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         "sort"
  14         "strconv"
  15         "strings"
  16
  17         "git.arvados.org/arvados.git/sdk/go/arvados"
  18         "github.com/arvados/lightning/hgvs"
  19         log "github.com/sirupsen/logrus"
  20 )
  21
  22 type annotatecmd struct {
  23         variantHash bool
  24 }
  25
  26 func (cmd *annotatecmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  27         var err error
  28         defer func() {
  29                 if err != nil {
  30                         fmt.Fprintf(stderr, "%s\n", err)
  31                 }
  32         }()
  33         flags := flag.NewFlagSet("", flag.ContinueOnError)
  34         flags.SetOutput(stderr)
  35         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  36         runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
  37         projectUUID := flags.String("project", "", "project `UUID` for output data")
  38         priority := flags.Int("priority", 500, "container request priority")
  39         inputFilename := flags.String("i", "-", "input `file` (library)")
  40         outputFilename := flags.String("o", "-", "output `file`")
  41         flags.BoolVar(&cmd.variantHash, "variant-hash", false, "output variant hash instead of index")
  42         err = flags.Parse(args)
  43         if err == flag.ErrHelp {
  44                 err = nil
  45                 return 0
  46         } else if err != nil {
  47                 return 2
  48         }
  49
  50         if *pprof != "" {
  51                 go func() {
  52                         log.Println(http.ListenAndServe(*pprof, nil))
  53                 }()
  54         }
  55         if !*runlocal {
  56                 if *outputFilename != "-" {
  57                         err = errors.New("cannot specify output file in container mode: not implemented")
  58                         return 1
  59                 }
  60                 runner := arvadosContainerRunner{
  61                         Name:        "lightning annotate",
  62                         Client:      arvados.NewClientFromEnv(),
  63                         ProjectUUID: *projectUUID,
  64                         RAM:         120000000000,
  65                         VCPUs:       2,
  66                         Priority:    *priority,
  67                 }
  68                 err = runner.TranslatePaths(inputFilename)
  69                 if err != nil {
  70                         return 1
  71                 }
  72                 runner.Args = []string{"annotate", "-local=true", fmt.Sprintf("-variant-hash=%v", cmd.variantHash), "-i", *inputFilename, "-o", "/mnt/output/tilevariants.tsv"}
  73                 var output string
  74                 output, err = runner.Run()
  75                 if err != nil {
  76                         return 1
  77                 }
  78                 fmt.Fprintln(stdout, output+"/tilevariants.tsv")
  79                 return 0
  80         }
  81
  82         var input io.ReadCloser
  83         if *inputFilename == "-" {
  84                 input = ioutil.NopCloser(stdin)
  85         } else {
  86                 input, err = os.Open(*inputFilename)
  87                 if err != nil {
  88                         return 1
  89                 }
  90                 defer input.Close()
  91         }
  92
  93         var output io.WriteCloser
  94         if *outputFilename == "-" {
  95                 output = nopCloser{stdout}
  96         } else {
  97                 output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0666)
  98                 if err != nil {
  99                         return 1
 100                 }
 101                 defer output.Close()
 102         }
 103         bufw := bufio.NewWriter(output)
 104
 105         err = cmd.exportTileDiffs(bufw, input)
 106         if err != nil {
 107                 return 1
 108         }
 109         err = bufw.Flush()
 110         if err != nil {
 111                 return 1
 112         }
 113         err = output.Close()
 114         if err != nil {
 115                 return 1
 116         }
 117         err = input.Close()
 118         if err != nil {
 119                 return 1
 120         }
 121         return 0
 122 }
 123
 124 func (cmd *annotatecmd) exportTileDiffs(outw io.Writer, librdr io.Reader) error {
 125         var refs []CompactSequence
 126         var tiles [][]TileVariant
 127         var tagset [][]byte
 128         var taglen int
 129         err := DecodeLibrary(librdr, func(ent *LibraryEntry) error {
 130                 if len(ent.TagSet) > 0 {
 131                         if tagset != nil {
 132                                 return errors.New("error: not implemented: input has multiple tagsets")
 133                         }
 134                         tagset = ent.TagSet
 135                         taglen = len(tagset[0])
 136                         tiles = make([][]TileVariant, len(tagset))
 137                 }
 138                 for _, tv := range ent.TileVariants {
 139                         if tv.Tag >= tagID(len(tiles)) {
 140                                 return fmt.Errorf("error: reading tile variant for tag %d but only %d tags were loaded", tv.Tag, len(tiles))
 141                         }
 142                         for len(tiles[tv.Tag]) <= int(tv.Variant) {
 143                                 tiles[tv.Tag] = append(tiles[tv.Tag], TileVariant{})
 144                         }
 145                         tiles[tv.Tag][tv.Variant] = tv
 146                 }
 147                 for _, cs := range ent.CompactSequences {
 148                         refs = append(refs, cs)
 149                 }
 150                 return nil
 151         })
 152         if err != nil {
 153                 return err
 154         }
 155         tag2tagid := make(map[string]tagID, len(tagset))
 156         for tagid, tagseq := range tagset {
 157                 tag2tagid[string(tagseq)] = tagID(tagid)
 158         }
 159         sort.Slice(refs, func(i, j int) bool { return refs[i].Name < refs[j].Name })
 160         log.Infof("len(refs) %d", len(refs))
 161         for _, refcs := range refs {
 162                 var seqnames []string
 163                 for seqname := range refcs.TileSequences {
 164                         seqnames = append(seqnames, seqname)
 165                 }
 166                 sort.Strings(seqnames)
 167                 for _, seqname := range seqnames {
 168                         var refseq []byte
 169                         // tilestart[123] is the index into refseq
 170                         // where the tile for tag 123 was placed.
