vcf2fasta.go

   1 package main
   2
   3 import (
   4         "bufio"
   5         "bytes"
   6         "compress/gzip"
   7         "context"
   8         "errors"
   9         "flag"
  10         "fmt"
  11         "io"
  12         "io/ioutil"
  13         "net/http"
  14         _ "net/http/pprof"
  15         "os"
  16         "os/exec"
  17         "path/filepath"
  18         "regexp"
  19         "runtime"
  20         "strconv"
  21         "strings"
  22         "sync"
  23         "syscall"
  24
  25         "git.arvados.org/arvados.git/sdk/go/arvados"
  26         log "github.com/sirupsen/logrus"
  27 )
  28
  29 type vcf2fasta struct {
  30         refFile           string
  31         genomeFile        string
  32         mask              bool
  33         gvcfRegionsPy     string
  34         gvcfRegionsPyData []byte
  35         gvcfType          string
  36         projectUUID       string
  37         outputDir         string
  38         runLocal          bool
  39         vcpus             int
  40         batchArgs
  41
  42         stderr io.Writer
  43 }
  44
  45 func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  46         var err error
  47         defer func() {
  48                 if err != nil {
  49                         fmt.Fprintf(stderr, "%s\n", err)
  50                 }
  51         }()
  52         flags := flag.NewFlagSet("", flag.ContinueOnError)
  53         flags.SetOutput(stderr)
  54         flags.StringVar(&cmd.refFile, "ref", "", "reference fasta `file`")
  55         flags.StringVar(&cmd.genomeFile, "genome", "", "reference genome `file`")
  56         flags.BoolVar(&cmd.mask, "mask", false, "mask uncalled regions (default: output hom ref)")
  57         flags.StringVar(&cmd.gvcfRegionsPy, "gvcf-regions.py", "https://raw.githubusercontent.com/lijiayong/gvcf_regions/master/gvcf_regions.py", "source of gvcf_regions.py")
  58         flags.StringVar(&cmd.gvcfType, "gvcf-type", "gatk", "gvcf_type argument to gvcf_regions.py: gatk, complete_genomics, freebayes")
  59         flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for containers and output data")
  60         flags.StringVar(&cmd.outputDir, "output-dir", "", "output directory")
  61         flags.IntVar(&cmd.vcpus, "vcpus", 0, "number of VCPUs to request for arvados container (default: 2*number of input files, max 32)")
  62         flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)")
  63         cmd.batchArgs.Flags(flags)
  64         priority := flags.Int("priority", 500, "container request priority")
  65         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  66         err = flags.Parse(args)
  67         if err == flag.ErrHelp {
  68                 err = nil
  69                 return 0
  70         } else if err != nil {
  71                 return 2
  72         } else if cmd.refFile == "" {
  73                 err = errors.New("reference data (-ref) not specified")
  74                 return 2
  75         } else if flags.NArg() == 0 {
  76                 flags.Usage()
  77                 return 2
  78         }
  79         cmd.stderr = stderr
  80
  81         if *pprof != "" {
  82                 go func() {
  83                         log.Println(http.ListenAndServe(*pprof, nil))
  84                 }()
  85         }
  86
  87         if cmd.mask {
  88                 err = cmd.loadRegionsPy()
  89                 if err != nil {
  90                         return 1
  91                 }
  92         }
  93
  94         if !cmd.runLocal {
  95                 if cmd.outputDir != "" {
  96                         err = errors.New("cannot specify output dir in non-local mode")
  97                         return 2
  98                 }
  99                 if cmd.vcpus < 1 {
 100                         var infiles []string
 101                         infiles, err = listInputFiles(flags.Args())
 102                         if err != nil {
 103                                 return 1
 104                         }
 105                         if cmd.vcpus = len(cmd.batchArgs.Slice(infiles)) * 2; cmd.vcpus > 32 {
 106                                 cmd.vcpus = 32
 107                         }
 108                 }
 109                 client := arvados.NewClientFromEnv()
 110                 runner := arvadosContainerRunner{
 111                         Name:        "lightning vcf2fasta",
 112                         Client:      client,
 113                         ProjectUUID: cmd.projectUUID,
 114                         RAM:         2<<30 + int64(cmd.vcpus)<<28,
 115                         VCPUs:       cmd.vcpus,
 116                         Priority:    *priority,
 117                         Mounts: map[string]map[string]interface{}{
