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         "strconv"
  20         "strings"
  21         "sync/atomic"
  22
  23         "git.arvados.org/arvados.git/sdk/go/arvados"
  24         "github.com/arvados/lightning/hgvs"
  25         "github.com/kshedden/gonpy"
  26         log "github.com/sirupsen/logrus"
  27         "golang.org/x/crypto/blake2b"
  28 )
  29
  30 type sliceNumpy struct {
  31         filter  filter
  32         threads int
  33 }
  34
  35 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  36         var err error
  37         defer func() {
  38                 if err != nil {
  39                         fmt.Fprintf(stderr, "%s\n", err)
  40                 }
  41         }()
  42         flags := flag.NewFlagSet("", flag.ContinueOnError)
  43         flags.SetOutput(stderr)
  44         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  45         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  46         projectUUID := flags.String("project", "", "project `UUID` for output data")
  47         priority := flags.Int("priority", 500, "container request priority")
  48         inputDir := flags.String("input-dir", "./in", "input `directory`")
  49         outputDir := flags.String("output-dir", "./out", "output `directory`")
  50         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  51         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  52         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  53         mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
  54         flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
  55         cmd.filter.Flags(flags)
  56         err = flags.Parse(args)
  57         if err == flag.ErrHelp {
  58                 err = nil
  59                 return 0
  60         } else if err != nil {
  61                 return 2
  62         }
  63
  64         if *pprof != "" {
  65                 go func() {
  66                         log.Println(http.ListenAndServe(*pprof, nil))
  67                 }()
  68         }
  69
  70         if !*runlocal {
  71                 runner := arvadosContainerRunner{
  72                         Name:        "lightning slice-numpy",
  73                         Client:      arvados.NewClientFromEnv(),
  74                         ProjectUUID: *projectUUID,
  75                         RAM:         650000000000,
  76                         VCPUs:       96,
  77                         Priority:    *priority,
  78                         KeepCache:   2,
  79                         APIAccess:   true,
  80                 }
  81                 err = runner.TranslatePaths(inputDir, regionsFilename)
  82                 if err != nil {
  83                         return 1
  84                 }
  85                 runner.Args = []string{"slice-numpy", "-local=true",
  86                         "-pprof=:6060",
  87                         "-input-dir=" + *inputDir,
  88                         "-output-dir=/mnt/output",
  89                         "-threads=" + fmt.Sprintf("%d", cmd.threads),
  90                         "-regions=" + *regionsFilename,
  91                         "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
  92                         "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
  93                 }
  94                 runner.Args = append(runner.Args, cmd.filter.Args()...)
  95                 var output string
  96                 output, err = runner.Run()
  97                 if err != nil {
  98                         return 1
  99                 }
 100                 fmt.Fprintln(stdout, output)
 101                 return 0
 102         }
 103
 104         infiles, err := allGobFiles(*inputDir)
 105         if err != nil {
 106                 return 1
 107         }
 108         if len(infiles) == 0 {
 109                 err = fmt.Errorf("no input files found in %s", *inputDir)
 110                 return 1
 111         }
 112         sort.Strings(infiles)
 113
 114         var cgnames []string
 115         var refseq map[string][]tileLibRef
 116         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 117         in0, err := open(infiles[0])
 118         if err != nil {
 119                 return 1
 120         }
 121
 122         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 123         if err != nil {
 124                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 125                 return 1
 126         }
 127
 128         taglen := -1
 129         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 130                 if len(ent.TagSet) > 0 {
 131                         taglen = len(ent.TagSet[0])
 132                 }
 133                 for _, cseq := range ent.CompactSequences {
 134                         if cseq.Name == *ref || *ref == "" {
 135                                 refseq = cseq.TileSequences
 136                         }
 137                 }
 138                 for _, cg := range ent.CompactGenomes {
 139                         if matchGenome.MatchString(cg.Name) {
 140                                 cgnames = append(cgnames, cg.Name)
 141                         }
 142                 }
 143                 for _, tv := range ent.TileVariants {
 144                         if tv.Ref {
 145                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 146                         }
 147                 }
 148                 return nil
 149         })
