exportnumpy.go

   1 package lightning
   2
   3 import (
   4         "bufio"
   5         "bytes"
   6         "context"
   7         "errors"
   8         "flag"
   9         "fmt"
  10         "io"
  11         "io/ioutil"
  12         "net/http"
  13         _ "net/http/pprof"
  14         "os"
  15         "sort"
  16         "strconv"
  17         "strings"
  18         "sync"
  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 )
  27
  28 type exportNumpy struct {
  29         filter filter
  30 }
  31
  32 func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  33         var err error
  34         defer func() {
  35                 if err != nil {
  36                         fmt.Fprintf(stderr, "%s\n", err)
  37                 }
  38         }()
  39         flags := flag.NewFlagSet("", flag.ContinueOnError)
  40         flags.SetOutput(stderr)
  41         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  42         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  43         projectUUID := flags.String("project", "", "project `UUID` for output data")
  44         priority := flags.Int("priority", 500, "container request priority")
  45         inputDir := flags.String("input-dir", "./in", "input `directory`")
  46         outputDir := flags.String("output-dir", "./out", "output `directory`")
  47         annotationsFilename := flags.String("output-annotations", "", "output `file` for tile variant annotations csv")
  48         librefsFilename := flags.String("output-onehot2tilevar", "", "when using -one-hot, create csv `file` mapping column# to tag# and variant#")
  49         labelsFilename := flags.String("output-labels", "", "output `file` for genome labels csv")
  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         onehot := flags.Bool("one-hot", false, "recode tile variants as one-hot")
  53         chunks := flags.Int("chunks", 1, "split output into `N` numpy files")
  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 export-numpy",
  72                         Client:      arvados.NewClientFromEnv(),
  73                         ProjectUUID: *projectUUID,
  74                         RAM:         500000000000,
  75                         VCPUs:       96,
  76                         Priority:    *priority,
  77                         KeepCache:   1,
  78                         APIAccess:   true,
  79                 }
  80                 err = runner.TranslatePaths(inputDir, regionsFilename)
  81                 if err != nil {
  82                         return 1
  83                 }
  84                 runner.Args = []string{"export-numpy", "-local=true",
  85                         "-pprof", ":6060",
  86                         fmt.Sprintf("-one-hot=%v", *onehot),
  87                         "-input-dir", *inputDir,
  88                         "-output-dir", "/mnt/output",
  89                         "-output-annotations", "/mnt/output/annotations.csv",
  90                         "-output-onehot2tilevar", "/mnt/output/onehot2tilevar.csv",
  91                         "-output-labels", "/mnt/output/labels.csv",
  92                         "-regions", *regionsFilename,
  93                         "-expand-regions", fmt.Sprintf("%d", *expandRegions),
  94                         "-max-variants", fmt.Sprintf("%d", cmd.filter.MaxVariants),
  95                         "-min-coverage", fmt.Sprintf("%f", cmd.filter.MinCoverage),
  96                         "-max-tag", fmt.Sprintf("%d", cmd.filter.MaxTag),
  97                         "-chunks", fmt.Sprintf("%d", *chunks),
  98                 }
  99                 var output string
 100                 output, err = runner.Run()
 101                 if err != nil {
 102                         return 1
 103                 }
 104                 fmt.Fprintln(stdout, output+"/matrix.npy")
 105                 return 0
 106         }
 107
 108         tilelib := &tileLibrary{
 109                 retainNoCalls:       true,
 110                 retainTileSequences: true,
 111                 compactGenomes:      map[string][]tileVariantID{},
 112         }
 113         err = tilelib.LoadDir(context.Background(), *inputDir, nil)
 114         if err != nil {
 115                 return 1
 116         }
 117
 118         log.Info("filtering")
 119         cmd.filter.Apply(tilelib)
 120         log.Info("tidying")
 121         tilelib.Tidy()
 122
 123         log.Info("building lowqual map")
 124         lowqual := lowqual(tilelib)
 125         names := cgnames(tilelib)
 126
 127         if *labelsFilename != "" {
 128                 log.Infof("writing labels to %s", *labelsFilename)
 129                 var f *os.File
 130                 f, err = os.OpenFile(*labelsFilename, os.O_CREATE|os.O_WRONLY, 0777)
 131                 if err != nil {
 132                         return 1
 133                 }
 134                 defer f.Close()
 135                 outBasename := "matrix.npy"
 136                 for i, name := range names {
 137                         _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), outBasename)
 138                         if err != nil {
 139                                 err = fmt.Errorf("write %s: %w", *labelsFilename, err)
 140                                 return 1
 141                         }
 142                 }
 143                 err = f.Close()
 144                 if err != nil {
 145                         err = fmt.Errorf("close %s: %w", *labelsFilename, err)
 146                         return 1
 147                 }
 148         }
 149
 150         log.Info("determining which tiles intersect given regions")
 151         dropTiles, err := chooseTiles(tilelib, *regionsFilename, *expandRegions)
 152         if err != nil {
 153                 return 1
 154         }
 155
 156         annotation2tvs := map[string]map[hgvs.Variant][]tileLibRef{}
