export.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "bytes"
   6         "context"
   7         "errors"
   8         "flag"
   9         "fmt"
  10         "io"
  11         "net/http"
  12         _ "net/http/pprof"
  13         "os"
  14         "sort"
  15         "strings"
  16         "sync"
  17         "time"
  18
  19         "git.arvados.org/arvados.git/sdk/go/arvados"
  20         "github.com/arvados/lightning/hgvs"
  21         log "github.com/sirupsen/logrus"
  22 )
  23
  24 type outputFormat struct {
  25         Print   func(out io.Writer, seqname string, varslice []hgvs.Variant)
  26         PadLeft bool
  27 }
  28
  29 var (
  30         outputFormats = map[string]outputFormat{
  31                 "hgvs": outputFormatHGVS,
  32                 "vcf":  outputFormatVCF,
  33         }
  34         outputFormatHGVS = outputFormat{Print: printHGVS}
  35         outputFormatVCF  = outputFormat{Print: printVCF, PadLeft: true}
  36 )
  37
  38 type exporter struct {
  39         outputFormat outputFormat
  40 }
  41
  42 func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  43         var err error
  44         defer func() {
  45                 if err != nil {
  46                         fmt.Fprintf(stderr, "%s\n", err)
  47                 }
  48         }()
  49         flags := flag.NewFlagSet("", flag.ContinueOnError)
  50         flags.SetOutput(stderr)
  51         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  52         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  53         projectUUID := flags.String("project", "", "project `UUID` for output data")
  54         priority := flags.Int("priority", 500, "container request priority")
  55         refname := flags.String("ref", "", "reference genome `name`")
  56         inputFilename := flags.String("i", "-", "input `file` (library)")
  57         outputFilename := flags.String("o", "-", "output `file`")
  58         outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs or vcf")
  59         outputBed := flags.String("output-bed", "", "also output bed `file`")
  60         pick := flags.String("pick", "", "`name` of single genome to export")
  61         err = flags.Parse(args)
  62         if err == flag.ErrHelp {
  63                 err = nil
  64                 return 0
  65         } else if err != nil {
  66                 return 2
  67         }
  68
  69         if f, ok := outputFormats[*outputFormatStr]; !ok {
  70                 err = fmt.Errorf("invalid output format %q", *outputFormatStr)
  71                 return 2
  72         } else {
  73                 cmd.outputFormat = f
  74         }
  75
  76         if *pprof != "" {
  77                 go func() {
  78                         log.Println(http.ListenAndServe(*pprof, nil))
  79                 }()
  80         }
  81
  82         if !*runlocal {
  83                 if *outputFilename != "-" {
  84                         err = errors.New("cannot specify output file in container mode: not implemented")
  85                         return 1
  86                 }
  87                 runner := arvadosContainerRunner{
  88                         Name:        "lightning export",
  89                         Client:      arvados.NewClientFromEnv(),
  90                         ProjectUUID: *projectUUID,
  91                         RAM:         128000000000,
  92                         VCPUs:       2,
  93                         Priority:    *priority,
  94                 }
  95                 err = runner.TranslatePaths(inputFilename)
  96                 if err != nil {
  97                         return 1
  98                 }
  99                 if *outputBed != "" {
 100                         if strings.Contains(*outputBed, "/") {
 101                                 err = fmt.Errorf("cannot use -output-bed filename %q containing '/' char", *outputBed)
 102                                 return 1
 103                         }
 104                         *outputBed = "/mnt/output/" + *outputBed
 105                 }
 106                 runner.Args = []string{"export", "-local=true", "-pick", *pick, "-ref", *refname, "-output-format", *outputFormatStr, "-output-bed", *outputBed, "-i", *inputFilename, "-o", "/mnt/output/export.csv"}
 107                 var output string
 108                 output, err = runner.Run()
 109                 if err != nil {
 110                         return 1
 111                 }
 112                 fmt.Fprintln(stdout, output+"/export.csv")
 113                 return 0
 114         }
 115
 116         input, err := os.Open(*inputFilename)
 117         if err != nil {
 118                 return 1
 119         }
 120         defer input.Close()
 121
 122         // Error out early if seeking doesn't work on the input file.
