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         "runtime"
  17         "sort"
  18         "strings"
  19         "sync/atomic"
  20
  21         "git.arvados.org/arvados.git/sdk/go/arvados"
  22         "github.com/arvados/lightning/hgvs"
  23         "github.com/kshedden/gonpy"
  24         "github.com/sirupsen/logrus"
  25         log "github.com/sirupsen/logrus"
  26         "golang.org/x/crypto/blake2b"
  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:         240000000000,
  74                         VCPUs:       64,
  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         in0, err := open(infiles[0])
 114         if err != nil {
 115                 return 1
 116         }
 117         taglen := -1
 118         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 119                 if len(ent.TagSet) > 0 {
 120                         taglen = len(ent.TagSet[0])
 121                 }
 122                 for _, cseq := range ent.CompactSequences {
 123                         if cseq.Name == *ref || *ref == "" {
 124                                 refseq = cseq.TileSequences
 125                         }
 126                 }
 127                 for _, cg := range ent.CompactGenomes {
 128                         cgnames = append(cgnames, cg.Name)
 129                 }
 130                 return nil
 131         })
 132         if err != nil {
 133                 return 1
 134         }
 135         in0.Close()
 136         if refseq == nil {
 137                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 138                 return 1
 139         }
 140         if taglen < 0 {
 141                 err = fmt.Errorf("tagset not found")
 142                 return 1
 143         }
 144         sort.Strings(cgnames)
 145
 146         {
 147                 labelsFilename := *outputDir + "/labels.csv"
 148                 log.Infof("writing labels to %s", labelsFilename)
 149                 var f *os.File
 150                 f, err = os.Create(labelsFilename)
 151                 if err != nil {
 152                         return 1
 153                 }
 154                 defer f.Close()
 155                 for i, name := range cgnames {
 156                         _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
 157                         if err != nil {
 158                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 159                                 return 1
 160                         }
 161                 }
 162                 err = f.Close()
 163                 if err != nil {
 164                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 165                         return 1
 166                 }
 167         }
 168
 169         log.Info("building list of reference tiles to load") // TODO: more efficient if we had saved all ref tiles in slice0
 170         type reftileinfo struct {
 171                 variant  tileVariantID
 172                 seqname  string // chr1
 173                 pos      int    // distance from start of chr1 to start of tile
 174                 tiledata []byte // acgtggcaa...
 175         }
 176         reftile := map[tagID]*reftileinfo{}
 177         for seqname, cseq := range refseq {
 178                 for _, libref := range cseq {
 179                         reftile[libref.Tag] = &reftileinfo{seqname: seqname, variant: libref.Variant}
 180                 }
 181         }
 182         log.Info("loading reference tiles from all slices")
 183         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 184         for _, infile := range infiles {
 185                 infile := infile
 186                 throttleCPU.Go(func() error {
 187                         defer log.Infof("%s: done", infile)
 188                         f, err := open(infile)
 189                         if err != nil {
 190                                 return err
 191                         }
 192                         defer f.Close()
 193                         return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 194                                 for _, tv := range ent.TileVariants {
 195                                         if dst, ok := reftile[tv.Tag]; ok && dst.variant == tv.Variant {
 196                                                 dst.tiledata = tv.Sequence
 197                                         }
 198                                 }
 199                                 return nil
 200                         })
 201                 })
 202         }
 203         if err = throttleCPU.Wait(); err != nil {
 204                 return 1
 205         }
 206
 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                                 pos += len(rt.tiledata) - taglen
 217                         }
 218                         return nil
 219                 })
 220         }
 221         throttleCPU.Wait()
 222
 223         log.Info("TODO: determining which tiles intersect given regions")
 224
 225         throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
 226         throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
 227         log.Info("generating annotations and numpy matrix for each slice")
 228         var done int64
 229         for infileIdx, infile := range infiles {
 230                 infileIdx, infile := infileIdx, infile
 231                 throttleMem.Go(func() error {
 232                         seq := make(map[tagID][]TileVariant, 50000)
 233                         cgs := make(map[string]CompactGenome, len(cgnames))
 234                         f, err := open(infile)
 235                         if err != nil {
 236                                 return err
 237                         }
 238                         defer f.Close()
 239                         log.Infof("reading %s", infile)
 240                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 241                                 for _, tv := range ent.TileVariants {
 242                                         variants := seq[tv.Tag]
 243                                         if len(variants) == 0 {
 244                                                 variants = make([]TileVariant, 100)
 245                                         }
 246                                         for len(variants) <= int(tv.Variant) {
 247                                                 variants = append(variants, TileVariant{})
 248                                         }
 249                                         variants[int(tv.Variant)] = tv
 250                                         seq[tv.Tag] = variants
 251                                 }
 252                                 for _, cg := range ent.CompactGenomes {
 253                                         cgs[cg.Name] = cg
 254                                 }
 255                                 return nil
 256                         })
 257                         if err != nil {
 258                                 return err
 259                         }
 260                         tagstart := cgs[cgnames[0]].StartTag
 261                         tagend := cgs[cgnames[0]].EndTag
 262
 263                         // TODO: filters
 264
 265                         log.Infof("renumber/dedup variants for tags %d-%d", tagstart, tagend)
 266                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 267                         throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
 268                         for tag, variants := range seq {
 269                                 tag, variants := tag, variants
 270                                 throttleCPU.Acquire()
 271                                 go func() {
 272                                         defer throttleCPU.Release()
 273                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 274                                         for _, cg := range cgs {
 275                                                 idx := (tag - tagstart) * 2
 276                                                 if int(idx) < len(cg.Variants) {
 277                                                         count[variants[cg.Variants[idx]].Blake2b]++
 278                                                         count[variants[cg.Variants[idx+1]].Blake2b]++
 279                                                 }
 280                                         }
 281                                         // hash[i] will be the hash of
 282                                         // the variant(s) that should
 283                                         // be at rank i (0-based).