 150         if err != nil {
 151                 return 1
 152         }
 153         in0.Close()
 154         if refseq == nil {
 155                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 156                 return 1
 157         }
 158         if taglen < 0 {
 159                 err = fmt.Errorf("tagset not found")
 160                 return 1
 161         }
 162         if len(cgnames) == 0 {
 163                 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
 164                 return 1
 165         }
 166         sort.Strings(cgnames)
 167
 168         {
 169                 labelsFilename := *outputDir + "/labels.csv"
 170                 log.Infof("writing labels to %s", labelsFilename)
 171                 var f *os.File
 172                 f, err = os.Create(labelsFilename)
 173                 if err != nil {
 174                         return 1
 175                 }
 176                 defer f.Close()
 177                 for i, name := range cgnames {
 178                         _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
 179                         if err != nil {
 180                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 181                                 return 1
 182                         }
 183                 }
 184                 err = f.Close()
 185                 if err != nil {
 186                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 187                         return 1
 188                 }
 189         }
 190
 191         log.Info("indexing reference tiles")
 192         type reftileinfo struct {
 193                 variant  tileVariantID
 194                 seqname  string // chr1
 195                 pos      int    // distance from start of chr1 to start of tile
 196                 tiledata []byte // acgtggcaa...
 197         }
 198         reftile := map[tagID]*reftileinfo{}
 199         for seqname, cseq := range refseq {
 200                 for _, libref := range cseq {
 201                         reftile[libref.Tag] = &reftileinfo{
 202                                 seqname:  seqname,
 203                                 variant:  libref.Variant,
 204                                 tiledata: reftiledata[libref],
 205                         }
 206                 }
 207         }
 208
 209         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 210         log.Info("reconstructing reference sequences")
 211         for seqname, cseq := range refseq {
 212                 seqname, cseq := seqname, cseq
 213                 throttleCPU.Go(func() error {
 214                         defer log.Printf("... %s done", seqname)
 215                         pos := 0
 216                         for _, libref := range cseq {
 217                                 rt := reftile[libref.Tag]
 218                                 rt.pos = pos
 219                                 if len(rt.tiledata) == 0 {
 220                                         return fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 221                                 }
 222                                 pos += len(rt.tiledata) - taglen
 223                         }
 224                         return nil
 225                 })
 226         }
 227         throttleCPU.Wait()
 228
 229         var mask *mask
 230         if *regionsFilename != "" {
 231                 mask, err = makeMask(*regionsFilename, *expandRegions)
 232                 if err != nil {
 233                         return 1
 234                 }
 235                 // Delete reftile entries for masked-out regions.
 236                 for tag, rt := range reftile {
 237                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 238                                 delete(reftile, tag)
 239                         }
 240                 }
 241         }
 242
 243         var toMerge [][]int16
 244         if *mergeOutput {
 245                 toMerge = make([][]int16, len(infiles))
 246         }
 247
 248         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 249         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 250         log.Info("generating annotations and numpy matrix for each slice")
 251         var done int64
 252         for infileIdx, infile := range infiles {
 253                 infileIdx, infile := infileIdx, infile
 254                 throttleMem.Go(func() error {
 255                         seq := make(map[tagID][]TileVariant, 50000)
 256                         cgs := make(map[string]CompactGenome, len(cgnames))
 257                         f, err := open(infile)
 258                         if err != nil {
 259                                 return err
 260                         }
 261                         defer f.Close()
 262                         log.Infof("%04d: reading %s", infileIdx, infile)
 263                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 264                                 for _, tv := range ent.TileVariants {
 265                                         if tv.Ref {
 266                                                 continue
 267                                         }
 268                                         if mask != nil && reftile[tv.Tag] == nil {
 269                                                 // Don't waste
 270                                                 // time/memory on
 271                                                 // masked-out tiles.
