1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
21 "git.arvados.org/arvados.git/sdk/go/arvados"
22 "github.com/arvados/lightning/hgvs"
23 "github.com/kshedden/gonpy"
24 "github.com/sirupsen/logrus"
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 in0, err := open(infiles[0])
118 DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
119 if len(ent.TagSet) > 0 {
120 taglen = len(ent.TagSet[0])
122 for _, cseq := range ent.CompactSequences {
123 if cseq.Name == *ref || *ref == "" {
124 refseq = cseq.TileSequences
127 for _, cg := range ent.CompactGenomes {
128 cgnames = append(cgnames, cg.Name)
137 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
141 err = fmt.Errorf("tagset not found")
144 sort.Strings(cgnames)
147 labelsFilename := *outputDir + "/labels.csv"
148 log.Infof("writing labels to %s", labelsFilename)
150 f, err = os.Create(labelsFilename)
155 for i, name := range cgnames {
156 _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
158 err = fmt.Errorf("write %s: %w", labelsFilename, err)
164 err = fmt.Errorf("close %s: %w", labelsFilename, err)
169 log.Info("building list of reference tiles to load") // TODO: more efficient if we had saved all ref tiles in slice0
170 type reftileinfo struct {
171 variant tileVariantID
172 seqname string // chr1
173 pos int // distance from start of chr1 to start of tile
174 tiledata []byte // acgtggcaa...
176 reftile := map[tagID]*reftileinfo{}
177 for seqname, cseq := range refseq {
178 for _, libref := range cseq {
179 reftile[libref.Tag] = &reftileinfo{seqname: seqname, variant: libref.Variant}
182 log.Info("loading reference tiles from all slices")
183 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
184 for _, infile := range infiles {
186 throttleCPU.Go(func() error {
187 defer log.Infof("%s: done", infile)
188 f, err := open(infile)
193 return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
194 for _, tv := range ent.TileVariants {
195 if dst, ok := reftile[tv.Tag]; ok && dst.variant == tv.Variant {
196 dst.tiledata = tv.Sequence
203 if err = throttleCPU.Wait(); err != nil {
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 pos += len(rt.tiledata) - taglen
223 log.Info("TODO: determining which tiles intersect given regions")
225 throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
226 throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
227 log.Info("generating annotations and numpy matrix for each slice")
229 for infileIdx, infile := range infiles {
230 infileIdx, infile := infileIdx, infile
231 throttleMem.Go(func() error {
232 seq := make(map[tagID][]TileVariant, 50000)
233 cgs := make(map[string]CompactGenome, len(cgnames))
234 f, err := open(infile)
239 log.Infof("%04d: reading %s", infileIdx, infile)
240 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
241 for _, tv := range ent.TileVariants {
242 variants := seq[tv.Tag]
243 if len(variants) == 0 {
244 variants = make([]TileVariant, 100)
246 for len(variants) <= int(tv.Variant) {
247 variants = append(variants, TileVariant{})
249 variants[int(tv.Variant)] = tv
250 seq[tv.Tag] = variants
252 for _, cg := range ent.CompactGenomes {
260 tagstart := cgs[cgnames[0]].StartTag
261 tagend := cgs[cgnames[0]].EndTag
265 log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
266 variantRemap := make([][]tileVariantID, tagend-tagstart)
267 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
268 for tag, variants := range seq {
269 tag, variants := tag, variants
270 throttleCPU.Acquire()
272 defer throttleCPU.Release()
273 count := make(map[[blake2b.Size256]byte]int, len(variants))
274 for _, cg := range cgs {
275 idx := (tag - tagstart) * 2
276 if int(idx) < len(cg.Variants) {
277 count[variants[cg.Variants[idx]].Blake2b]++
278 count[variants[cg.Variants[idx+1]].Blake2b]++
281 // hash[i] will be the hash of
282 // the variant(s) that should
283 // be at rank i (0-based).
284 hash := make([][blake2b.Size256]byte, 0, len(count))
285 for b := range count {
286 hash = append(hash, b)
288 sort.Slice(hash, func(i, j int) bool {
289 bi, bj := &hash[i], &hash[j]
290 if ci, cj := count[*bi], count[*bj]; ci != cj {
293 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
296 // rank[b] will be the 1-based
297 // new variant number for
298 // variants whose hash is b.
299 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
300 for i, h := range hash {
301 rank[h] = tileVariantID(i + 1)
303 // remap[v] will be the new
304 // variant number for original
306 remap := make([]tileVariantID, len(variants))
307 for i, tv := range variants {
308 remap[i] = rank[tv.Blake2b]
310 variantRemap[tag-tagstart] = remap
315 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
316 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
317 annof, err := os.Create(annotationsFilename)
321 annow := bufio.NewWriterSize(annof, 1<<20)
322 for tag, variants := range seq {
323 rt, ok := reftile[tag]
325 // Reference does not use any
326 // variant of this tile.
327 // TODO: log this? mention it
331 outcol := tag - tagID(tagstart)
332 reftilestr := strings.ToUpper(string(rt.tiledata))
333 remap := variantRemap[tag-tagstart]
334 for v, tv := range variants {
335 if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
338 if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
341 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
342 for _, diff := range diffs {
343 diff.Position += rt.pos
344 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, remap[v], rt.seqname, diff.String())
357 throttleNumpyMem.Acquire()
358 log.Infof("%04d: preparing numpy", infileIdx)
360 cols := 2 * int(tagend-tagstart)
361 out := make([]int16, rows*cols)
362 for row, name := range cgnames {
363 out := out[row*cols:]
364 for col, v := range cgs[name].Variants {
365 if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
366 out[col] = int16(variantRemap[col/2][v])
373 throttleNumpyMem.Release()
375 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
376 output, err := os.Create(fnm)
381 bufw := bufio.NewWriterSize(output, 1<<26)
382 npw, err := gonpy.NewWriter(nopCloser{bufw})
386 log.WithFields(logrus.Fields{
390 }).Infof("%04d: writing numpy", infileIdx)
391 npw.Shape = []int{rows, cols}
401 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
405 if err = throttleMem.Wait(); err != nil {