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         "github.com/sirupsen/logrus"
  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         flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
  54         cmd.filter.Flags(flags)
  55         err = flags.Parse(args)
  56         if err == flag.ErrHelp {
  57                 err = nil
  58                 return 0
  59         } else if err != nil {
  60                 return 2
  61         }
  62
  63         if *pprof != "" {
  64                 go func() {
  65                         log.Println(http.ListenAndServe(*pprof, nil))
  66                 }()
  67         }
  68
  69         if !*runlocal {
  70                 runner := arvadosContainerRunner{
  71                         Name:        "lightning slice-numpy",
  72                         Client:      arvados.NewClientFromEnv(),
  73                         ProjectUUID: *projectUUID,
  74                         RAM:         240000000000,
  75                         VCPUs:       64,
  76                         Priority:    *priority,
  77                         KeepCache:   2,
  78                         APIAccess:   true,
  79                 }
  80                 err = runner.TranslatePaths(inputDir, regionsFilename)
  81                 if err != nil {
  82                         return 1
  83                 }
  84                 runner.Args = []string{"slice-numpy", "-local=true",
  85                         "-pprof", ":6060",
  86                         "-input-dir", *inputDir,
  87                         "-output-dir", "/mnt/output",
  88                         "-threads", fmt.Sprintf("%d", cmd.threads),
  89                         "-regions", *regionsFilename,
  90                         "-expand-regions", fmt.Sprintf("%d", *expandRegions),
  91                 }
  92                 runner.Args = append(runner.Args, cmd.filter.Args()...)
  93                 var output string
  94                 output, err = runner.Run()
  95                 if err != nil {
  96                         return 1
  97                 }
  98                 fmt.Fprintln(stdout, output)
  99                 return 0
 100         }
 101
 102         infiles, err := allGobFiles(*inputDir)
 103         if err != nil {
 104                 return 1
 105         }
 106         if len(infiles) == 0 {
 107                 err = fmt.Errorf("no input files found in %s", *inputDir)
 108                 return 1
 109         }
 110         sort.Strings(infiles)
 111
 112         var cgnames []string
 113         var refseq map[string][]tileLibRef
 114         var reftiledata = make(map[tileLibRef][]byte, 11000000)
 115         in0, err := open(infiles[0])
 116         if err != nil {
 117                 return 1
 118         }
 119
 120         matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
 121         if err != nil {
 122                 err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
 123                 return 1
 124         }
 125
 126         taglen := -1
 127         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 128                 if len(ent.TagSet) > 0 {
 129                         taglen = len(ent.TagSet[0])
 130                 }
 131                 for _, cseq := range ent.CompactSequences {
 132                         if cseq.Name == *ref || *ref == "" {
 133                                 refseq = cseq.TileSequences
 134                         }
 135                 }
 136                 for _, cg := range ent.CompactGenomes {
 137                         if matchGenome.MatchString(cg.Name) {
 138                                 cgnames = append(cgnames, cg.Name)
 139                         }
 140                 }
 141                 for _, tv := range ent.TileVariants {
 142                         if tv.Ref {
 143                                 reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
 144                         }
 145                 }
 146                 return nil
 147         })
 148         if err != nil {
 149                 return 1
 150         }
 151         in0.Close()
 152         if refseq == nil {
 153                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 154                 return 1
 155         }
 156         if taglen < 0 {
 157                 err = fmt.Errorf("tagset not found")
 158                 return 1
 159         }
 160         if len(cgnames) == 0 {
 161                 err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
 162                 return 1
 163         }
 164         sort.Strings(cgnames)
 165
 166         {
 167                 labelsFilename := *outputDir + "/labels.csv"
 168                 log.Infof("writing labels to %s", labelsFilename)
 169                 var f *os.File
 170                 f, err = os.Create(labelsFilename)
 171                 if err != nil {
 172                         return 1
 173                 }
 174                 defer f.Close()
 175                 for i, name := range cgnames {
 176                         _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
 177                         if err != nil {
 178                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 179                                 return 1
 180                         }
 181                 }
 182                 err = f.Close()
 183                 if err != nil {
 184                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 185                         return 1
 186                 }
 187         }
 188
 189         log.Info("indexing reference tiles")
 190         type reftileinfo struct {
 191                 variant  tileVariantID
 192                 seqname  string // chr1
 193                 pos      int    // distance from start of chr1 to start of tile
 194                 tiledata []byte // acgtggcaa...