 157         if *annotationsFilename != "" {
 158                 log.Info("writing annotations")
 159                 var annow io.WriteCloser
 160                 annow, err = os.OpenFile(*annotationsFilename, os.O_CREATE|os.O_WRONLY, 0666)
 161                 if err != nil {
 162                         return 1
 163                 }
 164                 defer annow.Close()
 165                 var mtx sync.Mutex
 166                 err = (&annotatecmd{
 167                         maxTileSize: 5000,
 168                         dropTiles:   dropTiles,
 169                         reportAnnotation: func(tag tagID, _ int, variant tileVariantID, refname string, seqname string, pdi hgvs.Variant) {
 170                                 mtx.Lock()
 171                                 defer mtx.Unlock()
 172                                 if annotation2tvs[seqname] == nil {
 173                                         annotation2tvs[seqname] = map[hgvs.Variant][]tileLibRef{}
 174                                 }
 175                                 annotation2tvs[seqname][pdi] = append(annotation2tvs[seqname][pdi], tileLibRef{Tag: tag, Variant: variant})
 176                         },
 177                 }).exportTileDiffs(annow, tilelib)
 178                 if err != nil {
 179                         return 1
 180                 }
 181                 err = annow.Close()
 182                 if err != nil {
 183                         return 1
 184                 }
 185         }
 186
 187         var lastErr atomic.Value
 188         var wg sync.WaitGroup
 189         for seqname, pdivars := range annotation2tvs {
 190                 seqname, pdivars := seqname, pdivars
 191                 wg.Add(1)
 192                 go func() {
 193                         defer wg.Done()
 194                         log.Infof("choosing hgvs columns for seq %s", seqname)
 195                         var pdis []hgvs.Variant
 196                         for pdi, librefs := range pdivars {
 197                                 // Include this HGVS column if it was
 198                                 // seen in a variant of any
 199                                 // non-dropped tile.
 200                                 for _, libref := range librefs {
 201                                         if int(libref.Tag) >= len(dropTiles) || !dropTiles[libref.Tag] {
 202                                                 pdis = append(pdis, pdi)
 203                                                 break
 204                                         }
 205                                 }
 206                         }
 207                         sort.Slice(pdis, func(i, j int) bool {
 208                                 if cmp := pdis[i].Position - pdis[j].Position; cmp != 0 {
 209                                         return cmp < 0
 210                                 } else if pdis[i].Ref != pdis[j].Ref {
 211                                         return pdis[i].Ref < pdis[j].Ref
 212                                 } else {
 213                                         return pdis[i].New < pdis[j].New
 214                                 }
 215                         })
 216                         log.Infof("writing column labels for seq %s", seqname)
 217                         var buf bytes.Buffer
 218                         for _, pdi := range pdis {
 219                                 fmt.Fprintf(&buf, "%s:g.%s\n", seqname, pdi.String())
 220                         }
 221                         err := ioutil.WriteFile(*outputDir+"/"+seqname+".columns.csv", buf.Bytes(), 0777)
 222                         if err != nil {
 223                                 lastErr.Store(err)
 224                                 return
 225                         }
 226
 227                         log.Infof("building hgvs matrix for seq %s", seqname)
 228                         data := make([]int8, len(names)*len(pdis)*2)
 229                         for row, name := range names {
 230                                 cg := tilelib.compactGenomes[name]
 231                                 rowstart := row * len(pdis) * 2
 232                                 for col, pdi := range pdis {
 233                                         for _, libref := range pdivars[pdi] {
 234                                                 if len(cg) <= int(libref.Tag)*2+1 {
 235                                                         continue
 236                                                 }
 237                                                 for phase := 0; phase < 2; phase++ {
 238                                                         if cg[int(libref.Tag)*2+phase] == libref.Variant {
 239                                                                 data[rowstart+col*2+phase] = 1
 240                                                         }
 241                                                 }
 242                                         }
 243                                 }
 244                         }
 245                         log.Infof("writing hgvs numpy for seq %s", seqname)
 246                         f, err := os.OpenFile(*outputDir+"/"+seqname+".npy", os.O_CREATE|os.O_WRONLY, 0777)
 247                         if err != nil {
 248                                 lastErr.Store(err)
 249                                 return
 250                         }
 251                         defer f.Close()
 252                         npw, err := gonpy.NewWriter(f)
 253                         if err != nil {
 254                                 lastErr.Store(err)
 255                                 return
 256                         }
 257                         npw.Shape = []int{len(names), len(pdis) * 2}
 258                         npw.WriteInt8(data)
 259                         // gonpy closes f and ignores errors, doh.