 118                                 "/gvcf_regions.py": map[string]interface{}{
 119                                         "kind":    "text",
 120                                         "content": string(cmd.gvcfRegionsPyData),
 121                                 },
 122                         },
 123                 }
 124                 err = runner.TranslatePaths(&cmd.refFile, &cmd.genomeFile)
 125                 if err != nil {
 126                         return 1
 127                 }
 128                 inputs := flags.Args()
 129                 for i := range inputs {
 130                         err = runner.TranslatePaths(&inputs[i])
 131                         if err != nil {
 132                                 return 1
 133                         }
 134                 }
 135                 var outputs []string
 136                 outputs, err = cmd.batchArgs.RunBatches(context.Background(), func(ctx context.Context, batch int) (string, error) {
 137                         runner := runner
 138                         if cmd.mask {
 139                                 runner.RAM += int64(cmd.vcpus) << 31
 140                         }
 141                         runner.Args = []string{"vcf2fasta",
 142                                 "-local=true",
 143                                 "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask),
 144                                 "-genome", cmd.genomeFile,
 145                                 "-gvcf-regions.py", "/gvcf_regions.py",
 146                                 "-gvcf-type", cmd.gvcfType,
 147                                 "-output-dir", "/mnt/output",
 148                         }
 149                         runner.Args = append(runner.Args, cmd.batchArgs.Args(batch)...)
 150                         runner.Args = append(runner.Args, inputs...)
 151                         log.Printf("batch %d: %v", batch, runner.Args)
 152                         return runner.RunContext(ctx)
 153                 })
 154                 if err != nil {
 155                         return 1
 156                 }
 157                 fmt.Fprintln(stdout, strings.Join(outputs, " "))
 158                 return 0
 159         }
 160
 161         infiles, err := listInputFiles(flags.Args())
 162         if err != nil {
 163                 return 1
 164         }
 165         infiles = cmd.batchArgs.Slice(infiles)
 166
 167         type job struct {
 168                 vcffile string
 169                 phase   int
 170         }
 171         todo := make(chan job)
 172         go func() {
 173                 for _, infile := range infiles {
 174                         for phase := 1; phase <= 2; phase++ {
 175                                 todo <- job{vcffile: infile, phase: phase}
 176                         }
 177                 }
 178                 close(todo)
 179         }()
 180
 181         done := make(chan error, runtime.NumCPU()*2)
 182         var wg sync.WaitGroup
 183         for i := 0; i < runtime.NumCPU(); i++ {
 184                 wg.Add(1)
 185                 go func() {
 186                         defer wg.Done()
 187                         for job := range todo {
 188                                 if len(done) > 0 {
 189                                         // a different worker encountered an error
 190                                         return
 191                                 }
 192                                 err := cmd.vcf2fasta(job.vcffile, job.phase)
 193                                 if err != nil {
 194                                         done <- fmt.Errorf("%s phase %d: %s", job.vcffile, job.phase, err)
 195                                         return
 196                                 }
 197                         }
 198                 }()
 199         }
 200         go func() {
 201                 wg.Wait()
 202                 close(done)
 203         }()
 204
 205         err = <-done
 206         if err != nil {
 207                 return 1
 208         }
 209         return 0
 210 }
 211
 212 func maybeInDocker(args, mountfiles []string) []string {
 213         if out, err := exec.Command("docker", "image", "ls", "-q", "lightning-runtime").Output(); err != nil || len(out) == 0 {
 214                 return args
 215         }
 216         dockerrun := []string{
 217                 "docker", "run", "--rm", "-i",
 218                 "--log-driver=none",
 219         }
 220         for _, f := range mountfiles {
 221                 dockerrun = append(dockerrun, "--volume="+f+":"+f+":ro")
 222         }
 223         dockerrun = append(dockerrun, "lightning-runtime")
 224         dockerrun = append(dockerrun, args...)
