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 }
  32
  33 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  34         var err error
  35         defer func() {
  36                 if err != nil {
  37                         fmt.Fprintf(stderr, "%s\n", err)
  38                 }
  39         }()
  40         flags := flag.NewFlagSet("", flag.ContinueOnError)
  41         flags.SetOutput(stderr)
  42         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  43         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  44         projectUUID := flags.String("project", "", "project `UUID` for output data")
  45         priority := flags.Int("priority", 500, "container request priority")
  46         inputDir := flags.String("input-dir", "./in", "input `directory`")
  47         outputDir := flags.String("output-dir", "./out", "output `directory`")
  48         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  49         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  50         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  51         cmd.filter.Flags(flags)
  52         err = flags.Parse(args)
  53         if err == flag.ErrHelp {
  54                 err = nil
  55                 return 0
  56         } else if err != nil {
  57                 return 2
  58         }
  59
  60         if *pprof != "" {
  61                 go func() {
  62                         log.Println(http.ListenAndServe(*pprof, nil))
  63                 }()
  64         }
  65
  66         if !*runlocal {
  67                 runner := arvadosContainerRunner{
  68                         Name:        "lightning slice-numpy",
  69                         Client:      arvados.NewClientFromEnv(),
  70                         ProjectUUID: *projectUUID,
  71                         RAM:         250000000000,
  72                         VCPUs:       32,
  73                         Priority:    *priority,
  74                         KeepCache:   2,
  75                         APIAccess:   true,
  76                 }
  77                 err = runner.TranslatePaths(inputDir, regionsFilename)
  78                 if err != nil {
  79                         return 1
  80                 }
  81                 runner.Args = []string{"slice-numpy", "-local=true",
  82                         "-pprof", ":6060",
  83                         "-input-dir", *inputDir,
  84                         "-output-dir", "/mnt/output",
  85                         "-regions", *regionsFilename,
  86                         "-expand-regions", fmt.Sprintf("%d", *expandRegions),
  87                 }
  88                 runner.Args = append(runner.Args, cmd.filter.Args()...)
  89                 var output string
  90                 output, err = runner.Run()
  91                 if err != nil {
  92                         return 1
  93                 }
  94                 fmt.Fprintln(stdout, output)
  95                 return 0
  96         }
  97
  98         infiles, err := allGobFiles(*inputDir)
  99         if err != nil {
 100                 return 1
 101         }
 102         if len(infiles) == 0 {
 103                 err = fmt.Errorf("no input files found in %s", *inputDir)
 104                 return 1
 105         }
 106         sort.Strings(infiles)
 107
 108         var cgnames []string
 109         var refseq map[string][]tileLibRef
 110         in0, err := open(infiles[0])
 111         if err != nil {
 112                 return 1
 113         }
 114         taglen := -1
 115         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 116                 if len(ent.TagSet) > 0 {
 117                         taglen = len(ent.TagSet[0])
 118                 }
 119                 for _, cseq := range ent.CompactSequences {
 120                         if cseq.Name == *ref || *ref == "" {
 121                                 refseq = cseq.TileSequences
 122                         }
 123                 }
 124                 for _, cg := range ent.CompactGenomes {
 125                         cgnames = append(cgnames, cg.Name)
 126                 }
 127                 return nil
 128         })
 129         if err != nil {
 130                 return 1
 131         }
 132         in0.Close()
 133         if refseq == nil {
 134                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 135                 return 1
 136         }
 137         if taglen < 0 {
 138                 err = fmt.Errorf("tagset not found")
 139                 return 1
 140         }
 141         sort.Strings(cgnames)
 142
 143         {
 144                 labelsFilename := *outputDir + "/labels.csv"
 145                 log.Infof("writing labels to %s", labelsFilename)
 146                 var f *os.File
 147                 f, err = os.Create(labelsFilename)
 148                 if err != nil {
 149                         return 1
 150                 }
 151                 defer f.Close()
 152                 for i, name := range cgnames {
 153                         _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
 154                         if err != nil {
 155                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 156                                 return 1
 157                         }
 158                 }
 159                 err = f.Close()
 160                 if err != nil {
 161                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 162                         return 1
 163                 }
 164         }
 165
 166         log.Info("building list of reference tiles to load") // TODO: more efficient if we had saved all ref tiles in slice0
 167         type reftileinfo struct {
 168                 variant  tileVariantID
 169                 seqname  string // chr1
 170                 pos      int    // distance from start of chr1 to start of tile
 171                 tiledata []byte // acgtggcaa...