 272                                                 continue
 273                                         }
 274                                         variants := seq[tv.Tag]
 275                                         if len(variants) == 0 {
 276                                                 variants = make([]TileVariant, 100)
 277                                         }
 278                                         for len(variants) <= int(tv.Variant) {
 279                                                 variants = append(variants, TileVariant{})
 280                                         }
 281                                         variants[int(tv.Variant)] = tv
 282                                         seq[tv.Tag] = variants
 283                                 }
 284                                 for _, cg := range ent.CompactGenomes {
 285                                         if matchGenome.MatchString(cg.Name) {
 286                                                 cgs[cg.Name] = cg
 287                                         }
 288                                 }
 289                                 return nil
 290                         })
 291                         if err != nil {
 292                                 return err
 293                         }
 294                         tagstart := cgs[cgnames[0]].StartTag
 295                         tagend := cgs[cgnames[0]].EndTag
 296
 297                         // TODO: filters
 298
 299                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 300                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 301                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 302                         for tag, variants := range seq {
 303                                 tag, variants := tag, variants
 304                                 throttleCPU.Acquire()
 305                                 go func() {
 306                                         defer throttleCPU.Release()
 307                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 308                                         for _, cg := range cgs {
 309                                                 idx := int(tag-tagstart) * 2
 310                                                 if idx < len(cg.Variants) {
 311                                                         for allele := 0; allele < 2; allele++ {
 312                                                                 v := cg.Variants[idx+allele]
 313                                                                 if v > 0 && len(variants[v].Sequence) > 0 {
 314                                                                         count[variants[v].Blake2b]++
 315                                                                 }
 316                                                         }
 317                                                 }
 318                                         }
 319                                         // hash[i] will be the hash of
 320                                         // the variant(s) that should
 321                                         // be at rank i (0-based).
 322                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 323                                         for b := range count {
 324                                                 hash = append(hash, b)
 325                                         }
 326                                         sort.Slice(hash, func(i, j int) bool {
 327                                                 bi, bj := &hash[i], &hash[j]
 328                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 329                                                         return ci > cj
 330                                                 } else {
 331                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 332                                                 }
 333                                         })
 334                                         // rank[b] will be the 1-based
 335                                         // new variant number for
 336                                         // variants whose hash is b.
 337                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 338                                         for i, h := range hash {
 339                                                 rank[h] = tileVariantID(i + 1)
 340                                         }
 341                                         // remap[v] will be the new
 342                                         // variant number for original
 343                                         // variant number v.
 344                                         remap := make([]tileVariantID, len(variants))
 345                                         for i, tv := range variants {
 346                                                 remap[i] = rank[tv.Blake2b]
 347                                         }
 348                                         variantRemap[tag-tagstart] = remap
 349                                 }()
 350                         }
 351                         throttleCPU.Wait()
 352
 353                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 354                         log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 355                         annof, err := os.Create(annotationsFilename)
 356                         if err != nil {
 357                                 return err
 358                         }
 359                         annow := bufio.NewWriterSize(annof, 1<<20)
 360                         outcol := 0
 361                         for tag := tagstart; tag < tagend; tag++ {
 362                                 rt, ok := reftile[tag]
 363                                 if !ok {
 364                                         if mask == nil {
 365                                                 outcol++
 366                                         }
 367                                         // Excluded by specified
 368                                         // regions, or reference does
 369                                         // not use any variant of this
 370                                         // tile. (TODO: log this?
 371                                         // mention it in annotations?)
