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 chromosome to starttag
 196                 tiledata []byte // acgtggcaa...
 197         }
 198         isdup := map[tagID]bool{}
 199         reftile := map[tagID]*reftileinfo{}
 200         for seqname, cseq := range refseq {
 201                 pos := 0
 202                 for _, libref := range cseq {
 203                         tiledata := reftiledata[libref]
 204                         if len(tiledata) == 0 {
 205                                 err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 206                                 return 1
 207                         }
 208                         if isdup[libref.Tag] {
 209                                 log.Printf("dropping reference tile %+v from %s, tag not unique", libref, seqname)
 210                         } else if reftile[libref.Tag] != nil {
 211                                 log.Printf("dropping reference tile %+v from %s, tag not unique", tileLibRef{Tag: libref.Tag, Variant: reftile[libref.Tag].variant}, reftile[libref.Tag].seqname)
 212                                 delete(reftile, libref.Tag)
 213                                 log.Printf("dropping reference tile %+v from %s, tag not unique", libref, seqname)
 214                                 isdup[libref.Tag] = true
 215                         } else {
 216                                 reftile[libref.Tag] = &reftileinfo{
 217                                         seqname:  seqname,
 218                                         variant:  libref.Variant,
 219                                         tiledata: tiledata,
 220                                         pos:      pos,
 221                                 }
 222                         }
 223                         pos += len(tiledata) - taglen
 224                 }
 225                 log.Printf("... %s done, len %d", seqname, pos+taglen)
 226         }
 227
 228         var mask *mask
 229         if *regionsFilename != "" {
 230                 log.Printf("loading regions from %s", *regionsFilename)
 231                 mask, err = makeMask(*regionsFilename, *expandRegions)
 232                 if err != nil {
 233                         return 1
 234                 }
 235                 log.Printf("before applying mask, len(reftile) == %d", len(reftile))
 236                 log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
 237                 for tag, rt := range reftile {
 238                         if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
 239                                 delete(reftile, tag)
 240                         }
 241                 }
 242                 log.Printf("after applying mask, len(reftile) == %d", len(reftile))
 243         }
 244
 245         var toMerge [][]int16
 246         if *mergeOutput {
 247                 toMerge = make([][]int16, len(infiles))
 248         }
 249
 250         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 251         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 252         log.Info("generating annotations and numpy matrix for each slice")
 253         var done int64
 254         for infileIdx, infile := range infiles {
 255                 infileIdx, infile := infileIdx, infile
 256                 throttleMem.Go(func() error {
 257                         seq := make(map[tagID][]TileVariant, 50000)
 258                         cgs := make(map[string]CompactGenome, len(cgnames))
 259                         f, err := open(infile)
 260                         if err != nil {
 261                                 return err
 262                         }
 263                         defer f.Close()
 264                         log.Infof("%04d: reading %s", infileIdx, infile)
 265                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 266                                 for _, tv := range ent.TileVariants {
 267                                         if tv.Ref {
 268                                                 continue
 269                                         }
 270                                         if mask != nil && reftile[tv.Tag] == nil {
 271                                                 // Don't waste
 272                                                 // time/memory on
 273                                                 // masked-out tiles.
