annotate.go

   1 package lightning
   2
   3 import (
   4         "bufio"
   5         "context"
   6         "errors"
   7         "flag"
   8         "fmt"
   9         "io"
  10         "io/ioutil"
  11         "net/http"
  12         _ "net/http/pprof"
  13         "os"
  14         "runtime"
  15         "sort"
  16         "strconv"
  17         "strings"
  18         "sync"
  19
  20         "git.arvados.org/arvados.git/sdk/go/arvados"
  21         "github.com/arvados/lightning/hgvs"
  22         log "github.com/sirupsen/logrus"
  23 )
  24
  25 type annotatecmd struct {
  26         dropTiles   []bool
  27         variantHash bool
  28         maxTileSize int
  29         tag2tagid   map[string]tagID
  30 }
  31
  32 func (cmd *annotatecmd) 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         inputFilename := flags.String("i", "-", "input `file` (library)")
  46         outputFilename := flags.String("o", "-", "output `file`")
  47         flags.BoolVar(&cmd.variantHash, "variant-hash", false, "output variant hash instead of index")
  48         flags.IntVar(&cmd.maxTileSize, "max-tile-size", 50000, "don't try to make annotations for tiles bigger than given `size`")
  49         err = flags.Parse(args)
  50         if err == flag.ErrHelp {
  51                 err = nil
  52                 return 0
  53         } else if err != nil {
  54                 return 2
  55         }
  56
  57         if *pprof != "" {
  58                 go func() {
  59                         log.Println(http.ListenAndServe(*pprof, nil))
  60                 }()
  61         }
  62         if !*runlocal {
  63                 if *outputFilename != "-" {
  64                         err = errors.New("cannot specify output file in container mode: not implemented")
  65                         return 1
  66                 }
  67                 runner := arvadosContainerRunner{
  68                         Name:        "lightning annotate",
  69                         Client:      arvados.NewClientFromEnv(),
  70                         ProjectUUID: *projectUUID,
  71                         RAM:         80000000000,
  72                         VCPUs:       16,
  73                         Priority:    *priority,
  74                 }
  75                 err = runner.TranslatePaths(inputFilename)
  76                 if err != nil {
  77                         return 1
  78                 }
  79                 runner.Args = []string{"annotate", "-local=true", fmt.Sprintf("-variant-hash=%v", cmd.variantHash), "-max-tile-size", strconv.Itoa(cmd.maxTileSize), "-i", *inputFilename, "-o", "/mnt/output/tilevariants.csv"}
  80                 var output string
  81                 output, err = runner.Run()
  82                 if err != nil {
  83                         return 1
  84                 }
  85                 fmt.Fprintln(stdout, output+"/tilevariants.csv")
  86                 return 0
  87         }
  88
  89         var input io.ReadCloser
  90         if *inputFilename == "-" {
  91                 input = ioutil.NopCloser(stdin)
  92         } else {
  93                 input, err = os.Open(*inputFilename)
  94                 if err != nil {
  95                         return 1
  96                 }
  97                 defer input.Close()
  98         }
  99
 100         var output io.WriteCloser
 101         if *outputFilename == "-" {
 102                 output = nopCloser{stdout}
 103         } else {
 104                 output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0666)
 105                 if err != nil {
 106                         return 1
 107                 }
 108                 defer output.Close()
 109         }
 110         bufw := bufio.NewWriterSize(output, 4*1024*1024)
 111
 112         tilelib := &tileLibrary{
 113                 retainNoCalls:       true,
 114                 retainTileSequences: true,
 115         }
 116         err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), nil)
 117         if err != nil {
 118                 return 1
 119         }
 120         err = cmd.exportTileDiffs(bufw, tilelib)
 121         if err != nil {
 122                 return 1
 123         }
 124         err = bufw.Flush()
 125         if err != nil {
 126                 return 1
 127         }
 128         err = output.Close()
 129         if err != nil {
 130                 return 1
 131         }
 132         err = input.Close()
 133         if err != nil {