 123         _, err = input.Seek(0, io.SeekEnd)
 124         if err != nil {
 125                 return 1
 126         }
 127         _, err = input.Seek(0, io.SeekStart)
 128         if err != nil {
 129                 return 1
 130         }
 131
 132         var mtx sync.Mutex
 133         var cgs []CompactGenome
 134         var tilelib tileLibrary
 135         err = tilelib.LoadGob(context.Background(), input, func(cg CompactGenome) {
 136                 if *pick != "" && *pick != cg.Name {
 137                         return
 138                 }
 139                 log.Debugf("export: pick %q", cg.Name)
 140                 mtx.Lock()
 141                 defer mtx.Unlock()
 142                 cgs = append(cgs, cg)
 143         })
 144         if err != nil {
 145                 return 1
 146         }
 147         sort.Slice(cgs, func(i, j int) bool { return cgs[i].Name < cgs[j].Name })
 148         log.Printf("export: pick %q => %d genomes", *pick, len(cgs))
 149
 150         refseq, ok := tilelib.refseqs[*refname]
 151         if !ok {
 152                 err = fmt.Errorf("reference name %q not found in input; have %v", *refname, func() (names []string) {
 153                         for name := range tilelib.refseqs {
 154                                 names = append(names, name)
 155                         }
 156                         return
 157                 }())
 158                 return 1
 159         }
 160
 161         _, err = input.Seek(0, io.SeekStart)
 162         if err != nil {
 163                 return 1
 164         }
 165
 166         var output io.WriteCloser
 167         if *outputFilename == "-" {
 168                 output = nopCloser{stdout}
 169         } else {
 170                 output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0666)
 171                 if err != nil {
 172                         return 1
 173                 }
 174                 defer output.Close()
 175         }
 176         bufw := bufio.NewWriter(output)
 177
 178         var bedout *os.File
 179         var bedbufw *bufio.Writer
 180         if *outputBed != "" {
 181                 bedout, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
 182                 if err != nil {
 183                         return 1
 184                 }
 185                 defer bedout.Close()
 186                 bedbufw = bufio.NewWriter(bedout)
 187         }
 188
 189         err = cmd.export(bufw, bedout, input, tilelib.taglib.keylen, refseq, cgs)
 190         if err != nil {
 191                 return 1
 192         }
 193         err = bufw.Flush()
 194         if err != nil {
 195                 return 1
 196         }
 197         err = output.Close()
 198         if err != nil {
 199                 return 1
 200         }
 201         if bedout != nil {
 202                 err = bedbufw.Flush()
 203                 if err != nil {
 204                         return 1
 205                 }
 206                 err = bedout.Close()
 207                 if err != nil {
 208                         return 1
 209                 }
 210         }
 211         err = input.Close()
 212         if err != nil {
 213                 return 1
 214         }
 215         return 0
 216 }
 217
 218 func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
 219         need := map[tileLibRef]bool{}
 220         var seqnames []string
 221         for seqname, librefs := range refseq {
 222                 seqnames = append(seqnames, seqname)
 223                 for _, libref := range librefs {
 224                         if libref.Variant != 0 {
 225                                 need[libref] = true
 226                         }
 227                 }
 228         }
 229         sort.Strings(seqnames)
 230
 231         for _, cg := range cgs {
 232                 for i, variant := range cg.Variants {
 233                         if variant == 0 {
 234                                 continue
 235                         }
 236                         libref := tileLibRef{Tag: tagID(i / 2), Variant: variant}
 237                         need[libref] = true
 238                 }
 239         }
 240
 241         log.Infof("export: loading %d tile variants", len(need))
 242         tileVariant := map[tileLibRef]TileVariant{}
 243         err := DecodeLibrary(librdr, func(ent *LibraryEntry) error {
 244                 for _, tv := range ent.TileVariants {
 245                         libref := tileLibRef{Tag: tv.Tag, Variant: tv.Variant}
 246                         if need[libref] {
 247                                 tileVariant[libref] = tv
 248                         }
 249                 }
 250                 return nil
 251         })
 252         if err != nil {
 253                 return err
 254         }
 255
 256         log.Infof("export: loaded %d tile variants", len(tileVariant))
 257         var missing []tileLibRef
 258         for libref := range need {
 259                 if _, ok := tileVariant[libref]; !ok {
 260                         missing = append(missing, libref)
 261                 }
 262         }
 263         if len(missing) > 0 {
 264                 if limit := 100; len(missing) > limit {
 265                         log.Warnf("first %d missing tiles: %v", limit, missing[:limit])
 266                 } else {
 267                         log.Warnf("missing tiles: %v", missing)
 268                 }
 269                 return fmt.Errorf("%d needed tiles are missing from library", len(missing))
 270         }
 271
 272         refpos := 0
 273         for _, seqname := range seqnames {
 274                 variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
 275                 for refstep, libref := range refseq[seqname] {
 276                         reftile := tileVariant[libref]
 277                         coverage := int64(0) // number of ref bases that are called in genomes -- max is len(reftile.Sequence)*len(cgs)*2
 278                         for cgidx, cg := range cgs {
 279                                 for phase := 0; phase < 2; phase++ {
 280                                         if len(cg.Variants) <= int(libref.Tag)*2+phase {
 281                                                 continue
 282                                         }
 283                                         variant := cg.Variants[int(libref.Tag)*2+phase]
 284                                         if variant == 0 {
 285                                                 continue
 286                                         }
 287                                         genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
 288                                         if variant == libref.Variant {
 289                                                 continue
 290                                         }
 291                                         refSequence := reftile.Sequence
 292                                         // If needed, extend the
 293                                         // reference sequence up to
 294                                         // the tag at the end of the
 295                                         // genometile sequence.