 195         }
 196         reftile := map[tagID]*reftileinfo{}
 197         for seqname, cseq := range refseq {
 198                 for _, libref := range cseq {
 199                         reftile[libref.Tag] = &reftileinfo{
 200                                 seqname:  seqname,
 201                                 variant:  libref.Variant,
 202                                 tiledata: reftiledata[libref],
 203                         }
 204                 }
 205         }
 206
 207         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 208         log.Info("reconstructing reference sequences")
 209         for seqname, cseq := range refseq {
 210                 seqname, cseq := seqname, cseq
 211                 throttleCPU.Go(func() error {
 212                         defer log.Printf("... %s done", seqname)
 213                         pos := 0
 214                         for _, libref := range cseq {
 215                                 rt := reftile[libref.Tag]
 216                                 rt.pos = pos
 217                                 if len(rt.tiledata) == 0 {
 218                                         return fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
 219                                 }
 220                                 pos += len(rt.tiledata) - taglen
 221                         }
 222                         return nil
 223                 })
 224         }
 225         throttleCPU.Wait()
 226
 227         log.Info("TODO: determining which tiles intersect given regions")
 228
 229         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 230         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 231         log.Info("generating annotations and numpy matrix for each slice")
 232         var done int64
 233         for infileIdx, infile := range infiles {
 234                 infileIdx, infile := infileIdx, infile
 235                 throttleMem.Go(func() error {
 236                         seq := make(map[tagID][]TileVariant, 50000)
 237                         cgs := make(map[string]CompactGenome, len(cgnames))
 238                         f, err := open(infile)
 239                         if err != nil {
 240                                 return err
 241                         }
 242                         defer f.Close()
 243                         log.Infof("%04d: reading %s", infileIdx, infile)
 244                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 245                                 for _, tv := range ent.TileVariants {
 246                                         if tv.Ref {
 247                                                 continue
 248                                         }
 249                                         variants := seq[tv.Tag]
 250                                         if len(variants) == 0 {
 251                                                 variants = make([]TileVariant, 100)
 252                                         }
 253                                         for len(variants) <= int(tv.Variant) {
 254                                                 variants = append(variants, TileVariant{})
 255                                         }
 256                                         variants[int(tv.Variant)] = tv
 257                                         seq[tv.Tag] = variants
 258                                 }
 259                                 for _, cg := range ent.CompactGenomes {
 260                                         if matchGenome.MatchString(cg.Name) {
 261                                                 cgs[cg.Name] = cg
 262                                         }
 263                                 }
 264                                 return nil
 265                         })
 266                         if err != nil {
 267                                 return err
 268                         }
 269                         tagstart := cgs[cgnames[0]].StartTag
 270                         tagend := cgs[cgnames[0]].EndTag
 271
 272                         // TODO: filters
 273
 274                         log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
 275                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 276                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 277                         for tag, variants := range seq {
 278                                 tag, variants := tag, variants
 279                                 throttleCPU.Acquire()
 280                                 go func() {
 281                                         defer throttleCPU.Release()
 282                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 283                                         for _, cg := range cgs {
 284                                                 idx := (tag - tagstart) * 2
 285                                                 if int(idx) < len(cg.Variants) {
 286                                                         count[variants[cg.Variants[idx]].Blake2b]++
 287                                                         count[variants[cg.Variants[idx+1]].Blake2b]++
 288                                                 }
 289                                         }
 290                                         // hash[i] will be the hash of
 291                                         // the variant(s) that should
 292                                         // be at rank i (0-based).