 274                                                 continue
 275                                         }
 276                                         variants := seq[tv.Tag]
 277                                         if len(variants) == 0 {
 278                                                 variants = make([]TileVariant, 100)
 279                                         }
 280                                         for len(variants) <= int(tv.Variant) {
 281                                                 variants = append(variants, TileVariant{})
 282                                         }
 283                                         variants[int(tv.Variant)] = tv
 284                                         seq[tv.Tag] = variants
 285                                 }
 286                                 for _, cg := range ent.CompactGenomes {
 287                                         if matchGenome.MatchString(cg.Name) {
 288                                                 cgs[cg.Name] = cg
 289                                         }
 290                                 }
 291                                 return nil
 292                         })
 293                         if err != nil {
 294                                 return err
 295                         }
 296                         tagstart := cgs[cgnames[0]].StartTag
 297                         tagend := cgs[cgnames[0]].EndTag
 298
 299                         // TODO: filters
 300
 301                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 302                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 303                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 304                         for tag, variants := range seq {
 305                                 tag, variants := tag, variants
 306                                 throttleCPU.Acquire()
 307                                 go func() {
 308                                         defer throttleCPU.Release()
 309                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 310                                         for _, cg := range cgs {
 311                                                 idx := int(tag-tagstart) * 2
 312                                                 if idx < len(cg.Variants) {
 313                                                         for allele := 0; allele < 2; allele++ {
 314                                                                 v := cg.Variants[idx+allele]
 315                                                                 if v > 0 && len(variants[v].Sequence) > 0 {
 316                                                                         count[variants[v].Blake2b]++
 317                                                                 }
 318                                                         }
 319                                                 }
 320                                         }
 321                                         // hash[i] will be the hash of
 322                                         // the variant(s) that should
 323                                         // be at rank i (0-based).
 324                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 325                                         for b := range count {
 326                                                 hash = append(hash, b)
 327                                         }
 328                                         sort.Slice(hash, func(i, j int) bool {
 329                                                 bi, bj := &hash[i], &hash[j]
 330                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 331                                                         return ci > cj
 332                                                 } else {
 333                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 334                                                 }
 335                                         })
 336                                         // rank[b] will be the 1-based
 337                                         // new variant number for
 338                                         // variants whose hash is b.
 339                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 340                                         for i, h := range hash {
 341                                                 rank[h] = tileVariantID(i + 1)
 342                                         }
 343                                         // remap[v] will be the new
 344                                         // variant number for original
 345                                         // variant number v.
 346                                         remap := make([]tileVariantID, len(variants))
 347                                         for i, tv := range variants {
 348                                                 remap[i] = rank[tv.Blake2b]
 349                                         }
 350                                         variantRemap[tag-tagstart] = remap
 351                                 }()
 352                         }
 353                         throttleCPU.Wait()
 354
 355                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 356                         log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 357                         annof, err := os.Create(annotationsFilename)
 358                         if err != nil {
 359                                 return err
 360                         }
 361                         annow := bufio.NewWriterSize(annof, 1<<20)
 362                         outcol := 0
 363                         for tag := tagstart; tag < tagend; tag++ {
 364                                 rt, ok := reftile[tag]
 365                                 if !ok {
 366                                         if mask == nil {
 367                                                 outcol++
 368                                         }
 369                                         // Excluded by specified
 370                                         // regions, or reference does
 371                                         // not use any variant of this
 372                                         // tile. (TODO: log this?
 373                                         // mention it in annotations?)
