row++ {
936 copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
939 toMerge[outIdx] = nil
941 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
942 log.Infof("reading %s", annotationsFilename)
943 buf, err := os.ReadFile(annotationsFilename)
948 err = os.Remove(annotationsFilename)
953 for _, line := range bytes.Split(buf, []byte{'\n'}) {
957 fields := bytes.SplitN(line, []byte{','}, 9)
958 tag, _ := strconv.Atoi(string(fields[0]))
959 incol, _ := strconv.Atoi(string(fields[1]))
960 tileVariant, _ := strconv.Atoi(string(fields[2]))
961 hgvsID := string(fields[3])
962 seqname := string(fields[4])
963 pos, _ := strconv.Atoi(string(fields[5]))
966 // Null entry for un-diffable
971 // Null entry for ref tile
974 if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
975 // The tile intersects one of
976 // the selected regions, but
977 // this particular HGVS
981 hgvsColPair := hgvsCols[hgvsID]
982 if hgvsColPair[0] == nil {
983 // values in new columns start
984 // out as -1 ("no data yet")
985 // or 0 ("=ref") here, may
986 // change to 1 ("hgvs variant
987 // present") below, either on
988 // this line or a future line.
989 hgvsColPair = [2][]int16{make([]int16, len(cmd.cgnames)), make([]int16, len(cmd.cgnames))}
990 rt, ok := reftile[tagID(tag)]
992 err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
995 for ph := 0; ph < 2; ph++ {
996 for row := 0; row < rows; row++ {
997 v := chunk[row*chunkcols+incol*2+ph]
998 if tileVariantID(v) == rt.variant {
999 hgvsColPair[ph][row] = 0
1001 hgvsColPair[ph][row] = -1
1005 hgvsCols[hgvsID] = hgvsColPair
1007 hgvsref := hgvs.Variant{
1009 Ref: string(refseq),
1010 New: string(refseq),
1012 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])
1016 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])
1018 for ph := 0; ph < 2; ph++ {
1019 for row := 0; row < rows; row++ {
1020 v := chunk[row*chunkcols+incol*2+ph]
1021 if int(v) == tileVariant {
1022 hgvsColPair[ph][row] = 1
1028 startcol += chunkcols
1039 err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
1047 cols = len(hgvsCols) * 2
1048 log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
1049 out = make([]int16, rows*cols)
1050 hgvsIDs := make([]string, 0, cols/2)
1051 for hgvsID := range hgvsCols {
1052 hgvsIDs = append(hgvsIDs, hgvsID)
1054 sort.Strings(hgvsIDs)
1055 var hgvsLabels bytes.Buffer
1056 for idx, hgvsID := range hgvsIDs {
1057 fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
1058 for ph := 0; ph < 2; ph++ {
1059 hgvscol := hgvsCols[hgvsID][ph]
1060 for row, val := range hgvscol {
1061 out[row*cols+idx*2+ph] = val
1065 err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
1070 fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
1071 log.Printf("writing hgvs labels: %s", fnm)
1072 err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
1078 if *onehotSingle || *onlyPCA {
1080 for _, part := range onehotIndirect {
1081 nzCount += len(part[0])
1083 onehot := make([]uint32, nzCount*2) // [r,r,r,...,c,c,c,...]
1084 var xrefs []onehotXref
1085 chunkOffset := uint32(0)
1087 for i, part := range onehotIndirect {
1088 for i := range part[1] {
1089 part[1][i] += chunkOffset
1091 copy(onehot[outcol:], part[0])
1092 copy(onehot[outcol+nzCount:], part[1])
1093 xrefs = append(xrefs, onehotXrefs[i]...)
1095 outcol += len(part[0])
1096 chunkOffset += onehotChunkSize[i]
1100 onehotXrefs[i] = nil
1101 debug.FreeOSMemory()
1104 fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
1105 err = writeNumpyUint32(fnm, onehot, 2, nzCount)
1109 fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
1110 err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
1117 for _, c := range onehot[nzCount:] {
1123 return fmt.Errorf("cannot do PCA: one-hot matrix is empty")
1125 log.Printf("have %d one-hot cols", cols)
1127 for *maxPCATiles > 0 && cols > *maxPCATiles*2 {
1128 cols = (cols + 1) / 2
1131 log.Printf("creating matrix: %d rows, %d cols, stride %d", len(cmd.cgnames), cols, stride)
1132 mtx := mat.NewDense(len(cmd.cgnames), cols, nil)
1133 for i, c := range onehot[nzCount:] {
1134 if int(c/2)%stride == 0 {
1135 mtx.Set(int(onehot[i]), int(c/2)/stride*2+int(c)%2, 1)
1138 log.Print("fitting")
1139 transformer := nlp.NewPCA(*pcaComponents)
1140 transformer.Fit(mtx.T())
1141 log.Printf("transforming")
1142 pca, err := transformer.Transform(mtx.T())
1147 outrows, outcols := pca.Dims()
1148 log.Printf("copying result to numpy output array: %d rows, %d cols", outrows, outcols)
1149 out := make([]float64, outrows*outcols)
1150 for i := 0; i < outrows; i++ {
1151 for j := 0; j < outcols; j++ {
1152 out[i*outcols+j] = pca.At(i, j)
1155 fnm := fmt.Sprintf("%s/pca.npy", *outputDir)
1156 log.Printf("writing numpy: %s", fnm)
1157 output, err := os.OpenFile(fnm, os.O_CREATE|os.O_TRUNC|os.O_WRONLY, 0777)
1161 npw, err := gonpy.NewWriter(nopCloser{output})
1163 return fmt.Errorf("gonpy.NewWriter: %w", err)
1165 npw.Shape = []int{outrows, outcols}
1166 err = npw.WriteFloat64(out)
1168 return fmt.Errorf("WriteFloat64: %w", err)
1170 err = output.Close()
1177 if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
1178 tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
1179 log.Infof("writing tag offsets to %s", tagoffsetFilename)
1181 f, err = os.Create(tagoffsetFilename)
1186 for idx, offset := range chunkStartTag {
1187 _, err = fmt.Fprintf(f, "%q,%d\n", fmt.Sprintf("matrix.%04d.npy", idx), offset)
1189 err = fmt.Errorf("write %s: %w", tagoffsetFilename, err)
1195 err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
1202 // Read case/control files, remove non-case/control entries from
1203 // cmd.cgnames, and build cmd.chi2Cases.