 296                                         refstepend := refstep + 1
 297                                         for refstepend < len(refseq[seqname]) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) {
 298                                                 if &refSequence[0] == &reftile.Sequence[0] {
 299                                                         refSequence = append([]byte(nil), refSequence...)
 300                                                 }
 301                                                 refSequence = append(refSequence, tileVariant[refseq[seqname][refstepend]].Sequence...)
 302                                                 refstepend++
 303                                         }
 304                                         // (TODO: handle no-calls)
 305                                         vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genometile.Sequence)), time.Second)
 306                                         for _, v := range vars {
 307                                                 if cmd.outputFormat.PadLeft {
 308                                                         v = v.PadLeft()
 309                                                 }
 310                                                 v.Position += refpos
 311                                                 log.Debugf("%s seq %s phase %d tag %d tile diff %s\n", cg.Name, seqname, phase, libref.Tag, v.String())
 312                                                 varslice := variantAt[v.Position]
 313                                                 if varslice == nil {
 314                                                         varslice = make([]hgvs.Variant, len(cgs)*2)
 315                                                         variantAt[v.Position] = varslice
 316                                                 }
 317                                                 varslice[cgidx*2+phase] = v
 318                                         }
 319                                         coverage += int64(len(reftile.Sequence))
 320                                 }
 321                         }
 322                         refpos += len(reftile.Sequence) - taglen
 323
 324                         // Flush entries from variantAt that are
 325                         // behind refpos. Flush all entries if this is
 326                         // the last reftile of the path/chromosome.
 327                         var flushpos []int
 328                         lastrefstep := refstep == len(refseq[seqname])-1
 329                         for pos := range variantAt {
 330                                 if lastrefstep || pos <= refpos {
 331                                         flushpos = append(flushpos, pos)
 332                                 }
 333                         }
 334                         sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
 335                         for _, pos := range flushpos {
 336                                 varslice := variantAt[pos]
 337                                 delete(variantAt, pos)
 338                                 for i := range varslice {
 339                                         if varslice[i].Position == 0 {
 340                                                 varslice[i].Position = pos
 341                                         }
 342                                 }
 343                                 cmd.outputFormat.Print(out, seqname, varslice)
 344                         }
 345                         if bedout != nil && len(reftile.Sequence) > 0 {
 346                                 tilestart := refpos - len(reftile.Sequence) + taglen
 347                                 tileend := refpos
 348                                 if !lastrefstep {
 349                                         tileend += taglen
 350                                 }
 351                                 thickstart := tilestart + taglen
 352                                 if refstep == 0 {
 353                                         thickstart = 0
 354                                 }
 355                                 thickend := refpos
 356                                 // coverage score, 0 to 1000
 357                                 score := 1000 * coverage / int64(len(reftile.Sequence)) / int64(len(cgs)) / 2
 358                                 fmt.Fprintf(bedout, "%s %d %d %d %d . %d %d\n",
 359                                         seqname, tilestart, tileend,
 360                                         libref.Tag,
 361                                         score,
 362                                         thickstart, thickend)
 363                         }
 364                 }
 365         }
 366         return nil
 367 }
 368
 369 func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
 370         refs := map[string]map[string]int{}
 371         for _, v := range varslice {
 372                 if v.Ref == "" && v.New == "" {
 373                         continue
 374                 }
 375                 alts := refs[v.Ref]
 376                 if alts == nil {
 377                         alts = map[string]int{}
 378                         refs[v.Ref] = alts
 379                 }
 380                 alts[v.New] = 0
 381         }
 382         for ref, alts := range refs {
 383                 var altslice []string
 384                 for alt := range alts {
 385                         altslice = append(altslice, alt)
 386                 }
 387                 sort.Strings(altslice)
 388                 for i, a := range altslice {
 389                         alts[a] = i + 1
 390                 }
 391                 fmt.Fprintf(out, "%s\t%d\t%s\t%s", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
 392                 for i := 0; i < len(varslice)/2; i++ {
 393                         v1, v2 := varslice[i*2], varslice[i*2+1]
 394                         a1, a2 := alts[v1.New], alts[v2.New]
 395                         if v1.Ref != ref {
 396                                 a1 = 0
 397                         }
 398                         if v2.Ref != ref {
 399                                 a2 = 0
 400                         }
 401                         fmt.Fprintf(out, "\t%d/%d", a1, a2)
 402                 }
 403                 out.Write([]byte{'\n'})
 404         }
 405 }
 406
 407 func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
 408         for i := 0; i < len(varslice)/2; i++ {
 409                 if i > 0 {
 410                         out.Write([]byte{'\t'})
 411                 }
 412                 var1, var2 := varslice[i*2], varslice[i*2+1]
 413                 if var1 == var2 {
 414                         if var1.Ref == var1.New {
 415                                 out.Write([]byte{'.'})
 416                         } else {
 417                                 fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
 418                         }
 419                 } else {
 420                         fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
 421                 }
 422         }
 423         out.Write([]byte{'\n'})
 424 }