 374                                         continue
 375                                 }
 376                                 variants, ok := seq[tag]
 377                                 if !ok {
 378                                         outcol++
 379                                         continue
 380                                 }
 381                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 382                                 remap := variantRemap[tag-tagstart]
 383                                 done := make([]bool, len(variants))
 384                                 for v, tv := range variants {
 385                                         v := remap[v]
 386                                         if done[v] {
 387                                                 continue
 388                                         } else {
 389                                                 done[v] = true
 390                                         }
 391                                         if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 392                                                 continue
 393                                         }
 394                                         if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 395                                                 continue
 396                                         }
 397                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 398                                         for _, diff := range diffs {
 399                                                 diff.Position += rt.pos
 400                                                 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)
 401                                         }
 402                                 }
 403                                 outcol++
 404                         }
 405                         err = annow.Flush()
 406                         if err != nil {
 407                                 return err
 408                         }
 409                         err = annof.Close()
 410                         if err != nil {
 411                                 return err
 412                         }
 413
 414                         log.Infof("%04d: preparing numpy", infileIdx)
 415                         throttleNumpyMem.Acquire()
 416                         rows := len(cgnames)
 417                         cols := 2 * outcol
 418                         out := make([]int16, rows*cols)
 419                         for row, name := range cgnames {
 420                                 out := out[row*cols:]
 421                                 outcol := 0
 422                                 for col, v := range cgs[name].Variants {
 423                                         tag := tagstart + tagID(col/2)
 424                                         if mask != nil && reftile[tag] == nil {
 425                                                 continue
 426                                         }
 427                                         if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
 428                                                 out[outcol] = int16(variantRemap[tag-tagstart][v])
 429                                         } else {
 430                                                 out[outcol] = -1
 431                                         }
 432                                         outcol++
 433                                 }
 434                         }
 435                         seq = nil
 436                         throttleNumpyMem.Release()
 437
 438                         if *mergeOutput {
 439                                 log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
 440                                 toMerge[infileIdx] = out
 441                         } else {
 442                                 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 443                                 err = writeNumpyInt16(fnm, out, rows, cols)
 444                                 if err != nil {
 445                                         return err
 446                                 }
 447                         }
 448                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 449                         return nil
 450                 })
 451         }
 452         if err = throttleMem.Wait(); err != nil {
 453                 return 1
 454         }
 455         if *mergeOutput {
 456                 log.Info("merging output matrix and annotations")
 457
 458                 annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
 459                 annof, err := os.Create(annoFilename)
 460                 if err != nil {
 461                         return 1
 462                 }
 463                 annow := bufio.NewWriterSize(annof, 1<<20)
 464
 465                 rows := len(cgnames)
 466                 cols := 0
 467                 for _, chunk := range toMerge {
 468                         cols += len(chunk) / rows
 469                 }
 470                 out := make([]int16, rows*cols)
 471                 startcol := 0
 472                 for outIdx, chunk := range toMerge {
 473                         chunkcols := len(chunk) / rows
 474                         for row := 0; row < rows; row++ {
 475                                 copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
 476                         }
 477                         toMerge[outIdx] = nil
 478
 479                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
 480                         log.Infof("reading %s", annotationsFilename)
 481                         buf, err := os.ReadFile(annotationsFilename)
 482                         if err != nil {
 483                                 return 1
 484                         }
 485                         err = os.Remove(annotationsFilename)
 486                         if err != nil {
 487                                 return 1
 488                         }
 489                         for _, line := range bytes.Split(buf, []byte{'\n'}) {
 490                                 if len(line) == 0 {
 491                                         continue
 492                                 }
 493                                 fields := bytes.SplitN(line, []byte{','}, 3)
 494                                 incol, _ := strconv.Atoi(string(fields[1]))
 495                                 fmt.Fprintf(annow, "%s,%d,%s\n", fields[0], incol+startcol/2, fields[2])
 496                         }
 497
 498                         startcol += chunkcols
 499                 }
 500                 err = annow.Flush()
 501                 if err != nil {
 502                         return 1
 503                 }
 504                 err = annof.Close()
 505                 if err != nil {
 506                         return 1
 507                 }
 508                 err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
 509                 if err != nil {
 510                         return 1
 511                 }
 512         }
 513         return 0
 514 }
 515
 516 func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
 517         output, err := os.Create(fnm)
 518         if err != nil {
 519                 return err
 520         }
 521         defer output.Close()
 522         bufw := bufio.NewWriterSize(output, 1<<26)
 523         npw, err := gonpy.NewWriter(nopCloser{bufw})
 524         if err != nil {
 525                 return err
 526         }
 527         log.WithFields(log.Fields{
 528                 "filename": fnm,
 529                 "rows":     rows,
 530                 "cols":     cols,
 531         }).Infof("writing numpy: %s", fnm)
 532         npw.Shape = []int{rows, cols}
 533         npw.WriteInt16(out)
 534         err = bufw.Flush()
 535         if err != nil {
 536                 return err
 537         }
 538         return output.Close()
 539 }