 293                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 294                                         for b := range count {
 295                                                 hash = append(hash, b)
 296                                         }
 297                                         sort.Slice(hash, func(i, j int) bool {
 298                                                 bi, bj := &hash[i], &hash[j]
 299                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 300                                                         return ci > cj
 301                                                 } else {
 302                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 303                                                 }
 304                                         })
 305                                         // rank[b] will be the 1-based
 306                                         // new variant number for
 307                                         // variants whose hash is b.
 308                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 309                                         for i, h := range hash {
 310                                                 rank[h] = tileVariantID(i + 1)
 311                                         }
 312                                         // remap[v] will be the new
 313                                         // variant number for original
 314                                         // variant number v.
 315                                         remap := make([]tileVariantID, len(variants))
 316                                         for i, tv := range variants {
 317                                                 remap[i] = rank[tv.Blake2b]
 318                                         }
 319                                         variantRemap[tag-tagstart] = remap
 320                                 }()
 321                         }
 322                         throttleCPU.Wait()
 323
 324                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 325                         log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
 326                         annof, err := os.Create(annotationsFilename)
 327                         if err != nil {
 328                                 return err
 329                         }
 330                         annow := bufio.NewWriterSize(annof, 1<<20)
 331                         for tag, variants := range seq {
 332                                 rt, ok := reftile[tag]
 333                                 if !ok {
 334                                         // Reference does not use any
 335                                         // variant of this tile.
 336                                         // TODO: log this? mention it
 337                                         // in annotations?
 338                                         continue
 339                                 }
 340                                 outcol := tag - tagID(tagstart)
 341                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 342                                 remap := variantRemap[tag-tagstart]
 343                                 for v, tv := range variants {
 344                                         if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 345                                                 continue
 346                                         }
 347                                         if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 348                                                 continue
 349                                         }
 350                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 351                                         for _, diff := range diffs {
 352                                                 diff.Position += rt.pos
 353                                                 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, remap[v], rt.seqname, diff.String())
 354                                         }
 355                                 }
 356                         }
 357                         err = annow.Flush()
 358                         if err != nil {
 359                                 return err
 360                         }
 361                         err = annof.Close()
 362                         if err != nil {
 363                                 return err
 364                         }
 365
 366                         throttleNumpyMem.Acquire()
 367                         log.Infof("%04d: preparing numpy", infileIdx)
 368                         rows := len(cgnames)
 369                         cols := 2 * int(tagend-tagstart)
 370                         out := make([]int16, rows*cols)
 371                         for row, name := range cgnames {
 372                                 out := out[row*cols:]
 373                                 for col, v := range cgs[name].Variants {
 374                                         if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
 375                                                 out[col] = int16(variantRemap[col/2][v])
 376                                         } else {
 377                                                 out[col] = -1
 378                                         }
 379                                 }
 380                         }
 381                         seq = nil
 382                         throttleNumpyMem.Release()
 383
 384                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 385                         output, err := os.Create(fnm)
 386                         if err != nil {
 387                                 return err
 388                         }
 389                         defer output.Close()
 390                         bufw := bufio.NewWriterSize(output, 1<<26)
 391                         npw, err := gonpy.NewWriter(nopCloser{bufw})
 392                         if err != nil {
 393                                 return err
 394                         }
 395                         log.WithFields(logrus.Fields{
 396                                 "filename": fnm,
 397                                 "rows":     rows,
 398                                 "cols":     cols,
 399                         }).Infof("%04d: writing numpy", infileIdx)
 400                         npw.Shape = []int{rows, cols}
 401                         npw.WriteInt16(out)
 402                         err = bufw.Flush()
 403                         if err != nil {
 404                                 return err
 405                         }
 406                         err = output.Close()
 407                         if err != nil {
 408                                 return err
 409                         }
 410                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 411                         return nil
 412                 })
 413         }
 414         if err = throttleMem.Wait(); err != nil {
 415                 return 1
 416         }
 417         return 0
 418 }