1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
22 "git.arvados.org/arvados.git/sdk/go/arvados"
23 "github.com/arvados/lightning/hgvs"
24 "github.com/kshedden/gonpy"
25 log "github.com/sirupsen/logrus"
26 "golang.org/x/crypto/blake2b"
29 type sliceNumpy struct {
34 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
38 fmt.Fprintf(stderr, "%s\n", err)
41 flags := flag.NewFlagSet("", flag.ContinueOnError)
42 flags.SetOutput(stderr)
43 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
44 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
45 projectUUID := flags.String("project", "", "project `UUID` for output data")
46 priority := flags.Int("priority", 500, "container request priority")
47 inputDir := flags.String("input-dir", "./in", "input `directory`")
48 outputDir := flags.String("output-dir", "./out", "output `directory`")
49 ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
50 regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
51 expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
52 flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
53 cmd.filter.Flags(flags)
54 err = flags.Parse(args)
55 if err == flag.ErrHelp {
58 } else if err != nil {
64 log.Println(http.ListenAndServe(*pprof, nil))
69 runner := arvadosContainerRunner{
70 Name: "lightning slice-numpy",
71 Client: arvados.NewClientFromEnv(),
72 ProjectUUID: *projectUUID,
79 err = runner.TranslatePaths(inputDir, regionsFilename)
83 runner.Args = []string{"slice-numpy", "-local=true",
85 "-input-dir", *inputDir,
86 "-output-dir", "/mnt/output",
87 "-threads", fmt.Sprintf("%d", cmd.threads),
88 "-regions", *regionsFilename,
89 "-expand-regions", fmt.Sprintf("%d", *expandRegions),
91 runner.Args = append(runner.Args, cmd.filter.Args()...)
93 output, err = runner.Run()
97 fmt.Fprintln(stdout, output)
101 infiles, err := allGobFiles(*inputDir)
105 if len(infiles) == 0 {
106 err = fmt.Errorf("no input files found in %s", *inputDir)
109 sort.Strings(infiles)
112 var refseq map[string][]tileLibRef
113 var reftiledata = make(map[tileLibRef][]byte, 11000000)
114 in0, err := open(infiles[0])
119 matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
121 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
126 DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
127 if len(ent.TagSet) > 0 {
128 taglen = len(ent.TagSet[0])
130 for _, cseq := range ent.CompactSequences {
131 if cseq.Name == *ref || *ref == "" {
132 refseq = cseq.TileSequences
135 for _, cg := range ent.CompactGenomes {
136 if matchGenome.MatchString(cg.Name) {
137 cgnames = append(cgnames, cg.Name)
140 for _, tv := range ent.TileVariants {
142 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
152 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
156 err = fmt.Errorf("tagset not found")
159 if len(cgnames) == 0 {
160 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
163 sort.Strings(cgnames)
166 labelsFilename := *outputDir + "/labels.csv"
167 log.Infof("writing labels to %s", labelsFilename)
169 f, err = os.Create(labelsFilename)
174 for i, name := range cgnames {
175 _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
177 err = fmt.Errorf("write %s: %w", labelsFilename, err)
183 err = fmt.Errorf("close %s: %w", labelsFilename, err)
188 log.Info("indexing reference tiles")
189 type reftileinfo struct {
190 variant tileVariantID
191 seqname string // chr1
192 pos int // distance from start of chr1 to start of tile
193 tiledata []byte // acgtggcaa...