 260                         // err = f.Close()
 261                         // if err != nil {
 262                         //      lastErr.Store(err)
 263                         //      return
 264                         // }
 265                 }()
 266         }
 267         wg.Wait()
 268         if e, ok := lastErr.Load().(error); ok {
 269                 err = e
 270                 return 1
 271         }
 272
 273         chunksize := (len(tilelib.variant) + *chunks - 1) / *chunks
 274         for chunk := 0; chunk < *chunks; chunk++ {
 275                 log.Infof("preparing chunk %d of %d", chunk+1, *chunks)
 276                 tagstart := chunk * chunksize
 277                 tagend := tagstart + chunksize
 278                 if tagend > len(tilelib.variant) {
 279                         tagend = len(tilelib.variant)
 280                 }
 281                 out, rows, cols := cgs2array(tilelib, names, lowqual, dropTiles, tagstart, tagend)
 282
 283                 var npw *gonpy.NpyWriter
 284                 var output io.WriteCloser
 285                 fnm := *outputDir + "/matrix.npy"
 286                 if *chunks > 1 {
 287                         fnm = fmt.Sprintf("%s/matrix.%d.npy", *outputDir, chunk)
 288                 }
 289                 output, err = os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY, 0777)
 290                 if err != nil {
 291                         return 1
 292                 }
 293                 defer output.Close()
 294                 bufw := bufio.NewWriter(output)
 295                 npw, err = gonpy.NewWriter(nopCloser{bufw})
 296                 if err != nil {
 297                         return 1
 298                 }
 299                 if *onehot {
 300                         log.Info("recoding to onehot")
 301                         recoded, librefs, recodedcols := recodeOnehot(out, cols)
 302                         out, cols = recoded, recodedcols
 303                         if *librefsFilename != "" {
 304                                 log.Infof("writing onehot column mapping")
 305                                 err = cmd.writeLibRefs(*librefsFilename, tilelib, librefs)
 306                                 if err != nil {
 307                                         return 1
 308                                 }
 309                         }
 310                 }
 311                 log.WithFields(logrus.Fields{
 312                         "filename": fnm,
 313                         "rows":     rows,
 314                         "cols":     cols,
 315                 }).Info("writing numpy")
 316                 npw.Shape = []int{rows, cols}
 317                 npw.WriteInt16(out)
 318                 err = bufw.Flush()
 319                 if err != nil {
 320                         return 1
 321                 }
 322                 err = output.Close()
 323                 if err != nil {
 324                         return 1
 325                 }
 326         }
 327         return 0
 328 }
 329
 330 func (*exportNumpy) writeLibRefs(fnm string, tilelib *tileLibrary, librefs []tileLibRef) error {
 331         f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY, 0666)
 332         if err != nil {
 333                 return err
 334         }
 335         defer f.Close()
 336         for i, libref := range librefs {
 337                 _, err = fmt.Fprintf(f, "%d,%d,%d\n", i, libref.Tag, libref.Variant)
 338                 if err != nil {
 339                         return err
 340                 }
 341         }
 342         return f.Close()
 343 }
 344
 345 func cgnames(tilelib *tileLibrary) (cgnames []string) {
 346         for name := range tilelib.compactGenomes {
 347                 cgnames = append(cgnames, name)
 348         }
 349         sort.Slice(cgnames, func(i, j int) bool {
 350                 return trimFilenameForLabel(cgnames[i]) < trimFilenameForLabel(cgnames[j])
 351         })
 352         return
 353 }
 354
 355 func lowqual(tilelib *tileLibrary) (lowqual []map[tileVariantID]bool) {
 356         lowqual = make([]map[tileVariantID]bool, len(tilelib.variant))
 357         for tag, variants := range tilelib.variant {
 358                 lq := lowqual[tag]
 359                 for varidx, hash := range variants {
 360                         if len(tilelib.seq[hash]) == 0 {
