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 var reftiledata = make(map[tileLibRef][]byte, 11000000)
114 in0, err := open(infiles[0])
120 DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
121 if len(ent.TagSet) > 0 {
122 taglen = len(ent.TagSet[0])
124 for _, cseq := range ent.CompactSequences {
125 if cseq.Name == *ref || *ref == "" {
126 refseq = cseq.TileSequences
129 for _, cg := range ent.CompactGenomes {
130 cgnames = append(cgnames, cg.Name)
132 for _, tv := range ent.TileVariants {
134 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
144 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
148 err = fmt.Errorf("tagset not found")
151 sort.Strings(cgnames)
154 labelsFilename := *outputDir + "/labels.csv"
155 log.Infof("writing labels to %s", labelsFilename)
157 f, err = os.Create(labelsFilename)
162 for i, name := range cgnames {
163 _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
165 err = fmt.Errorf("write %s: %w", labelsFilename, err)
171 err = fmt.Errorf("close %s: %w", labelsFilename, err)
176 log.Info("indexing reference tiles")
177 type reftileinfo struct {
178 variant tileVariantID
179 seqname string // chr1
180 pos int // distance from start of chr1 to start of tile
181 tiledata []byte // acgtggcaa...
183 reftile := map[tagID]*reftileinfo{}
184 for seqname, cseq := range refseq {
185 for _, libref := range cseq {
186 reftile[libref.Tag] = &reftileinfo{
188 variant: libref.Variant,
189 tiledata: reftiledata[libref],
194 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
195 log.Info("reconstructing reference sequences")
196 for seqname, cseq := range refseq {
197 seqname, cseq := seqname, cseq
198 throttleCPU.Go(func() error {
199 defer log.Printf("... %s done", seqname)
201 for _, libref := range cseq {
202 rt := reftile[libref.Tag]
204 if len(rt.tiledata) == 0 {
205 return fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
207 pos += len(rt.tiledata) - taglen
214 log.Info("TODO: determining which tiles intersect given regions")
216 throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
217 throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
218 log.Info("generating annotations and numpy matrix for each slice")
220 for infileIdx, infile := range infiles {
221 infileIdx, infile := infileIdx, infile
222 throttleMem.Go(func() error {
223 seq := make(map[tagID][]TileVariant, 50000)
224 cgs := make(map[string]CompactGenome, len(cgnames))
225 f, err := open(infile)
230 log.Infof("%04d: reading %s", infileIdx, infile)
231 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
232 for _, tv := range ent.TileVariants {
236 variants := seq[tv.Tag]
237 if len(variants) == 0 {
238 variants = make([]TileVariant, 100)
240 for len(variants) <= int(tv.Variant) {
241 variants = append(variants, TileVariant{})
243 variants[int(tv.Variant)] = tv
244 seq[tv.Tag] = variants
246 for _, cg := range ent.CompactGenomes {
254 tagstart := cgs[cgnames[0]].StartTag
255 tagend := cgs[cgnames[0]].EndTag
259 log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
260 variantRemap := make([][]tileVariantID, tagend-tagstart)
261 throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
262 for tag, variants := range seq {
263 tag, variants := tag, variants
264 throttleCPU.Acquire()
266 defer throttleCPU.Release()
267 count := make(map[[blake2b.Size256]byte]int, len(variants))
268 for _, cg := range cgs {
269 idx := (tag - tagstart) * 2
270 if int(idx) < len(cg.Variants) {
271 count[variants[cg.Variants[idx]].Blake2b]++
272 count[variants[cg.Variants[idx+1]].Blake2b]++
275 // hash[i] will be the hash of
276 // the variant(s) that should
277 // be at rank i (0-based).
278 hash := make([][blake2b.Size256]byte, 0, len(count))
279 for b := range count {
280 hash = append(hash, b)
282 sort.Slice(hash, func(i, j int) bool {
283 bi, bj := &hash[i], &hash[j]
284 if ci, cj := count[*bi], count[*bj]; ci != cj {
287 return bytes.Compare((*bi)[:], (*bj)[:]) < 0
290 // rank[b] will be the 1-based
291 // new variant number for
292 // variants whose hash is b.
293 rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
294 for i, h := range hash {
295 rank[h] = tileVariantID(i + 1)
297 // remap[v] will be the new
298 // variant number for original
300 remap := make([]tileVariantID, len(variants))
301 for i, tv := range variants {
302 remap[i] = rank[tv.Blake2b]
304 variantRemap[tag-tagstart] = remap
309 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
310 log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
311 annof, err := os.Create(annotationsFilename)
315 annow := bufio.NewWriterSize(annof, 1<<20)
316 for tag, variants := range seq {
317 rt, ok := reftile[tag]
319 // Reference does not use any
320 // variant of this tile.
321 // TODO: log this? mention it
325 outcol := tag - tagID(tagstart)
326 reftilestr := strings.ToUpper(string(rt.tiledata))
327 remap := variantRemap[tag-tagstart]
328 for v, tv := range variants {
329 if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
332 if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
335 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
336 for _, diff := range diffs {
337 diff.Position += rt.pos
338 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, remap[v], rt.seqname, diff.String())
351 throttleNumpyMem.Acquire()
352 log.Infof("%04d: preparing numpy", infileIdx)
354 cols := 2 * int(tagend-tagstart)
355 out := make([]int16, rows*cols)
356 for row, name := range cgnames {
357 out := out[row*cols:]
358 for col, v := range cgs[name].Variants {
359 if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
360 out[col] = int16(variantRemap[col/2][v])
367 throttleNumpyMem.Release()
369 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
370 output, err := os.Create(fnm)
375 bufw := bufio.NewWriterSize(output, 1<<26)
376 npw, err := gonpy.NewWriter(nopCloser{bufw})
380 log.WithFields(logrus.Fields{
384 }).Infof("%04d: writing numpy", infileIdx)
385 npw.Shape = []int{rows, cols}
395 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
399 if err = throttleMem.Wait(); err != nil {