slicenumpy.go

   1 // Copyright (C) The Lightning Authors. All rights reserved.
   2 //
   3 // SPDX-License-Identifier: AGPL-3.0
   4
   5 package lightning
   6
   7 import (
   8         "bufio"
   9         "bytes"
  10         "flag"
  11         "fmt"
  12         "io"
  13         "net/http"
  14         _ "net/http/pprof"
  15         "os"
  16         "regexp"
  17         "runtime"
  18         "sort"
  19         "strings"
  20         "sync/atomic"
  21
  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"
  27 )
  28
  29 type sliceNumpy struct {
  30         filter  filter
  31         threads int
  32 }
  33
  34 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  35         var err error
  36         defer func() {
  37                 if err != nil {
  38                         fmt.Fprintf(stderr, "%s\n", err)
  39                 }
  40         }()
  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 {
  56                 err = nil
  57                 return 0
  58         } else if err != nil {
  59                 return 2
  60         }
  61
  62         if *pprof != "" {
  63                 go func() {
  64                         log.Println(http.ListenAndServe(*pprof, nil))
  65                 }()
  66         }
  67
  68         if !*runlocal {
  69                 runner := arvadosContainerRunner{
  70                         Name:        "lightning slice-numpy",
  71                         Client:      arvados.NewClientFromEnv(),
  72                         ProjectUUID: *projectUUID,
  73                         RAM:         650000000000,
  74                         VCPUs:       96,
  75                         Priority:    *priority,
  76                         KeepCache:   2,
  77                         APIAccess:   true,
  78                 }
  79                 err = runner.TranslatePaths(inputDir, regionsFilename)
  80                 if err != nil {
  81                         return 1
  82                 }
  83                 runner.Args = []string{"slice-numpy", "-local=true",
  84                         "-pprof=:6060",
  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),
  90                 }
  91                 runner.Args = append(runner.Args, cmd.filter.Args()...)
  92                 var output string
  93                 output, err = runner.Run()
  94                 if err != nil {
  95                         return 1
  96                 }
  97                 fmt.Fprintln(stdout, output)
  98                 return 0
  99         }
 100
 101         infiles, err := allGobFiles(*inputDir)
 102         if err != nil {
 103                 return 1
 104         }
 105         if len(infiles) == 0 {
 106                 err = fmt.Errorf("no input files found in %s", *inputDir)
 107                 return 1
 108         }
 109         sort.Strings(infiles)
 110
 111         var cgnames []string
 112         var refseq map[string][]tileLibRef
 113         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 114         in0, err := open(infiles[0])
 115         if err != nil {
 116                 return 1
 117         }
 118
 119         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 120         if err != nil {
 121                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 122                 return 1
 123         }
 124
 125         taglen := -1
 126         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 127                 if len(ent.TagSet) > 0 {
 128                         taglen = len(ent.TagSet[0])
 129                 }
 130                 for _, cseq := range ent.CompactSequences {
 131                         if cseq.Name == *ref || *ref == "" {
 132                                 refseq = cseq.TileSequences
 133                         }
 134                 }
 135                 for _, cg := range ent.CompactGenomes {
 136                         if matchGenome.MatchString(cg.Name) {
 137                                 cgnames = append(cgnames, cg.Name)
 138                         }
 139                 }
 140                 for _, tv := range ent.TileVariants {
 141                         if tv.Ref {
 142                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 143                         }
 144                 }
 145                 return nil
 146         })
 147         if err != nil {
 148                 return 1
 149         }
 150         in0.Close()
 151         if refseq == nil {
 152                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 153                 return 1
 154         }
 155         if taglen < 0 {
 156                 err = fmt.Errorf("tagset not found")
 157                 return 1
 158         }
 159         if len(cgnames) == 0 {
 160                 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
 161                 return 1
 162         }
 163         sort.Strings(cgnames)
 164
 165         {
 166                 labelsFilename := *outputDir + "/labels.csv"
 167                 log.Infof("writing labels to %s", labelsFilename)
 168                 var f *os.File
 169                 f, err = os.Create(labelsFilename)
 170                 if err != nil {
 171                         return 1
 172                 }
 173                 defer f.Close()
 174                 for i, name := range cgnames {
 175                         _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
 176                         if err != nil {
 177                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 178                                 return 1
 179                         }
 180                 }
 181                 err = f.Close()
 182                 if err != nil {
 183                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 184                         return 1
 185                 }
 186         }
 187
 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...