1204 func (cmd *sliceNumpy) useCaseControlFiles() error {
1205 if cmd.chi2CaseControlFile == "" {
1208 infiles, err := allFiles(cmd.chi2CaseControlFile, nil)
1212 // index in cmd.cgnames => case(true) / control(false)
1213 cc := map[int]bool{}
1214 for _, infile := range infiles {
1215 f, err := open(infile)
1219 buf, err := io.ReadAll(f)
1225 for _, tsv := range bytes.Split(buf, []byte{'\n'}) {
1229 split := strings.Split(string(tsv), "\t")
1232 for col, name := range split {
1233 if name == cmd.chi2CaseControlColumn {
1239 return fmt.Errorf("%s: no column named %q in header row %q", infile, cmd.chi2CaseControlColumn, tsv)
1243 if len(split) <= ccCol {
1248 for i, name := range cmd.cgnames {
1249 if strings.Contains(name, pattern) {
1251 log.Warnf("pattern %q in %s matches multiple genome IDs (%qs, %q)", pattern, infile, cmd.cgnames[found], name)
1257 log.Warnf("pattern %q in %s does not match any genome IDs", pattern, infile)
1260 if split[ccCol] == "0" {
1263 if split[ccCol] == "1" {
1268 allnames := cmd.cgnames
1272 for i, name := range allnames {
1273 if cc, ok := cc[i]; ok {
1274 cmd.cgnames = append(cmd.cgnames, name)
1275 cmd.chi2Cases = append(cmd.chi2Cases, cc)
1281 log.Printf("%d cases, %d controls, %d neither (dropped)", ncases, len(cmd.cgnames)-ncases, len(allnames)-len(cmd.cgnames))
1285 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
1286 if cmd.chi2PValue >= 1 {
1289 col0 := make([]bool, 0, len(cmd.chi2Cases))
1290 col1 := make([]bool, 0, len(cmd.chi2Cases))
1291 cases := make([]bool, 0, len(cmd.chi2Cases))
1292 for i, c := range cmd.chi2Cases {
1293 if colpair[0][i] < 0 {
1296 col0 = append(col0, colpair[0][i] != 0)
1297 col1 = append(col1, colpair[1][i] != 0)
1298 cases = append(cases, c)
1300 return len(cases) >= cmd.minCoverage &&
1301 (pvalue(col0, cases) <= cmd.chi2PValue || pvalue(col1, cases) <= cmd.chi2PValue)
1304 func writeNumpyUint32(fnm string, out []uint32, rows, cols int) error {
1305 output, err := os.Create(fnm)
1309 defer output.Close()
1310 bufw := bufio.NewWriterSize(output, 1<<26)
1311 npw, err := gonpy.NewWriter(nopCloser{bufw})
1315 log.WithFields(log.Fields{
1319 "bytes": rows * cols * 4,
1320 }).Infof("writing numpy: %s", fnm)
1321 npw.Shape = []int{rows, cols}
1322 npw.WriteUint32(out)
1327 return output.Close()
1330 func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
1331 output, err := os.Create(fnm)
1335 defer output.Close()
1336 bufw := bufio.NewWriterSize(output, 1<<26)
1337 npw, err := gonpy.NewWriter(nopCloser{bufw})
1341 log.WithFields(log.Fields{
1345 "bytes": rows * cols * 4,
1346 }).Infof("writing numpy: %s", fnm)
1347 npw.Shape = []int{rows, cols}
1353 return output.Close()
1356 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
1357 output, err := os.Create(fnm)
1361 defer output.Close()
1362 bufw := bufio.NewWriterSize(output, 1<<26)
1363 npw, err := gonpy.NewWriter(nopCloser{bufw})
1367 log.WithFields(log.Fields{
1371 "bytes": rows * cols * 2,
1372 }).Infof("writing numpy: %s", fnm)
1373 npw.Shape = []int{rows, cols}
1379 return output.Close()
1382 func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
1383 output, err := os.Create(fnm)
1387 defer output.Close()
1388 bufw := bufio.NewWriterSize(output, 1<<26)
1389 npw, err := gonpy.NewWriter(nopCloser{bufw})
1393 log.WithFields(log.Fields{
1397 "bytes": rows * cols,
1398 }).Infof("writing numpy: %s", fnm)
1399 npw.Shape = []int{rows, cols}
1405 return output.Close()
1408 func allele2homhet(colpair [2][]int8) {
1409 a, b := colpair[0], colpair[1]
1410 for i, av := range a {
1412 if av < 0 || bv < 0 {
1415 } else if av > 0 && bv > 0 {
1418 } else if av > 0 || bv > 0 {
1422 // ref (or a different variant in same position)
1423 // (this is a no-op) a[i], b[i] = 0, 0
1428 type onehotXref struct {
1430 variant tileVariantID
1435 const onehotXrefSize = unsafe.Sizeof(onehotXref{})
1437 // Build onehot matrix (m[tileVariantIndex][genome] == 0 or 1) for all
1438 // variants of a single tile/tag#.
