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 )
  27
  28 type sliceNumpy struct {
  29         filter filter
  30 }
  31
  32 func (cmd *sliceNumpy) 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         ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
  48         regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
  49         expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
  50         cmd.filter.Flags(flags)
  51         err = flags.Parse(args)
  52         if err == flag.ErrHelp {
  53                 err = nil
  54                 return 0
  55         } else if err != nil {
  56                 return 2
  57         }
  58
  59         if *pprof != "" {
  60                 go func() {
  61                         log.Println(http.ListenAndServe(*pprof, nil))
  62                 }()
  63         }
  64
  65         if !*runlocal {
  66                 runner := arvadosContainerRunner{
  67                         Name:        "lightning slice-numpy",
  68                         Client:      arvados.NewClientFromEnv(),
  69                         ProjectUUID: *projectUUID,
  70                         RAM:         250000000000,
  71                         VCPUs:       32,
  72                         Priority:    *priority,
  73                         KeepCache:   2,
  74                         APIAccess:   true,
  75                 }
  76                 err = runner.TranslatePaths(inputDir, regionsFilename)
  77                 if err != nil {
  78                         return 1
  79                 }
  80                 runner.Args = []string{"slice-numpy", "-local=true",
  81                         "-pprof", ":6060",
  82                         "-input-dir", *inputDir,
  83                         "-output-dir", "/mnt/output",
  84                         "-regions", *regionsFilename,
  85                         "-expand-regions", fmt.Sprintf("%d", *expandRegions),
  86                 }
  87                 runner.Args = append(runner.Args, cmd.filter.Args()...)
  88                 var output string
  89                 output, err = runner.Run()
  90                 if err != nil {
  91                         return 1
  92                 }
  93                 fmt.Fprintln(stdout, output)
  94                 return 0
  95         }
  96
  97         infiles, err := allGobFiles(*inputDir)
  98         if err != nil {
  99                 return 1
 100         }
 101         if len(infiles) == 0 {
 102                 err = fmt.Errorf("no input files found in %s", *inputDir)
 103                 return 1
 104         }
 105         sort.Strings(infiles)
 106
 107         var cgnames []string
 108         var refseq map[string][]tileLibRef
 109         in0, err := open(infiles[0])
 110         if err != nil {
 111                 return 1
 112         }
 113         taglen := -1
 114         DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
 115                 if len(ent.TagSet) > 0 {
 116                         taglen = len(ent.TagSet[0])
 117                 }
 118                 for _, cseq := range ent.CompactSequences {
 119                         if cseq.Name == *ref || *ref == "" {
 120                                 refseq = cseq.TileSequences
 121                         }
 122                 }
 123                 for _, cg := range ent.CompactGenomes {
 124                         cgnames = append(cgnames, cg.Name)
 125                 }
 126                 return nil
 127         })
 128         if err != nil {
 129                 return 1
 130         }
 131         in0.Close()
 132         if refseq == nil {
 133                 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
 134                 return 1
 135         }
 136         if taglen < 0 {
 137                 err = fmt.Errorf("tagset not found")
 138                 return 1
 139         }
 140         sort.Strings(cgnames)
 141
 142         {
 143                 labelsFilename := *outputDir + "/labels.csv"
 144                 log.Infof("writing labels to %s", labelsFilename)
 145                 var f *os.File
 146                 f, err = os.Create(labelsFilename)
 147                 if err != nil {
 148                         return 1
 149                 }
 150                 defer f.Close()
 151                 for i, name := range cgnames {
 152                         _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
 153                         if err != nil {
 154                                 err = fmt.Errorf("write %s: %w", labelsFilename, err)
 155                                 return 1
 156                         }
 157                 }
 158                 err = f.Close()
 159                 if err != nil {
 160                         err = fmt.Errorf("close %s: %w", labelsFilename, err)
 161                         return 1
 162                 }
 163         }
 164
 165         log.Info("building list of reference tiles to load") // TODO: more efficient if we had saved all ref tiles in slice0
 166         type reftileinfo struct {
 167                 seqname  string // chr1
 168                 pos      int    // distance from start of chr1 to start of tile
 169                 tiledata []byte // acgtggcaa...