 194         }
 195         reftile := map[tagID]*reftileinfo{}
 196         for seqname, cseq := range refseq {
 197                 for _, libref := range cseq {
 198                         reftile[libref.Tag] = &reftileinfo{
 199                                 seqname:  seqname,
 200                                 variant:  libref.Variant,
 201                                 tiledata: reftiledata[libref],
 202                         }
 203                 }
 204         }
 205
 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)
 212                         pos := 0
 213                         for _, libref := range cseq {
 214                                 rt := reftile[libref.Tag]
 215                                 rt.pos = pos
 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)
 218                                 }
 219                                 pos += len(rt.tiledata) - taglen
 220                         }
 221                         return nil
 222                 })
 223         }
 224         throttleCPU.Wait()
 225
 226         var mask *mask
 227         if *regionsFilename != "" {
 228                 mask, err = makeMask(*regionsFilename, *expandRegions)
 229                 if err != nil {
 230                         return 1
 231                 }
 232                 // Delete reftile entries for masked-out regions.
 233                 for tag, rt := range reftile {
 234                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 235                                 delete(reftile, tag)
 236                         }
 237                 }
 238         }
 239
 240         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 241         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 242         log.Info("generating annotations and numpy matrix for each slice")
 243         var done int64
 244         for infileIdx, infile := range infiles {
 245                 infileIdx, infile := infileIdx, infile
 246                 throttleMem.Go(func() error {
 247                         seq := make(map[tagID][]TileVariant, 50000)
 248                         cgs := make(map[string]CompactGenome, len(cgnames))
 249                         f, err := open(infile)
 250                         if err != nil {
 251                                 return err
 252                         }
 253                         defer f.Close()
 254                         log.Infof("%04d: reading %s", infileIdx, infile)
 255                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 256                                 for _, tv := range ent.TileVariants {
 257                                         if tv.Ref {
 258                                                 continue
 259                                         }
 260                                         if mask != nil && reftile[tv.Tag] == nil {
 261                                                 // Don't waste
 262                                                 // time/memory on
 263                                                 // masked-out tiles.
 264                                                 continue
 265                                         }
 266                                         variants := seq[tv.Tag]
 267                                         if len(variants) == 0 {
 268                                                 variants = make([]TileVariant, 100)
 269                                         }
 270                                         for len(variants) <= int(tv.Variant) {
 271                                                 variants = append(variants, TileVariant{})
 272                                         }
 273                                         variants[int(tv.Variant)] = tv
 274                                         seq[tv.Tag] = variants
 275                                 }
 276                                 for _, cg := range ent.CompactGenomes {
 277                                         if matchGenome.MatchString(cg.Name) {
 278                                                 cgs[cg.Name] = cg
 279                                         }
 280                                 }
 281                                 return nil
 282                         })
 283                         if err != nil {
 284                                 return err
 285                         }
 286                         tagstart := cgs[cgnames[0]].StartTag
 287                         tagend := cgs[cgnames[0]].EndTag
 288
 289                         // TODO: filters
 290
 291                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 292                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 293                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 294                         for tag, variants := range seq {
 295                                 tag, variants := tag, variants
 296                                 throttleCPU.Acquire()
 297                                 go func() {
 298                                         defer throttleCPU.Release()
 299                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 300                                         for _, cg := range cgs {
 301                                                 idx := int(tag-tagstart) * 2
 302                                                 if idx < len(cg.Variants) {
 303                                                         for allele := 0; allele < 2; allele++ {
 304                                                                 v := cg.Variants[idx+allele]
 305                                                                 if v > 0 && len(variants[v].Sequence) > 0 {
 306                                                                         count[variants[v].Blake2b]++
 307                                                                 }
 308                                                         }
 309                                                 }
 310                                         }
 311                                         // hash[i] will be the hash of
 312                                         // the variant(s) that should
 313                                         // be at rank i (0-based).
 314                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 315                                         for b := range count {
 316                                                 hash = append(hash, b)
 317                                         }
 318                                         sort.Slice(hash, func(i, j int) bool {
 319                                                 bi, bj := &hash[i], &hash[j]
 320                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 321                                                         return ci > cj
 322                                                 } else {
 323                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 324                                                 }
 325                                         })
 326                                         // rank[b] will be the 1-based
 327                                         // new variant number for
 328                                         // variants whose hash is b.
