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         pick := flags.String("pick", "", "`name` of single genome to export")
  60         err = flags.Parse(args)
  61         if err == flag.ErrHelp {
  62                 err = nil
  63                 return 0
  64         } else if err != nil {
  65                 return 2
  66         }
  67
  68         if f, ok := outputFormats[*outputFormatStr]; !ok {
  69                 err = fmt.Errorf("invalid output format %q", *outputFormatStr)
  70                 return 2
  71         } else {
  72                 cmd.outputFormat = f
  73         }
  74
  75         if *pprof != "" {
  76                 go func() {
  77                         log.Println(http.ListenAndServe(*pprof, nil))
  78                 }()
  79         }
  80
  81         if !*runlocal {
  82                 if *outputFilename != "-" {
  83                         err = errors.New("cannot specify output file in container mode: not implemented")
  84                         return 1
  85                 }
  86                 runner := arvadosContainerRunner{
  87                         Name:        "lightning export",
  88                         Client:      arvados.NewClientFromEnv(),
  89                         ProjectUUID: *projectUUID,
  90                         RAM:         128000000000,
  91                         VCPUs:       2,
  92                         Priority:    *priority,
  93                 }
  94                 err = runner.TranslatePaths(inputFilename)
  95                 if err != nil {
  96                         return 1
  97                 }
  98                 runner.Args = []string{"export", "-local=true", "-pick", *pick, "-ref", *refname, "-output-format", *outputFormatStr, "-i", *inputFilename, "-o", "/mnt/output/export.csv"}
  99                 var output string
 100                 output, err = runner.Run()
 101                 if err != nil {
 102                         return 1
 103                 }
 104                 fmt.Fprintln(stdout, output+"/export.csv")
 105                 return 0
 106         }
 107
 108         input, err := os.Open(*inputFilename)
 109         if err != nil {
 110                 return 1
 111         }
 112         defer input.Close()
 113
 114         // Error out early if seeking doesn't work on the input file.
 115         _, err = input.Seek(0, io.SeekEnd)
 116         if err != nil {
 117                 return 1
 118         }
 119         _, err = input.Seek(0, io.SeekStart)
 120         if err != nil {
 121                 return 1
 122         }
 123
 124         var mtx sync.Mutex
 125         var cgs []CompactGenome
 126         var tilelib tileLibrary
 127         err = tilelib.LoadGob(context.Background(), input, func(cg CompactGenome) {
 128                 if *pick != "" && *pick != cg.Name {
 129                         return
 130                 }
 131                 log.Debugf("export: pick %q", cg.Name)
 132                 mtx.Lock()
 133                 defer mtx.Unlock()
 134                 cgs = append(cgs, cg)
 135         })
 136         if err != nil {
 137                 return 1
 138         }
 139         sort.Slice(cgs, func(i, j int) bool { return cgs[i].Name < cgs[j].Name })
 140         log.Printf("export: pick %q => %d genomes", *pick, len(cgs))
 141
 142         refseq, ok := tilelib.refseqs[*refname]
 143         if !ok {
 144                 err = fmt.Errorf("reference name %q not found in input; have %v", *refname, func() (names []string) {
 145                         for name := range tilelib.refseqs {
 146                                 names = append(names, name)
 147                         }
 148                         return
 149                 }())
 150                 return 1
 151         }
 152
 153         _, err = input.Seek(0, io.SeekStart)
 154         if err != nil {
 155                 return 1
 156         }
 157
 158         var output io.WriteCloser
 159         if *outputFilename == "-" {
 160                 output = nopCloser{stdout}
 161         } else {
 162                 output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0777)
 163                 if err != nil {
 164                         return 1
 165                 }
 166                 defer output.Close()
 167         }
 168         bufw := bufio.NewWriter(output)
 169         err = cmd.export(bufw, input, tilelib.taglib.keylen, refseq, cgs)
 170         if err != nil {
 171                 return 1
 172         }
 173         err = bufw.Flush()
 174         if err != nil {
 175                 return 1
 176         }
 177         err = output.Close()
 178         if err != nil {
 179                 return 1
 180         }
 181         err = input.Close()
 182         if err != nil {
 183                 return 1
 184         }
 185         return 0
 186 }
 187
 188 func (cmd *exporter) export(out io.Writer, librdr io.Reader, taglen int, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
 189         need := map[tileLibRef]bool{}
 190         var seqnames []string
 191         for seqname, librefs := range refseq {
 192                 seqnames = append(seqnames, seqname)
 193                 for _, libref := range librefs {
 194                         if libref.Variant != 0 {
 195                                 need[libref] = true
 196                         }
 197                 }
 198         }
 199         sort.Strings(seqnames)
 200
 201         for _, cg := range cgs {
 202                 for i, variant := range cg.Variants {
 203                         if variant == 0 {
 204                                 continue
 205                         }
 206                         libref := tileLibRef{Tag: tagID(i / 2), Variant: variant}
 207                         need[libref] = true
 208                 }
 209         }
 210
 211         log.Infof("export: loading %d tile variants", len(need))
 212         tileVariant := map[tileLibRef]TileVariant{}
 213         err := DecodeLibrary(librdr, func(ent *LibraryEntry) error {
 214                 for _, tv := range ent.TileVariants {
 215                         libref := tileLibRef{Tag: tv.Tag, Variant: tv.Variant}
 216                         if need[libref] {
 217                                 tileVariant[libref] = tv
 218                         }
 219                 }
 220                 return nil
 221         })
 222         if err != nil {
 223                 return err
 224         }
 225
 226         log.Infof("export: loaded %d tile variants", len(tileVariant))
 227         var missing []tileLibRef
 228         for libref := range need {
 229                 if _, ok := tileVariant[libref]; !ok {
 230                         missing = append(missing, libref)
 231                 }
 232         }
 233         if len(missing) > 0 {
 234                 if limit := 100; len(missing) > limit {
 235                         log.Warnf("first %d missing tiles: %v", limit, missing[:limit])
 236                 } else {
 237                         log.Warnf("missing tiles: %v", missing)
 238                 }
 239                 return fmt.Errorf("%d needed tiles are missing from library", len(missing))
 240         }
 241
 242         refpos := 0
 243         for _, seqname := range seqnames {
 244                 variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
 245                 for refstep, libref := range refseq[seqname] {
 246                         reftile := tileVariant[libref]
 247                         for cgidx, cg := range cgs {
 248                                 for phase := 0; phase < 2; phase++ {
 249                                         if len(cg.Variants) <= int(libref.Tag)*2+phase {
 250                                                 continue
 251                                         }
 252                                         variant := cg.Variants[int(libref.Tag)*2+phase]
 253                                         if variant == 0 {
 254                                                 continue
 255                                         }
 256                                         genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
 257                                         if variant == libref.Variant {
 258                                                 continue
 259                                         }
 260                                         refSequence := reftile.Sequence
 261                                         // If needed, extend the
 262                                         // reference sequence up to
 263                                         // the tag at the end of the
 264                                         // genometile sequence.