 170         }
 171         reftile := map[tagID]*reftileinfo{}
 172         for seqname, cseq := range refseq {
 173                 for _, libref := range cseq {
 174                         reftile[libref.Tag] = &reftileinfo{seqname: seqname}
 175                 }
 176         }
 177         log.Info("loading reference tiles from all slices")
 178         throttle := throttle{Max: runtime.GOMAXPROCS(0)}
 179         for _, infile := range infiles {
 180                 infile := infile
 181                 throttle.Go(func() error {
 182                         defer log.Infof("%s: done", infile)
 183                         f, err := open(infile)
 184                         if err != nil {
 185                                 return err
 186                         }
 187                         defer f.Close()
 188                         return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 189                                 for _, tv := range ent.TileVariants {
 190                                         if dst, ok := reftile[tv.Tag]; ok {
 191                                                 dst.tiledata = tv.Sequence
 192                                         }
 193                                 }
 194                                 return nil
 195                         })
 196                 })
 197         }
 198         throttle.Wait()
 199
 200         log.Info("reconstructing reference sequences")
 201         for seqname, cseq := range refseq {
 202                 seqname, cseq := seqname, cseq
 203                 throttle.Go(func() error {
 204                         defer log.Printf("... %s done", seqname)
 205                         pos := 0
 206                         for _, libref := range cseq {
 207                                 rt := reftile[libref.Tag]
 208                                 rt.pos = pos
 209                                 pos += len(rt.tiledata) - taglen
 210                         }
 211                         return nil
 212                 })
 213         }
 214         throttle.Wait()
 215
 216         log.Info("TODO: determining which tiles intersect given regions")
 217
 218         log.Info("generating annotations and numpy matrix for each slice")
 219         var done int64
 220         for infileIdx, infile := range infiles {
 221                 infileIdx, infile := infileIdx, infile
 222                 throttle.Go(func() error {
 223                         seq := map[tagID][][]byte{}
 224                         cgs := make(map[string]CompactGenome, len(cgnames))
 225                         f, err := open(infile)
 226                         if err != nil {
 227                                 return err
 228                         }
 229                         defer f.Close()
 230                         log.Infof("reading %s", infile)
 231                         err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
 232                                 for _, tv := range ent.TileVariants {
 233                                         variants := seq[tv.Tag]
 234                                         for len(variants) <= int(tv.Variant) {
 235                                                 variants = append(variants, nil)
 236                                         }
 237                                         variants[int(tv.Variant)] = tv.Sequence
 238                                         seq[tv.Tag] = variants
 239                                 }
 240                                 for _, cg := range ent.CompactGenomes {
 241                                         cgs[cg.Name] = cg
 242                                 }
 243                                 return nil
 244                         })
 245                         if err != nil {
 246                                 return err
 247                         }
 248                         tagstart := cgs[cgnames[0]].StartTag
 249                         tagend := cgs[cgnames[0]].EndTag
 250
 251                         // TODO: filters
 252                         // TODO: tidy/renumber
 253
 254                         annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
 255                         log.Infof("writing %s", annotationsFilename)
 256                         annof, err := os.Create(annotationsFilename)
 257                         if err != nil {
 258                                 return err
 259                         }
 260                         annow := bufio.NewWriterSize(annof, 1<<20)
 261                         for tag, variants := range seq {
 262                                 rt, ok := reftile[tag]
 263                                 if !ok {
 264                                         // Reference does not use any
 265                                         // variant of this tile.
 266                                         // TODO: log this? mention it
 267                                         // in annotations?
 268                                         continue
 269                                 }
 270                                 outcol := tag - tagID(tagstart)
 271                                 reftilestr := strings.ToUpper(string(rt.tiledata))
 272                                 for v, seq := range variants {
 273                                         if len(seq) == 0 || !bytes.HasSuffix(rt.tiledata, seq[len(seq)-taglen:]) {
 274                                                 continue
 275                                         }
 276                                         if lendiff := len(rt.tiledata) - len(seq); lendiff < -1000 || lendiff > 1000 {
 277                                                 continue
 278                                         }
 279                                         diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(seq)), 0)
 280                                         for _, diff := range diffs {
 281                                                 diff.Position += rt.pos
 282                                                 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, v, rt.seqname, diff.String())
 283                                         }
 284                                 }
 285                         }
 286                         err = annow.Flush()
 287                         if err != nil {
 288                                 return err
 289                         }
 290                         err = annof.Close()
 291                         if err != nil {
 292                                 return err
 293                         }
 294
 295                         log.Infof("%s: preparing numpy", infile)
 296                         rows := len(cgnames)
 297                         cols := 2 * int(tagend-tagstart)
 298                         out := make([]int16, rows*cols)
 299                         for row, name := range cgnames {
 300                                 out := out[row*cols:]
 301                                 for col, v := range cgs[name].Variants {
 302                                         if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v]) > 0 {
 303                                                 out[col] = int16(v)
 304                                         } else {
 305                                                 out[col] = -1
 306                                         }
 307                                 }
 308                         }
 309
 310                         fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
 311                         output, err := os.Create(fnm)
 312                         if err != nil {
 313                                 return err
 314                         }
 315                         defer output.Close()
 316                         bufw := bufio.NewWriterSize(output, 1<<26)
 317                         npw, err := gonpy.NewWriter(nopCloser{bufw})
 318                         if err != nil {
 319                                 return err
 320                         }
 321                         log.WithFields(logrus.Fields{
 322                                 "filename": fnm,
 323                                 "rows":     rows,
 324                                 "cols":     cols,
 325                         }).Info("writing numpy")
 326                         npw.Shape = []int{rows, cols}
 327                         npw.WriteInt16(out)
 328                         err = bufw.Flush()
 329                         if err != nil {
 330                                 return err
 331                         }
 332                         err = output.Close()
 333                         if err != nil {
 334                                 return err
 335                         }
 336                         log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
 337                         return nil
 338                 })
 339         }
 340         if err = throttle.Wait(); err != nil {
 341                 return 1
 342         }
 343         return 0
 344 }
 345
 346 func (*sliceNumpy) writeLibRefs(fnm string, tilelib *tileLibrary, librefs []tileLibRef) error {
 347         f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY, 0666)
 348         if err != nil {
 349                 return err
 350         }
 351         defer f.Close()
 352         for i, libref := range librefs {
 353                 _, err = fmt.Fprintf(f, "%d,%d,%d\n", i, libref.Tag, libref.Variant)
 354                 if err != nil {
 355                         return err
 356                 }
 357         }
 358         return f.Close()
 359 }