195 reftile := map[tagID]*reftileinfo{}
196 for seqname, cseq := range refseq {
197 for _, libref := range cseq {
198 reftile[libref.Tag] = &reftileinfo{
200 variant: libref.Variant,
201 tiledata: reftiledata[libref],
206 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
207 log.Info("reconstructing reference sequences")
208 for seqname, cseq := range refseq {
209 seqname, cseq := seqname, cseq
210 throttleCPU.Go(func() error {
211 defer log.Printf("... %s done", seqname)
213 for _, libref := range cseq {
214 rt := reftile[libref.Tag]
216 if len(rt.tiledata) == 0 {
217 return fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
219 pos += len(rt.tiledata) - taglen
226 log.Info("TODO: determining which tiles intersect given regions")
228 throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
229 throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
230 log.Info("generating annotations and numpy matrix for each slice")
232 for infileIdx, infile := range infiles {
233 infileIdx, infile := infileIdx, infile
234 throttleMem.Go(func() error {
235 seq := make(map[tagID][]TileVariant, 50000)
236 cgs := make(map[string]CompactGenome, len(cgnames))
237 f, err := open(infile)
242 log.Infof("%04d: reading %s", infileIdx, infile)
243 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
244 for _, tv := range ent.TileVariants {
248 variants := seq[tv.Tag]
249 if len(variants) == 0 {
250 variants = make([]TileVariant, 100)
252 for len(variants) <= int(tv.Variant) {
253 variants = append(variants, TileVariant{})
255 variants[int(tv.Variant)] = tv
256 seq[tv.Tag] = variants
258 for _, cg := range ent.CompactGenomes {
259 if matchGenome.MatchString(cg.Name) {
268 tagstart := cgs[cgnames[0]].StartTag
269 tagend := cgs[cgnames[0]].EndTag
273 log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
274 variantRemap := make([][]tileVariantID, tagend-tagstart)
275 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
276 for tag, variants := range seq {
277 tag, variants := tag, variants
278 throttleCPU.Acquire()
280 defer throttleCPU.Release()
281 count := make(map[[blake2b.Size256]byte]int, len(variants))
282 for _, cg := range cgs {
283 idx := (tag - tagstart) * 2
284 if int(idx) < len(cg.Variants) {
285 count[variants[cg.Variants[idx]].Blake2b]++
286 count[variants[cg.Variants[idx+1]].Blake2b]++
289 // hash[i] will be the hash of
290 // the variant(s) that should
291 // be at rank i (0-based).
292 hash := make([][blake2b.Size256]byte, 0, len(count))
293 for b := range count {
294 hash = append(hash, b)
296 sort.Slice(hash, func(i, j int) bool {
297 bi, bj := &hash[i], &hash[j]
298 if ci, cj := count[*bi], count[*bj]; ci != cj {
301 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
304 // rank[b] will be the 1-based
305 // new variant number for
306 // variants whose hash is b.
307 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
308 for i, h := range hash {
309 rank[h] = tileVariantID(i + 1)
311 // remap[v] will be the new
312 // variant number for original
314 remap := make([]tileVariantID, len(variants))
315 for i, tv := range variants {
316 remap[i] = rank[tv.Blake2b]
318 variantRemap[tag-tagstart] = remap
323 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
324 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
325 annof, err := os.Create(annotationsFilename)
329 annow := bufio.NewWriterSize(annof, 1<<20)
330 for tag, variants := range seq {
331 rt, ok := reftile[tag]
333 // Reference does not use any
334 // variant of this tile.
335 // TODO: log this? mention it
339 outcol := tag - tagID(tagstart)
340 reftilestr := strings.ToUpper(string(rt.tiledata))
341 remap := variantRemap[tag-tagstart]
342 for v, tv := range variants {
343 if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
346 if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
349 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
350 for _, diff := range diffs {
351 diff.Position += rt.pos
352 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s\n", tag, outcol, remap[v], rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New)
365 throttleNumpyMem.Acquire()
366 log.Infof("%04d: preparing numpy", infileIdx)
368 cols := 2 * int(tagend-tagstart)
369 out := make([]int16, rows*cols)
370 for row, name := range cgnames {
371 out := out[row*cols:]
372 for col, v := range cgs[name].Variants {
373 if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
374 out[col] = int16(variantRemap[col/2][v])
381 throttleNumpyMem.Release()
383 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
384 output, err := os.Create(fnm)
389 bufw := bufio.NewWriterSize(output, 1<<26)
390 npw, err := gonpy.NewWriter(nopCloser{bufw})
394 log.WithFields(log.Fields{
398 }).Infof("%04d: writing numpy", infileIdx)
399 npw.Shape = []int{rows, cols}
409 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
413 if err = throttleMem.Wait(); err != nil {