 171                         tilestart := map[tagID]int{}
 172                         tileend := map[tagID]int{}
 173                         for _, libref := range refcs.TileSequences[seqname] {
 174                                 if libref.Variant < 1 {
 175                                         return fmt.Errorf("reference %q seq %q uses variant zero at tag %d", refcs.Name, seqname, libref.Tag)
 176                                 }
 177                                 seq := tiles[libref.Tag][libref.Variant].Sequence
 178                                 if len(seq) < taglen {
 179                                         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)
 180                                 }
 181                                 overlap := taglen
 182                                 if len(refseq) == 0 {
 183                                         overlap = 0
 184                                 }
 185                                 tilestart[libref.Tag] = len(refseq) - overlap
 186                                 refseq = append(refseq, seq[overlap:]...)
 187                                 tileend[libref.Tag] = len(refseq)
 188                         }
 189                         log.Infof("seq %s len(refseq) %d len(tilestart) %d", seqname, len(refseq), len(tilestart))
 190                         for tag, tvs := range tiles {
 191                                 tag := tagID(tag)
 192                                 refstart, ok := tilestart[tag]
 193                                 if !ok {
 194                                         // Tag didn't place on this
 195                                         // reference sequence. (It
 196                                         // might place on the same
 197                                         // chromosome in a genome
 198                                         // anyway, but we don't output
 199                                         // the annotations that would
 200                                         // result.)
 201                                         continue
 202                                 }
 203                                 for variant, tv := range tvs {
 204                                         if variant == 0 {
 205                                                 continue
 206                                         }
 207                                         if len(tv.Sequence) < taglen {
 208                                                 return fmt.Errorf("tilevar %d,%d has sequence len %d < taglen %d", tag, variant, len(tv.Sequence), taglen)
 209                                         }
 210                                         var refpart []byte
 211                                         endtag := string(tv.Sequence[len(tv.Sequence)-taglen:])
 212                                         if endtagid, ok := tag2tagid[endtag]; !ok {
 213                                                 // Tile variant doesn't end on a tag, so it can only place at the end of a chromosome.
 214                                                 refpart = refseq[refstart:]
 215                                                 log.Warnf("%x tilevar %d,%d endtag not in ref: %s", tv.Blake2b[:13], tag, variant, endtag)
 216                                         } else if refendtagstart, ok := tilestart[endtagid]; !ok {
 217                                                 // Ref ends a chromsome with a (possibly very large) variant of this tile, but genomes with this tile don't.
 218                                                 // Give up. (TODO: something smarter)
 219                                                 log.Warnf("%x not annotating tilevar %d,%d because end tag %d is not in ref", tv.Blake2b[:13], tag, variant, endtagid)
 220                                                 continue
 221                                         } else {
 222                                                 // Non-terminal tile vs. non-terminal reference.
 223                                                 refpart = refseq[refstart : refendtagstart+taglen]
 224                                                 log.Tracef("\n%x tilevar %d,%d endtag %s endtagid %d refendtagstart %d", tv.Blake2b[:13], tag, variant, endtag, endtagid, refendtagstart)
 225                                         }
 226                                         // log.Printf("\n%x @ refstart %d \n< %s\n> %s\n", tv.Blake2b, refstart, refpart, tv.Sequence)
 227                                         diffs, _ := hgvs.Diff(strings.ToUpper(string(refpart)), strings.ToUpper(string(tv.Sequence)), 0)
 228                                         for _, diff := range diffs {
 229                                                 diff.Position += refstart
 230                                                 var varid string
 231                                                 if cmd.variantHash {
 232                                                         varid = fmt.Sprintf("%x", tv.Blake2b)[:13]
 233                                                 } else {
 234                                                         varid = strconv.Itoa(variant)
 235                                                 }
 236                                                 fmt.Fprintf(outw, "%d\t%s\t%s\t%s:g.%s\n", tag, varid, refcs.Name, seqname, diff.String())
 237                                         }
 238                                 }
 239                         }
 240                 }
 241         }
 242         return nil
 243 }