 134                 return 1
 135         }
 136         return 0
 137 }
 138
 139 func (cmd *annotatecmd) exportTileDiffs(outw io.Writer, tilelib *tileLibrary) error {
 140         tagset := tilelib.taglib.Tags()
 141         if len(tagset) == 0 {
 142                 return errors.New("cannot annotate library without tags")
 143         }
 144         taglen := len(tagset[0])
 145         var refs []string
 146         for name := range tilelib.refseqs {
 147                 refs = append(refs, name)
 148         }
 149         cmd.tag2tagid = make(map[string]tagID, len(tagset))
 150         for tagid, tagseq := range tagset {
 151                 cmd.tag2tagid[string(tagseq)] = tagID(tagid)
 152         }
 153         sort.Strings(refs)
 154         log.Infof("len(refs) %d", len(refs))
 155
 156         outch := make(chan string, runtime.NumCPU()*2)
 157         var outwg sync.WaitGroup
 158         defer outwg.Wait()
 159         outwg.Add(1)
 160         go func() {
 161                 defer outwg.Done()
 162                 for s := range outch {
 163                         io.WriteString(outw, s)
 164                 }
 165         }()
 166         defer close(outch)
 167
 168         nseqs := 0
 169         for _, refcs := range tilelib.refseqs {
 170                 nseqs += len(refcs)
 171         }
 172
 173         throttle := &throttle{Max: runtime.NumCPU()*2 + nseqs*2 + 1}
 174         defer throttle.Wait()
 175
 176         for _, refname := range refs {
 177                 refname := refname
 178                 refcs := tilelib.refseqs[refname]
 179                 var seqnames []string
 180                 for seqname := range refcs {
 181                         seqnames = append(seqnames, seqname)
 182                 }
 183                 sort.Strings(seqnames)
 184                 for _, seqname := range seqnames {
 185                         seqname := seqname
 186                         throttle.Acquire()
 187                         if throttle.Err() != nil {
 188                                 break
 189                         }
 190                         go func() {
 191                                 defer throttle.Release()
 192                                 throttle.Report(cmd.annotateSequence(throttle, outch, tilelib, taglen, refname, seqname, refcs[seqname], len(refs) > 1))
 193                         }()
 194                 }
 195         }
 196         throttle.Wait()
 197         return throttle.Err()
 198 }
 199
 200 func (cmd *annotatecmd) annotateSequence(throttle *throttle, outch chan<- string, tilelib *tileLibrary, taglen int, refname, seqname string, reftiles []tileLibRef, refnamecol bool) error {
 201         refnamefield := ""
 202         if refnamecol {
 203                 refnamefield = "," + trimFilenameForLabel(refname)
 204         }
 205         var refseq []byte
 206         // tilestart[123] is the index into refseq
 207         // where the tile for tag 123 was placed.
 208         tilestart := map[tagID]int{}
 209         tileend := map[tagID]int{}
 210         for _, libref := range reftiles {
 211                 if libref.Variant < 1 {
 212                         return fmt.Errorf("reference %q seq %q uses variant zero at tag %d", refname, seqname, libref.Tag)
 213                 }
 214                 seq := tilelib.TileVariantSequence(libref)
 215                 if len(seq) < taglen {
 216                         return fmt.Errorf("reference %q seq %q uses tile %d variant %d with sequence len %d < taglen %d", refname, seqname, libref.Tag, libref.Variant, len(seq), taglen)
 217                 }
 218                 overlap := taglen
 219                 if len(refseq) == 0 {
 220                         overlap = 0
 221                 }
 222                 tilestart[libref.Tag] = len(refseq) - overlap
 223                 refseq = append(refseq, seq[overlap:]...)
 224                 tileend[libref.Tag] = len(refseq)
 225         }
 226         log.Infof("seq %s len(refseq) %d len(tilestart) %d", seqname, len(refseq), len(tilestart))
 227         // outtag is tag's index in the subset of tags that aren't
 228         // dropped. If there are 10M tags and half are dropped by
 229         // dropTiles, tag ranges from 0 to 10M-1 and outtag ranges
 230         // from 0 to 5M-1.
 231         //
 232         // IOW, in the matrix built by cgs2array(), {tag} is
 233         // represented by columns {outtag}*2 and {outtag}*2+1.