 265                                         refstepend := refstep + 1
 266                                         for refstepend < len(refseq[seqname]) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) {
 267                                                 if &refSequence[0] == &reftile.Sequence[0] {
 268                                                         refSequence = append([]byte(nil), refSequence...)
 269                                                 }
 270                                                 refSequence = append(refSequence, tileVariant[refseq[seqname][refstepend]].Sequence...)
 271                                                 refstepend++
 272                                         }
 273                                         vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genometile.Sequence)), time.Second)
 274                                         for _, v := range vars {
 275                                                 if cmd.outputFormat.PadLeft {
 276                                                         v = v.PadLeft()
 277                                                 }
 278                                                 v.Position += refpos
 279                                                 log.Debugf("%s seq %s phase %d tag %d tile diff %s\n", cg.Name, seqname, phase, libref.Tag, v.String())
 280                                                 varslice := variantAt[v.Position]
 281                                                 if varslice == nil {
 282                                                         varslice = make([]hgvs.Variant, len(cgs)*2)
 283                                                         variantAt[v.Position] = varslice
 284                                                 }
 285                                                 varslice[cgidx*2+phase] = v
 286                                         }
 287                                 }
 288                         }
 289                         refpos += len(reftile.Sequence) - taglen
 290
 291                         // Flush entries from variantAt that are
 292                         // behind refpos. Flush all entries if this is
 293                         // the last reftile of the path/chromosome.
 294                         var flushpos []int
 295                         lastrefstep := refstep == len(refseq[seqname])-1
 296                         for pos := range variantAt {
 297                                 if lastrefstep || pos <= refpos {
 298                                         flushpos = append(flushpos, pos)
 299                                 }
 300                         }
 301                         sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
 302                         for _, pos := range flushpos {
 303                                 varslice := variantAt[pos]
 304                                 delete(variantAt, pos)
 305                                 for i := range varslice {
 306                                         if varslice[i].Position == 0 {
 307                                                 varslice[i].Position = pos
 308                                         }
 309                                 }
 310                                 cmd.outputFormat.Print(out, seqname, varslice)
 311                         }
 312                 }
 313         }
 314         return nil
 315 }
 316
 317 func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
 318         refs := map[string]map[string]int{}
 319         for _, v := range varslice {
 320                 if v.Ref == "" && v.New == "" {
 321                         continue
 322                 }
 323                 alts := refs[v.Ref]
 324                 if alts == nil {
 325                         alts = map[string]int{}
 326                         refs[v.Ref] = alts
 327                 }
 328                 alts[v.New] = 0
 329         }
 330         for ref, alts := range refs {
 331                 var altslice []string
 332                 for alt := range alts {
 333                         altslice = append(altslice, alt)
 334                 }
 335                 sort.Strings(altslice)
 336                 for i, a := range altslice {
 337                         alts[a] = i + 1
 338                 }
 339                 fmt.Fprintf(out, "%s\t%d\t%s\t%s", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
 340                 for i := 0; i < len(varslice)/2; i++ {
 341                         v1, v2 := varslice[i*2], varslice[i*2+1]
 342                         a1, a2 := alts[v1.New], alts[v2.New]
 343                         if v1.Ref != ref {
 344                                 a1 = 0
 345                         }
 346                         if v2.Ref != ref {
 347                                 a2 = 0
 348                         }
 349                         fmt.Fprintf(out, "\t%d/%d", a1, a2)
 350                 }
 351                 out.Write([]byte{'\n'})
 352         }
 353 }
 354
 355 func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
 356         for i := 0; i < len(varslice)/2; i++ {
 357                 if i > 0 {
 358                         out.Write([]byte{'\t'})
 359                 }
 360                 var1, var2 := varslice[i*2], varslice[i*2+1]
 361                 if var1 == var2 {
 362                         if var1.Ref == var1.New {
 363                                 out.Write([]byte{'.'})
 364                         } else {
 365                                 fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
 366                         }
 367                 } else {
 368                         fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
 369                 }
 370         }
 371         out.Write([]byte{'\n'})
 372 }