1440 // Return nil if no tile variant passes Χ² filter.
1441 func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID, seq map[tagID][]TileVariant) ([][]int8, []onehotXref) {
1442 if tag == cmd.debugTag {
1443 tv := make([]tileVariantID, len(cmd.cgnames)*2)
1444 for i, name := range cmd.cgnames {
1445 copy(tv[i*2:(i+1)*2], cgs[name].Variants[(tag-chunkstarttag)*2:])
1447 log.WithFields(logrus.Fields{
1448 "cgs[i].Variants[tag*2+j]": tv,
1452 "chunkstarttag": chunkstarttag,
1453 }).Info("tv2homhet()")
1455 if maxv < 1 || (maxv < 2 && !cmd.includeVariant1) {
1456 // everyone has the most common variant (of the variants we don't drop)
1459 tagoffset := tag - chunkstarttag
1461 for _, cg := range cgs {
1463 for _, v := range cg.Variants[tagoffset*2 : tagoffset*2+2] {
1464 if v > 0 && int(v) < len(seq[tag]) && len(seq[tag][v].Sequence) > 0 {
1472 if coverage < cmd.minCoverage {
1475 obs := make([][]bool, (maxv+1)*2) // 2 slices (hom + het) for each variant#
1476 for i := range obs {
1477 obs[i] = make([]bool, len(cmd.cgnames))
1479 for cgid, name := range cmd.cgnames {
1480 cgvars := cgs[name].Variants[tagoffset*2:]
1481 tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
1482 for v := tileVariantID(1); v <= maxv; v++ {
1483 if tv0 == v && tv1 == v {
1484 obs[v*2][cgid] = true
1485 } else if tv0 == v || tv1 == v {
1486 obs[v*2+1][cgid] = true
1491 var xref []onehotXref
1492 for col := 2; col < len(obs); col++ {
1493 // col 0,1 correspond to tile variant 0, i.e.,
1494 // no-call; col 2,3 correspond to the most common
1495 // variant; so we (normally) start at col 4.
1496 if col < 4 && !cmd.includeVariant1 {
1499 p := pvalue(obs[col], cmd.chi2Cases)
1500 if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
1503 onehot = append(onehot, bool2int8(obs[col]))
1504 xref = append(xref, onehotXref{
1506 variant: tileVariantID(col >> 1),
1514 func bool2int8(in []bool) []int8 {
1515 out := make([]int8, len(in))
1516 for i, v := range in {
1524 // convert a []onehotXref with length N to a numpy-style []int32
1525 // matrix with N columns, one row per field of onehotXref struct.
1527 // Hom/het row contains hom=0, het=1.
1529 // P-value row contains 1000000x actual p-value.
1530 func onehotXref2int32(xrefs []onehotXref) []int32 {
1532 xdata := make([]int32, 5*xcols)
1533 for i, xref := range xrefs {
1534 xdata[i] = int32(xref.tag)
1535 xdata[xcols+i] = int32(xref.variant)
1537 xdata[xcols*2+i] = 1
1539 xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
1540 xdata[xcols*4+i] = int32(-math.Log10(xref.pvalue) * 1000000)
1545 // transpose onehot data from in[col][row] to numpy-style
1546 // out[row*cols+col].
1547 func onehotcols2int8(in [][]int8) []int8 {
1553 out := make([]int8, rows*cols)
1554 for row := 0; row < rows; row++ {
1555 outrow := out[row*cols:]
1556 for col, incol := range in {
1557 outrow[col] = incol[row]
1563 // Return [2][]uint32{rowIndices, colIndices} indicating which
1564 // elements of matrixT[c][r] have non-zero values.
1565 func onehotChunk2Indirect(matrixT [][]int8) [2][]uint32 {
1567 for c, col := range matrixT {
1568 for r, val := range col {
1570 nz[0] = append(nz[0], uint32(r))
1571 nz[1] = append(nz[1], uint32(c))