 361                                 if lq == nil {
 362                                         lq = map[tileVariantID]bool{}
 363                                         lowqual[tag] = lq
 364                                 }
 365                                 lq[tileVariantID(varidx+1)] = true
 366                         }
 367                 }
 368         }
 369         return
 370 }
 371
 372 func cgs2array(tilelib *tileLibrary, names []string, lowqual []map[tileVariantID]bool, dropTiles []bool, tagstart, tagend int) (data []int16, rows, cols int) {
 373         rows = len(tilelib.compactGenomes)
 374         for tag := tagstart; tag < tagend; tag++ {
 375                 if len(dropTiles) <= tag || !dropTiles[tag] {
 376                         cols += 2
 377                 }
 378         }
 379         data = make([]int16, rows*cols)
 380         for row, name := range names {
 381                 cg := tilelib.compactGenomes[name]
 382                 outidx := 0
 383                 for tag := tagstart; tag < tagend && tag*2+1 < len(cg); tag++ {
 384                         if len(dropTiles) > tag && dropTiles[tag] {
 385                                 continue
 386                         }
 387                         for phase := 0; phase < 2; phase++ {
 388                                 v := cg[tag*2+phase]
 389                                 if v > 0 && lowqual[tag][v] {
 390                                         data[row*cols+outidx] = -1
 391                                 } else {
 392                                         data[row*cols+outidx] = int16(v)
 393                                 }
 394                                 outidx++
 395                         }
 396                 }
 397         }
 398         return
 399 }
 400
 401 func chooseTiles(tilelib *tileLibrary, regionsFilename string, expandRegions int) (drop []bool, err error) {
 402         if regionsFilename == "" {
 403                 return
 404         }
 405         rfile, err := zopen(regionsFilename)
 406         if err != nil {
 407                 return
 408         }
 409         defer rfile.Close()
 410         regions, err := ioutil.ReadAll(rfile)
 411         if err != nil {
 412                 return
 413         }
 414
 415         log.Print("chooseTiles: building mask")
 416         mask := &mask{}
 417         for _, line := range bytes.Split(regions, []byte{'\n'}) {
 418                 if bytes.HasPrefix(line, []byte{'#'}) {
 419                         continue
 420                 }
 421                 fields := bytes.Split(line, []byte{'\t'})
 422                 if len(fields) < 3 {
 423                         continue
 424                 }
 425                 refseqname := string(fields[0])
 426                 if strings.HasPrefix(refseqname, "chr") {
 427                         refseqname = refseqname[3:]
 428                 }
 429                 start, err1 := strconv.Atoi(string(fields[1]))
 430                 end, err2 := strconv.Atoi(string(fields[2]))
 431                 if err1 == nil && err2 == nil {
 432                         // BED
 433                 } else {
 434                         start, err1 = strconv.Atoi(string(fields[3]))
 435                         end, err2 = strconv.Atoi(string(fields[4]))
 436                         if err1 == nil && err2 == nil {
 437                                 // GFF/GTF
 438                                 end++
 439                         } else {
 440                                 err = fmt.Errorf("cannot parse input line as BED or GFF/GTF: %q", line)
 441                                 return
 442                         }
 443                 }
 444                 mask.Add(refseqname, start-expandRegions, end+expandRegions)
 445         }
 446         log.Print("chooseTiles: mask.Freeze")
 447         mask.Freeze()
 448
 449         tagset := tilelib.taglib.Tags()
 450         if len(tagset) == 0 {
 451                 err = errors.New("cannot choose tiles by region in a library without tags")
 452                 return
 453         }
 454         taglen := len(tagset[0])
 455
 456         log.Print("chooseTiles: check ref tiles")
 457         // Find position+size of each reference tile, and if it
 458         // intersects any of the desired regions, set drop[tag]=false.
