annotate.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "errors"
   6         "flag"
   7         "fmt"
   8         "io"
   9         "io/ioutil"
  10         "net/http"
  11         _ "net/http/pprof"
  12         "os"
  13         "runtime"
  14         "sort"
  15         "strconv"
  16         "strings"
  17         "sync"
  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 annotatecmd struct {
  25         variantHash bool
  26 }
  27
  28 func (cmd *annotatecmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  29         var err error
  30         defer func() {
  31                 if err != nil {
  32                         fmt.Fprintf(stderr, "%s\n", err)
  33                 }
  34         }()
  35         flags := flag.NewFlagSet("", flag.ContinueOnError)
  36         flags.SetOutput(stderr)
  37         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  38         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  39         projectUUID := flags.String("project", "", "project `UUID` for output data")
  40         priority := flags.Int("priority", 500, "container request priority")
  41         inputFilename := flags.String("i", "-", "input `file` (library)")
  42         outputFilename := flags.String("o", "-", "output `file`")
  43         flags.BoolVar(&cmd.variantHash, "variant-hash", false, "output variant hash instead of index")
  44         err = flags.Parse(args)
  45         if err == flag.ErrHelp {
  46                 err = nil
  47                 return 0
  48         } else if err != nil {
  49                 return 2
  50         }
  51
  52         if *pprof != "" {
  53                 go func() {
  54                         log.Println(http.ListenAndServe(*pprof, nil))
  55                 }()
  56         }
  57         if !*runlocal {
  58                 if *outputFilename != "-" {
  59                         err = errors.New("cannot specify output file in container mode: not implemented")
  60                         return 1
  61                 }
  62                 runner := arvadosContainerRunner{
  63                         Name:        "lightning annotate",
  64                         Client:      arvados.NewClientFromEnv(),
  65                         ProjectUUID: *projectUUID,
  66                         RAM:         120000000000,
  67                         VCPUs:       32,
  68                         Priority:    *priority,
  69                 }
  70                 err = runner.TranslatePaths(inputFilename)
  71                 if err != nil {
  72                         return 1
  73                 }
  74                 runner.Args = []string{"annotate", "-local=true", fmt.Sprintf("-variant-hash=%v", cmd.variantHash), "-i", *inputFilename, "-o", "/mnt/output/tilevariants.tsv"}
  75                 var output string
  76                 output, err = runner.Run()
  77                 if err != nil {
  78                         return 1
  79                 }
  80                 fmt.Fprintln(stdout, output+"/tilevariants.tsv")
  81                 return 0
  82         }
  83
  84         var input io.ReadCloser
  85         if *inputFilename == "-" {
  86                 input = ioutil.NopCloser(stdin)
  87         } else {
  88                 input, err = os.Open(*inputFilename)
  89                 if err != nil {
  90                         return 1
  91                 }
  92                 defer input.Close()
  93         }
  94
  95         var output io.WriteCloser
  96         if *outputFilename == "-" {
  97                 output = nopCloser{stdout}
  98         } else {
  99                 output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0666)
 100                 if err != nil {
 101                         return 1
 102                 }
 103                 defer output.Close()
 104         }
 105         bufw := bufio.NewWriter(output)
 106
 107         err = cmd.exportTileDiffs(bufw, input)
 108         if err != nil {
 109                 return 1
 110         }
 111         err = bufw.Flush()
 112         if err != nil {
 113                 return 1
 114         }
 115         err = output.Close()
 116         if err != nil {
 117                 return 1
 118         }
 119         err = input.Close()
 120         if err != nil {
 121                 return 1
 122         }
 123         return 0
 124 }
 125
 126 func (cmd *annotatecmd) exportTileDiffs(outw io.Writer, librdr io.Reader) error {
 127         var refs []CompactSequence
 128         var tiles [][]TileVariant
 129         var tagset [][]byte
 130         var taglen int
 131         err := DecodeLibrary(librdr, func(ent *LibraryEntry) error {
 132                 if len(ent.TagSet) > 0 {
 133                         if tagset != nil {
 134                                 return errors.New("error: not implemented: input has multiple tagsets")
 135                         }
 136                         tagset = ent.TagSet
 137                         taglen = len(tagset[0])
 138                         tiles = make([][]TileVariant, len(tagset))
 139                 }
 140                 for _, tv := range ent.TileVariants {
 141                         if tv.Tag >= tagID(len(tiles)) {
 142                                 return fmt.Errorf("error: reading tile variant for tag %d but only %d tags were loaded", tv.Tag, len(tiles))
 143                         }
 144                         for len(tiles[tv.Tag]) <= int(tv.Variant) {
 145                                 tiles[tv.Tag] = append(tiles[tv.Tag], TileVariant{})
 146                         }
 147                         tiles[tv.Tag][tv.Variant] = tv
 148                 }
 149                 for _, cs := range ent.CompactSequences {
 150                         refs = append(refs, cs)
 151                 }
 152                 return nil
 153         })
 154         if err != nil {
 155                 return err
 156         }
 157         tag2tagid := make(map[string]tagID, len(tagset))
 158         for tagid, tagseq := range tagset {
 159                 tag2tagid[string(tagseq)] = tagID(tagid)
 160         }
 161         sort.Slice(refs, func(i, j int) bool { return refs[i].Name < refs[j].Name })
 162         log.Infof("len(refs) %d", len(refs))
 163
 164         outch := make(chan string, 1)
 165         var outwg sync.WaitGroup
 166         defer outwg.Wait()
 167         outwg.Add(1)
 168         go func() {
 169                 defer outwg.Done()
 170                 for s := range outch {
 171                         io.WriteString(outw, s)
 172                 }
 173         }()
 174         defer close(outch)
 175
 176         limiter := make(chan bool, runtime.NumCPU()+1)
 177         var diffwg sync.WaitGroup
 178         defer diffwg.Wait()
 179
 180         for _, refcs := range refs {
 181                 refcs := refcs
 182                 var seqnames []string
 183                 for seqname := range refcs.TileSequences {
 184                         seqnames = append(seqnames, seqname)
 185                 }
 186                 sort.Strings(seqnames)
 187                 for _, seqname := range seqnames {
 188                         seqname := seqname
 189                         var refseq []byte
 190                         // tilestart[123] is the index into refseq
 191                         // where the tile for tag 123 was placed.