 172         }
 173         reftile := map[tagID]*reftileinfo{}
 174         for seqname, cseq := range refseq {
 175                 for _, libref := range cseq {
 176                         reftile[libref.Tag] = &reftileinfo{seqname: seqname, variant: libref.Variant}
 177                 }
 178         }
 179         log.Info("loading reference tiles from all slices")
 180         throttle1 := throttle{Max: runtime.GOMAXPROCS(0)}
 181         for _, infile := range infiles {
 182                 infile := infile
 183                 throttle1.Go(func() error {
 184                         defer log.Infof("%s: done", infile)
 185                         f, err := open(infile)
 186                         if err != nil {
 187                                 return err
 188                         }
 189                         defer f.Close()
 190                         return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 191                                 for _, tv := range ent.TileVariants {
 192                                         if dst, ok := reftile[tv.Tag]; ok && dst.variant == tv.Variant {
 193                                                 dst.tiledata = tv.Sequence
 194                                         }
 195                                 }
 196                                 return nil
 197                         })
 198                 })
 199         }
 200         throttle1.Wait()
 201
 202         log.Info("reconstructing reference sequences")
 203         for seqname, cseq := range refseq {
 204                 seqname, cseq := seqname, cseq
 205                 throttle1.Go(func() error {
 206                         defer log.Printf("... %s done", seqname)
 207                         pos := 0
 208                         for _, libref := range cseq {
 209                                 rt := reftile[libref.Tag]
 210                                 rt.pos = pos
 211                                 pos += len(rt.tiledata) - taglen
 212                         }
 213                         return nil
 214                 })
 215         }
 216         throttle1.Wait()
 217
 218         log.Info("TODO: determining which tiles intersect given regions")
 219
 220         log.Info("generating annotations and numpy matrix for each slice")
 221         var done int64
 222         for infileIdx, infile := range infiles {
 223                 infileIdx, infile := infileIdx, infile
 224                 throttle1.Go(func() error {
 225                         seq := make(map[tagID][]TileVariant, 50000)
 226                         cgs := make(map[string]CompactGenome, len(cgnames))
 227                         f, err := open(infile)
 228                         if err != nil {
 229                                 return err
 230                         }
 231                         defer f.Close()
 232                         log.Infof("reading %s", infile)
 233                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 234                                 for _, tv := range ent.TileVariants {
 235                                         variants := seq[tv.Tag]
 236                                         if len(variants) == 0 {
 237                                                 variants = make([]TileVariant, 100)
 238                                         }
 239                                         for len(variants) <= int(tv.Variant) {
 240                                                 variants = append(variants, TileVariant{})
 241                                         }
 242                                         variants[int(tv.Variant)] = tv
 243                                         seq[tv.Tag] = variants
 244                                 }
 245                                 for _, cg := range ent.CompactGenomes {
 246                                         cgs[cg.Name] = cg
 247                                 }
 248                                 return nil
 249                         })
 250                         if err != nil {
 251                                 return err
 252                         }
 253                         tagstart := cgs[cgnames[0]].StartTag
 254                         tagend := cgs[cgnames[0]].EndTag
 255
 256                         // TODO: filters
 257
 258                         log.Infof("renumber/dedup variants for tags %d-%d", tagstart, tagend)
 259                         variantRemap := make([][]tileVariantID, tagend-tagstart)
 260                         throttle2 := throttle{Max: runtime.GOMAXPROCS(0)}
 261                         for tag, variants := range seq {
 262                                 tag, variants := tag, variants
 263                                 throttle2.Acquire()
 264                                 go func() {
 265                                         defer throttle2.Release()
 266                                         count := make(map[[blake2b.Size256]byte]int, len(variants))
 267                                         for _, cg := range cgs {
 268                                                 idx := (tag - tagstart) * 2
 269                                                 if int(idx) < len(cg.Variants) {
 270                                                         count[variants[cg.Variants[idx]].Blake2b]++
 271                                                         count[variants[cg.Variants[idx+1]].Blake2b]++
 272                                                 }
 273                                         }
 274                                         // hash[i] will be the hash of
 275                                         // the variant(s) that should
 276                                         // be at rank i (0-based).