 372                                         continue
 373                                 }
 374                                 variants, ok := seq[tag]
 375                                 if !ok {
 376                                         outcol++
 377                                         continue
 378                                 }
 379                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 380                                 remap := variantRemap[tag-tagstart]
 381                                 done := make([]bool, len(variants))
 382                                 for v, tv := range variants {
 383                                         v := remap[v]
 384                                         if done[v] {
 385                                                 continue
 386                                         } else {
 387                                                 done[v] = true
 388                                         }
 389                                         if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 390                                                 continue
 391                                         }
 392                                         if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 393                                                 continue
 394                                         }
 395                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 396                                         for _, diff := range diffs {
 397                                                 diff.Position += rt.pos
 398                                                 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)
 399                                         }
 400                                 }
 401                                 outcol++
 402                         }
 403                         err = annow.Flush()
 404                         if err != nil {
 405                                 return err
 406                         }
 407                         err = annof.Close()
 408                         if err != nil {
 409                                 return err
 410                         }
 411
 412                         log.Infof("%04d: preparing numpy", infileIdx)
 413                         throttleNumpyMem.Acquire()
 414                         rows := len(cgnames)
 415                         cols := 2 * outcol
 416                         out := make([]int16, rows*cols)
 417                         for row, name := range cgnames {
 418                                 out := out[row*cols:]
 419                                 outcol := 0
 420                                 for col, v := range cgs[name].Variants {
 421                                         tag := tagstart + tagID(col/2)
 422                                         if mask != nil && reftile[tag] == nil {
 423                                                 continue
 424                                         }
 425                                         if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
 426                                                 out[outcol] = int16(variantRemap[tag-tagstart][v])
 427                                         } else {
 428                                                 out[outcol] = -1
 429                                         }
 430                                         outcol++
 431                                 }
 432                         }
 433                         seq = nil
 434                         throttleNumpyMem.Release()
 435
 436                         if *mergeOutput {
 437                                 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 438                                 toMerge[infileIdx] = out
 439                         } else {
 440                                 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 441                                 err = writeNumpyInt16(fnm, out, rows, cols)
 442                                 if err != nil {
 443                                         return err
 444                                 }
 445                         }
 446                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 447                         return nil
 448                 })
 449         }
 450         if err = throttleMem.Wait(); err != nil {
 451                 return 1
 452         }
 453         if *mergeOutput {
 454                 log.Info("merging output matrix and annotations")
 455
 456                 annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 457                 annof, err := os.Create(annoFilename)
 458                 if err != nil {
 459                         return 1
 460                 }
 461                 annow := bufio.NewWriterSize(annof, 1<<20)
 462
 463                 rows := len(cgnames)
 464                 cols := 0
 465                 for _, chunk := range toMerge {
 466                         cols += len(chunk) / rows
 467                 }
 468                 out := make([]int16, rows*cols)
 469                 startcol := 0
 470                 for outIdx, chunk := range toMerge {
 471                         chunkcols := len(chunk) / rows
 472                         for row := 0; row < rows; row++ {
 473                                 copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
 474                         }
 475                         toMerge[outIdx] = nil
 476
 477                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
 478                         log.Infof("reading %s", annotationsFilename)
 479                         buf, err := os.ReadFile(annotationsFilename)
 480                         if err != nil {
 481                                 return 1
 482                         }
 483                         err = os.Remove(annotationsFilename)
 484                         if err != nil {
 485                                 return 1
 486                         }
 487                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
 488                                 if len(line) == 0 {
 489                                         continue
 490                                 }
 491                                 fields := bytes.SplitN(line, []byte{','}, 3)
 492                                 incol, _ := strconv.Atoi(string(fields[1]))
 493                                 fmt.Fprintf(annow, "%s,%d,%s\n", fields[0], incol+startcol/2, fields[2])
 494                         }
 495
 496                         startcol += chunkcols
 497                 }
 498                 err = annow.Flush()
 499                 if err != nil {
 500                         return 1
 501                 }
 502                 err = annof.Close()
 503                 if err != nil {
 504                         return 1
 505                 }
 506                 err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
 507                 if err != nil {
 508                         return 1
 509                 }
 510         }
 511         return 0
 512 }
 513
 514 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
 515         output, err := os.Create(fnm)
 516         if err != nil {
 517                 return err
 518         }
 519         defer output.Close()
 520         bufw := bufio.NewWriterSize(output, 1<<26)
 521         npw, err := gonpy.NewWriter(nopCloser{bufw})
 522         if err != nil {
 523                 return err
 524         }
 525         log.WithFields(log.Fields{
 526                 "filename": fnm,
 527                 "rows":     rows,
 528                 "cols":     cols,
 529         }).Infof("writing numpy: %s", fnm)
 530         npw.Shape = []int{rows, cols}
 531         npw.WriteInt16(out)
 532         err = bufw.Flush()
 533         if err != nil {
 534                 return err
 535         }
 536         return output.Close()
 537 }