 284                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 285                                         for b := range count {
 286                                                 hash = append(hash, b)
 287                                         }
 288                                         sort.Slice(hash, func(i, j int) bool {
 289                                                 bi, bj := &hash[i], &hash[j]
 290                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 291                                                         return ci > cj
 292                                                 } else {
 293                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 294                                                 }
 295                                         })
 296                                         // rank[b] will be the 1-based
 297                                         // new variant number for
 298                                         // variants whose hash is b.
 299                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 300                                         for i, h := range hash {
 301                                                 rank[h] = tileVariantID(i + 1)
 302                                         }
 303                                         // remap[v] will be the new
 304                                         // variant number for original
 305                                         // variant number v.
 306                                         remap := make([]tileVariantID, len(variants))
 307                                         for i, tv := range variants {
 308                                                 remap[i] = rank[tv.Blake2b]
 309                                         }
 310                                         variantRemap[tag-tagstart] = remap
 311                                 }()
 312                         }
 313                         throttleCPU.Wait()
 314
 315                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 316                         log.Infof("writing %s", annotationsFilename)
 317                         annof, err := os.Create(annotationsFilename)
 318                         if err != nil {
 319                                 return err
 320                         }
 321                         annow := bufio.NewWriterSize(annof, 1<<20)
 322                         for tag, variants := range seq {
 323                                 rt, ok := reftile[tag]
 324                                 if !ok {
 325                                         // Reference does not use any
 326                                         // variant of this tile.
 327                                         // TODO: log this? mention it
 328                                         // in annotations?
 329                                         continue
 330                                 }
 331                                 outcol := tag - tagID(tagstart)
 332                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 333                                 remap := variantRemap[tag-tagstart]
 334                                 for v, tv := range variants {
 335                                         if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 336                                                 continue
 337                                         }
 338                                         if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 339                                                 continue
 340                                         }
 341                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 342                                         for _, diff := range diffs {
 343                                                 diff.Position += rt.pos
 344                                                 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, remap[v], rt.seqname, diff.String())
 345                                         }
 346                                 }
 347                         }
 348                         err = annow.Flush()
 349                         if err != nil {
 350                                 return err
 351                         }
 352                         err = annof.Close()
 353                         if err != nil {
 354                                 return err
 355                         }
 356
 357                         throttleNumpyMem.Acquire()
 358                         log.Infof("%s: preparing numpy", infile)
 359                         rows := len(cgnames)
 360                         cols := 2 * int(tagend-tagstart)
 361                         out := make([]int16, rows*cols)
 362                         for row, name := range cgnames {
 363                                 out := out[row*cols:]
 364                                 for col, v := range cgs[name].Variants {
 365                                         if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
 366                                                 out[col] = int16(variantRemap[col/2][v])
 367                                         } else {
 368                                                 out[col] = -1
 369                                         }
 370                                 }
 371                         }
 372                         seq = nil
 373                         throttleNumpyMem.Release()
 374
 375                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 376                         output, err := os.Create(fnm)
 377                         if err != nil {
 378                                 return err
 379                         }
 380                         defer output.Close()
 381                         bufw := bufio.NewWriterSize(output, 1<<26)
 382                         npw, err := gonpy.NewWriter(nopCloser{bufw})
 383                         if err != nil {
 384                                 return err
 385                         }
 386                         log.WithFields(logrus.Fields{
 387                                 "filename": fnm,
 388                                 "rows":     rows,
 389                                 "cols":     cols,
 390                         }).Info("writing numpy")
 391                         npw.Shape = []int{rows, cols}
 392                         npw.WriteInt16(out)
 393                         err = bufw.Flush()
 394                         if err != nil {
 395                                 return err
 396                         }
 397                         err = output.Close()
 398                         if err != nil {
 399                                 return err
 400                         }
 401                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 402                         return nil
 403                 })
 404         }
 405         if err = throttleMem.Wait(); err != nil {
 406                 return 1
 407         }
 408         return 0
 409 }