 459         //
 460         // (Note it doesn't quite work to do the more obvious thing --
 461         // start with drop=false and change to true when ref tiles
 462         // intersect target regions -- because that would give us
 463         // drop=false for tiles that don't appear at all in the
 464         // reference.)
 465         //
 466         // TODO: (optionally?) don't drop tags for which some tile
 467         // variants are spanning tiles, i.e., where the reference tile
 468         // does not intersect the desired regions, but a spanning tile
 469         // from a genome does.
 470         drop = make([]bool, len(tilelib.variant))
 471         for i := range drop {
 472                 drop[i] = true
 473         }
 474         for refname, refseqs := range tilelib.refseqs {
 475                 for refseqname, reftiles := range refseqs {
 476                         if strings.HasPrefix(refseqname, "chr") {
 477                                 refseqname = refseqname[3:]
 478                         }
 479                         tileend := 0
 480                         for _, libref := range reftiles {
 481                                 if libref.Variant < 1 {
 482                                         err = fmt.Errorf("reference %q seq %q uses variant zero at tag %d", refname, refseqname, libref.Tag)
 483                                         return
 484                                 }
 485                                 seq := tilelib.TileVariantSequence(libref)
 486                                 if len(seq) < taglen {
 487                                         err = fmt.Errorf("reference %q seq %q uses tile %d variant %d with sequence len %d < taglen %d", refname, refseqname, libref.Tag, libref.Variant, len(seq), taglen)
 488                                         return
 489                                 }
 490                                 tilestart := tileend
 491                                 tileend = tilestart + len(seq) - taglen
 492                                 if mask.Check(refseqname, tilestart, tileend) {
 493                                         drop[libref.Tag] = false
 494                                 }
 495                         }
 496                 }
 497         }
 498
 499         log.Print("chooseTiles: done")
 500         return
 501 }
 502
 503 func recodeOnehot(in []int16, incols int) (out []int16, librefs []tileLibRef, outcols int) {
 504         rows := len(in) / incols
 505         maxvalue := make([]int16, incols)
 506         for row := 0; row < rows; row++ {
 507                 for col := 0; col < incols; col++ {
 508                         if v := in[row*incols+col]; maxvalue[col] < v {
 509                                 maxvalue[col] = v
 510                         }
 511                 }
 512         }
 513         outcol := make([]int, incols)
 514         dropped := 0
 515         for incol, maxv := range maxvalue {
 516                 outcol[incol] = outcols
 517                 if maxv == 0 {
 518                         dropped++
 519                 }
 520                 for v := 1; v <= int(maxv); v++ {
 521                         librefs = append(librefs, tileLibRef{Tag: tagID(incol), Variant: tileVariantID(v)})
 522                         outcols++
 523                 }
 524         }
 525         log.Printf("recodeOnehot: dropped %d input cols with zero maxvalue", dropped)
 526
 527         out = make([]int16, rows*outcols)
 528         for inidx, row := 0, 0; row < rows; row++ {
 529                 outrow := out[row*outcols:]
 530                 for col := 0; col < incols; col++ {
 531                         if v := in[inidx]; v > 0 {
 532                                 outrow[outcol[col]+int(v)-1] = 1
 533                         }
 534                         inidx++
 535                 }
 536         }
 537         return
 538 }
 539
 540 type nopCloser struct {
 541         io.Writer
 542 }
 543
 544 func (nopCloser) Close() error { return nil }
 545
 546 func trimFilenameForLabel(s string) string {
 547         if i := strings.LastIndex(s, "/"); i >= 0 {
 548                 s = s[i+1:]
 549         }
 550         s = strings.TrimSuffix(s, ".gz")
 551         s = strings.TrimSuffix(s, ".fa")
 552         s = strings.TrimSuffix(s, ".fasta")
 553         s = strings.TrimSuffix(s, ".1")
 554         s = strings.TrimSuffix(s, ".2")
 555         s = strings.TrimSuffix(s, ".gz")
 556         s = strings.TrimSuffix(s, ".vcf")
 557         return s
 558 }