 329                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 330                                         for i, h := range hash {
 331                                                 rank[h] = tileVariantID(i + 1)
 332                                         }
 333                                         // remap[v] will be the new
 334                                         // variant number for original
 335                                         // variant number v.
 336                                         remap := make([]tileVariantID, len(variants))
 337                                         for i, tv := range variants {
 338                                                 remap[i] = rank[tv.Blake2b]
 339                                         }
 340                                         variantRemap[tag-tagstart] = remap
 341                                 }()
 342                         }
 343                         throttleCPU.Wait()
 344
 345                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 346                         log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 347                         annof, err := os.Create(annotationsFilename)
 348                         if err != nil {
 349                                 return err
 350                         }
 351                         annow := bufio.NewWriterSize(annof, 1<<20)
 352                         outcol := 0
 353                         for tag := tagstart; tag < tagend; tag++ {
 354                                 rt, ok := reftile[tag]
 355                                 if !ok {
 356                                         if mask == nil {
 357                                                 outcol++
 358                                         }
 359                                         // Excluded by specified
 360                                         // regions, or reference does
 361                                         // not use any variant of this
 362                                         // tile. (TODO: log this?
 363                                         // mention it in annotations?)
 364                                         continue
 365                                 }
 366                                 variants, ok := seq[tag]
 367                                 if !ok {
 368                                         outcol++
 369                                         continue
 370                                 }
 371                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 372                                 remap := variantRemap[tag-tagstart]
 373                                 done := make([]bool, len(variants))
 374                                 for v, tv := range variants {
 375                                         v := remap[v]
 376                                         if done[v] {
 377                                                 continue
 378                                         } else {
 379                                                 done[v] = true
 380                                         }
 381                                         if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 382                                                 continue
 383                                         }
 384                                         if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 385                                                 continue
 386                                         }
 387                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 388                                         for _, diff := range diffs {
 389                                                 diff.Position += rt.pos
 390                                                 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)
 391                                         }
 392                                 }
 393                                 outcol++
 394                         }
 395                         err = annow.Flush()
 396                         if err != nil {
 397                                 return err
 398                         }
 399                         err = annof.Close()
 400                         if err != nil {
 401                                 return err
 402                         }
 403
 404                         log.Infof("%04d: preparing numpy", infileIdx)
 405                         throttleNumpyMem.Acquire()
 406                         rows := len(cgnames)
 407                         cols := 2 * outcol
 408                         out := make([]int16, rows*cols)
 409                         for row, name := range cgnames {
 410                                 out := out[row*cols:]
 411                                 outcol := 0
 412                                 for col, v := range cgs[name].Variants {
 413                                         tag := tagstart + tagID(col/2)
 414                                         if mask != nil && reftile[tag] == nil {
 415                                                 continue
 416                                         }
 417                                         if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
 418                                                 out[outcol] = int16(variantRemap[tag-tagstart][v])
 419                                         } else {
 420                                                 out[outcol] = -1
 421                                         }
 422                                         outcol++
 423                                 }
 424                         }
 425                         seq = nil
 426                         throttleNumpyMem.Release()
 427
 428                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 429                         output, err := os.Create(fnm)
 430                         if err != nil {
 431                                 return err
 432                         }
 433                         defer output.Close()
 434                         bufw := bufio.NewWriterSize(output, 1<<26)
 435                         npw, err := gonpy.NewWriter(nopCloser{bufw})
 436                         if err != nil {
 437                                 return err
 438                         }
 439                         log.WithFields(log.Fields{
 440                                 "filename": fnm,
 441                                 "rows":     rows,
 442                                 "cols":     cols,
 443                         }).Infof("%04d: writing numpy", infileIdx)
 444                         npw.Shape = []int{rows, cols}
 445                         npw.WriteInt16(out)
 446                         err = bufw.Flush()
 447                         if err != nil {
 448                                 return err
 449                         }
 450                         err = output.Close()
 451                         if err != nil {
 452                                 return err
 453                         }
 454                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 455                         return nil
 456                 })
 457         }
 458         if err = throttleMem.Wait(); err != nil {
 459                 return 1
 460         }
 461         return 0
 462 }