 192                         tilestart := map[tagID]int{}
 193                         tileend := map[tagID]int{}
 194                         for _, libref := range refcs.TileSequences[seqname] {
 195                                 if libref.Variant < 1 {
 196                                         return fmt.Errorf("reference %q seq %q uses variant zero at tag %d", refcs.Name, seqname, libref.Tag)
 197                                 }
 198                                 seq := tiles[libref.Tag][libref.Variant].Sequence
 199                                 if len(seq) < taglen {
 200                                         return fmt.Errorf("reference %q seq %q uses tile %d variant %d with sequence len %d < taglen %d", refcs.Name, seqname, libref.Tag, libref.Variant, len(seq), taglen)
 201                                 }
 202                                 overlap := taglen
 203                                 if len(refseq) == 0 {
 204                                         overlap = 0
 205                                 }
 206                                 tilestart[libref.Tag] = len(refseq) - overlap
 207                                 refseq = append(refseq, seq[overlap:]...)
 208                                 tileend[libref.Tag] = len(refseq)
 209                         }
 210                         log.Infof("seq %s len(refseq) %d len(tilestart) %d", seqname, len(refseq), len(tilestart))
 211                         for tag, tvs := range tiles {
 212                                 tag := tagID(tag)
 213                                 refstart, ok := tilestart[tag]
 214                                 if !ok {
 215                                         // Tag didn't place on this
 216                                         // reference sequence. (It
 217                                         // might place on the same
 218                                         // chromosome in a genome
 219                                         // anyway, but we don't output
 220                                         // the annotations that would
 221                                         // result.)
 222                                         continue
 223                                 }
 224                                 for variant, tv := range tvs {
 225                                         variant, tv := variant, tv
 226                                         if variant == 0 {
 227                                                 continue
 228                                         }
 229                                         if len(tv.Sequence) < taglen {
 230                                                 return fmt.Errorf("tilevar %d,%d has sequence len %d < taglen %d", tag, variant, len(tv.Sequence), taglen)
 231                                         }
 232                                         var refpart []byte
 233                                         endtag := string(tv.Sequence[len(tv.Sequence)-taglen:])
 234                                         if endtagid, ok := tag2tagid[endtag]; !ok {
 235                                                 // Tile variant doesn't end on a tag, so it can only place at the end of a chromosome.
 236                                                 refpart = refseq[refstart:]
 237                                                 log.Warnf("%x tilevar %d,%d endtag not in ref: %s", tv.Blake2b[:13], tag, variant, endtag)
 238                                         } else if refendtagstart, ok := tilestart[endtagid]; !ok {
 239                                                 // Ref ends a chromsome with a (possibly very large) variant of this tile, but genomes with this tile don't.
 240                                                 // Give up. (TODO: something smarter)
 241                                                 log.Debugf("%x not annotating tilevar %d,%d because end tag %d is not in ref", tv.Blake2b[:13], tag, variant, endtagid)
 242                                                 continue
 243                                         } else {
 244                                                 // Non-terminal tile vs. non-terminal reference.
 245                                                 refpart = refseq[refstart : refendtagstart+taglen]
 246                                                 log.Tracef("\n%x tilevar %d,%d endtag %s endtagid %d refendtagstart %d", tv.Blake2b[:13], tag, variant, endtag, endtagid, refendtagstart)
 247                                         }
 248                                         if len(refpart) > 10000 {
 249                                                 log.Warnf("%x tilevar %d,%d skipping long diff, ref %s seq %s ref len %d", tv.Blake2b[:13], tag, variant, refcs.Name, seqname, len(refpart))
 250                                                 continue
 251                                         }
 252                                         if len(tv.Sequence) > 10000 {
 253                                                 log.Warnf("%x tilevar %d,%d skipping long diff, ref %s seq %s variant len %d", tv.Blake2b[:13], tag, variant, refcs.Name, seqname, len(tv.Sequence))
 254                                                 continue
 255                                         }
 256                                         // log.Printf("\n%x @ refstart %d \n< %s\n> %s\n", tv.Blake2b, refstart, refpart, tv.Sequence)
 257
 258                                         diffwg.Add(1)
 259                                         limiter <- true
 260                                         go func() {
 261                                                 defer func() {
 262                                                         <-limiter
 263                                                         diffwg.Done()
 264                                                 }()
 265                                                 diffs, _ := hgvs.Diff(strings.ToUpper(string(refpart)), strings.ToUpper(string(tv.Sequence)), 0)
 266                                                 for _, diff := range diffs {
 267                                                         diff.Position += refstart
 268                                                         var varid string
 269                                                         if cmd.variantHash {
 270                                                                 varid = fmt.Sprintf("%x", tv.Blake2b)[:13]
 271                                                         } else {
 272                                                                 varid = strconv.Itoa(variant)
 273                                                         }
 274                                                         outch <- fmt.Sprintf("%d\t%s\t%s\t%s:g.%s\n", tag, varid, refcs.Name, seqname, diff.String())
 275                                                 }
 276                                         }()
 277                                 }
 278                         }
 279                 }
 280         }
 281         return nil
 282 }