 277                                         hash := make([][blake2b.Size256]byte, 0, len(count))
 278                                         for b := range count {
 279                                                 hash = append(hash, b)
 280                                         }
 281                                         sort.Slice(hash, func(i, j int) bool {
 282                                                 bi, bj := &hash[i], &hash[j]
 283                                                 if ci, cj := count[*bi], count[*bj]; ci != cj {
 284                                                         return ci > cj
 285                                                 } else {
 286                                                         return bytes.Compare((*bi)[:], (*bj)[:]) < 0
 287                                                 }
 288                                         })
 289                                         // rank[b] will be the 1-based
 290                                         // new variant number for
 291                                         // variants whose hash is b.
 292                                         rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
 293                                         for i, h := range hash {
 294                                                 rank[h] = tileVariantID(i + 1)
 295                                         }
 296                                         // remap[v] will be the new
 297                                         // variant number for original
 298                                         // variant number v.
 299                                         remap := make([]tileVariantID, len(variants))
 300                                         for i, tv := range variants {
 301                                                 remap[i] = rank[tv.Blake2b]
 302                                         }
 303                                         variantRemap[tag-tagstart] = remap
 304                                 }()
 305                         }
 306                         throttle2.Wait()
 307
 308                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 309                         log.Infof("writing %s", annotationsFilename)
 310                         annof, err := os.Create(annotationsFilename)
 311                         if err != nil {
 312                                 return err
 313                         }
 314                         annow := bufio.NewWriterSize(annof, 1<<20)
 315                         for tag, variants := range seq {
 316                                 rt, ok := reftile[tag]
 317                                 if !ok {
 318                                         // Reference does not use any
 319                                         // variant of this tile.
 320                                         // TODO: log this? mention it
 321                                         // in annotations?
 322                                         continue
 323                                 }
 324                                 outcol := tag - tagID(tagstart)
 325                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 326                                 remap := variantRemap[tag-tagstart]
 327                                 for v, tv := range variants {
 328                                         if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
 329                                                 continue
 330                                         }
 331                                         if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
 332                                                 continue
 333                                         }
 334                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
 335                                         for _, diff := range diffs {
 336                                                 diff.Position += rt.pos
 337                                                 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, remap[v], rt.seqname, diff.String())
 338                                         }
 339                                 }
 340                         }
 341                         err = annow.Flush()
 342                         if err != nil {
 343                                 return err
 344                         }
 345                         err = annof.Close()
 346                         if err != nil {
 347                                 return err
 348                         }
 349
 350                         log.Infof("%s: preparing numpy", infile)
 351                         rows := len(cgnames)
 352                         cols := 2 * int(tagend-tagstart)
 353                         out := make([]int16, rows*cols)
 354                         for row, name := range cgnames {
 355                                 out := out[row*cols:]
 356                                 for col, v := range cgs[name].Variants {
 357                                         if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
 358                                                 out[col] = int16(variantRemap[col/2][v])
 359                                         } else {
 360                                                 out[col] = -1
 361                                         }
 362                                 }
 363                         }
 364
 365                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 366                         output, err := os.Create(fnm)
 367                         if err != nil {
 368                                 return err
 369                         }
 370                         defer output.Close()
 371                         bufw := bufio.NewWriterSize(output, 1<<26)
 372                         npw, err := gonpy.NewWriter(nopCloser{bufw})
 373                         if err != nil {
 374                                 return err
 375                         }
 376                         log.WithFields(logrus.Fields{
 377                                 "filename": fnm,
 378                                 "rows":     rows,
 379                                 "cols":     cols,
 380                         }).Info("writing numpy")
 381                         npw.Shape = []int{rows, cols}
 382                         npw.WriteInt16(out)
 383                         err = bufw.Flush()
 384                         if err != nil {
 385                                 return err
 386                         }
 387                         err = output.Close()
 388                         if err != nil {
 389                                 return err
 390                         }
 391                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 392                         return nil
 393                 })
 394         }
 395         if err = throttle1.Wait(); err != nil {
 396                 return 1
 397         }
 398         return 0
 399 }