 234         outcol := -1
 235         for tag, tvs := range tilelib.variant {
 236                 if len(cmd.dropTiles) > tag && cmd.dropTiles[tag] {
 237                         continue
 238                 }
 239                 tag := tagID(tag)
 240                 outcol++
 241                 // Must shadow outcol var to use safely in goroutine below.
 242                 outcol := outcol
 243                 refstart, ok := tilestart[tag]
 244                 if !ok {
 245                         // Tag didn't place on this
 246                         // reference sequence. (It
 247                         // might place on the same
 248                         // chromosome in a genome
 249                         // anyway, but we don't output
 250                         // the annotations that would
 251                         // result.)
 252                         // outch <- fmt.Sprintf("%d,%d,-1%s\n", tag, outcol, refnamefield)
 253                         continue
 254                 }
 255                 for variant := 1; variant <= len(tvs); variant++ {
 256                         variant, hash := tileVariantID(variant), tvs[variant-1]
 257                         tileseq := tilelib.TileVariantSequence(tileLibRef{Tag: tag, Variant: variant})
 258                         if len(tileseq) == 0 {
 259                                 continue
 260                         } else if len(tileseq) < taglen {
 261                                 return fmt.Errorf("tilevar %d,%d has sequence len %d < taglen %d", tag, variant, len(tileseq), taglen)
 262                         }
 263                         var refpart []byte
 264                         endtag := string(tileseq[len(tileseq)-taglen:])
 265                         if endtagid, ok := cmd.tag2tagid[endtag]; !ok {
 266                                 // Tile variant doesn't end on a tag, so it can only place at the end of a chromosome.
 267                                 refpart = refseq[refstart:]
 268                                 log.Warnf("%x tilevar %d,%d endtag not in ref: %s", hash[:13], tag, variant, endtag)
 269                         } else if refendtagstart, ok := tilestart[endtagid]; !ok {
 270                                 // Ref ends a chromsome with a (possibly very large) variant of this tile, but genomes with this tile don't.
 271                                 // Give up. (TODO: something smarter)
 272                                 log.Debugf("%x not annotating tilevar %d,%d because end tag %d is not in ref", hash[:13], tag, variant, endtagid)
 273                                 continue
 274                         } else {
 275                                 // Non-terminal tile vs. non-terminal reference.
 276                                 refpart = refseq[refstart : refendtagstart+taglen]
 277                                 log.Tracef("\n%x tilevar %d,%d endtag %s endtagid %d refendtagstart %d", hash[:13], tag, variant, endtag, endtagid, refendtagstart)
 278                         }
 279                         if len(refpart) > cmd.maxTileSize {
 280                                 log.Warnf("%x tilevar %d,%d skipping long diff, ref %s seq %s pos %d ref len %d", hash[:13], tag, variant, refname, seqname, refstart, len(refpart))
 281                                 continue
 282                         }
 283                         if len(tileseq) > cmd.maxTileSize {
 284                                 log.Warnf("%x tilevar %d,%d skipping long diff, ref %s seq %s variant len %d", hash[:13], tag, variant, refname, seqname, len(tileseq))
 285                                 continue
 286                         }
 287                         // log.Printf("\n%x @ refstart %d \n< %s\n> %s\n", tv.Blake2b, refstart, refpart, tileseq)
 288
 289                         throttle.Acquire()
 290                         go func() {
 291                                 defer throttle.Release()
 292                                 diffs, _ := hgvs.Diff(strings.ToUpper(string(refpart)), strings.ToUpper(string(tileseq)), 0)
 293                                 for _, diff := range diffs {
 294                                         diff.Position += refstart
 295                                         var varid string
 296                                         if cmd.variantHash {
 297                                                 varid = fmt.Sprintf("%x", hash)[:13]
 298                                         } else {
 299                                                 varid = fmt.Sprintf("%d", variant)
 300                                         }
 301                                         outch <- fmt.Sprintf("%d,%d,%s%s,%s:g.%s\n", tag, outcol, varid, refnamefield, seqname, diff.String())
 302                                 }
 303                         }()
 304                 }
 305         }
 306         return nil
 307 }