 225         return dockerrun
 226 }
 227
 228 func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 229         ctx, cancel := context.WithCancel(context.Background())
 230         defer cancel()
 231
 232         _, basename := filepath.Split(infile)
 233         outfile := filepath.Join(cmd.outputDir, fmt.Sprintf("%s.%d.fasta.gz", basename, phase))
 234         outf, err := os.OpenFile(outfile, os.O_CREATE|os.O_WRONLY, 0777)
 235         if err != nil {
 236                 return fmt.Errorf("error opening output file: %s", err)
 237         }
 238         defer outf.Close()
 239         bufw := bufio.NewWriterSize(outf, 8*1024*1024)
 240         gzipw := gzip.NewWriter(bufw)
 241         defer gzipw.Close()
 242
 243         var maskfifo string // filename of mask fifo if we're running bedtools, otherwise ""
 244
 245         var wg sync.WaitGroup
 246         errs := make(chan error, 2)
 247         if cmd.mask {
 248                 chrSize := map[string]int{}
 249
 250                 vcffile, err := os.Open(infile)
 251                 if err != nil {
 252                         return err
 253                 }
 254                 defer vcffile.Close()
 255                 var rdr io.Reader = vcffile
 256                 if strings.HasSuffix(infile, ".gz") {
 257                         rdr, err = gzip.NewReader(vcffile)
 258                         if err != nil {
 259                                 return err
 260                         }
 261                 }
 262                 contigre := regexp.MustCompile(`([^=,]*)=([^>,]*)`)
 263                 scanner := bufio.NewScanner(rdr)
 264                 for scanner.Scan() {
 265                         if s := scanner.Text(); !strings.HasPrefix(s, "##") {
 266                                 break
 267                         } else if !strings.HasPrefix(s, "##contig=<") {
 268                                 continue
 269                         } else {
 270                                 kv := map[string]string{}
 271                                 for _, m := range contigre.FindAllStringSubmatch(s[10:], -1) {
 272                                         kv[m[1]] = m[2]
 273                                 }
 274                                 if kv["ID"] != "" && kv["length"] != "" {
 275                                         chrSize[kv["ID"]], _ = strconv.Atoi(kv["length"])
 276                                 }
 277                         }
 278                 }
 279                 if err = scanner.Err(); err != nil {
 280                         return fmt.Errorf("error scanning input file %q: %s", infile, err)
 281                 }
 282                 var regions bytes.Buffer
 283                 bedargs := []string{"python2", "-", "--gvcf_type", cmd.gvcfType, infile}
 284                 bed := exec.CommandContext(ctx, bedargs[0], bedargs[1:]...)
 285                 bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
 286                 bed.Stdout = &regions
 287                 bed.Stderr = cmd.stderr
 288                 log.Printf("running %v", bed.Args)
 289                 err = bed.Run()
 290                 log.Printf("exited %v", bed.Args)
 291                 if err != nil {
 292                         return fmt.Errorf("gvcf_regions: %s", err)
 293                 }
 294
 295                 if cmd.genomeFile != "" {
 296                         // Read chromosome sizes from genome file in
 297                         // case any weren't specified in the VCF
 298                         // header.
 299                         genomeFile, err := os.Open(cmd.genomeFile)
 300                         if err != nil {
 301                                 return fmt.Errorf("error opening genome file %q: %s", cmd.genomeFile, err)
 302                         }
 303                         scanner := bufio.NewScanner(genomeFile)
 304                         for scanner.Scan() {
 305                                 var chr string
 306                                 var size int
 307                                 _, err := fmt.Sscanf(scanner.Text(), "%s\t%d", &chr, &size)
 308                                 if err != nil {
 309                                         return fmt.Errorf("error parsing genome file %q: %s", cmd.genomeFile, err)
 310                                 }
 311                                 if chrSize[chr] == 0 {
 312                                         chrSize[chr] = size
 313                                 }
 314                         }
 315                         if err = scanner.Err(); err != nil {
 316                                 return fmt.Errorf("error scanning genome file %q: %s", cmd.genomeFile, err)
 317                         }
 318                 }
 319
 320                 // "bedtools complement" expects the chromosome sizes
 321                 // ("genome file") to appear in the same order as the
 322                 // chromosomes in the input vcf, so we need to sort
 323                 // them.
 324                 scanner = bufio.NewScanner(bytes.NewBuffer(append([]byte(nil), regions.Bytes()...)))
 325                 var sortedGenomeFile bytes.Buffer
 326                 for scanner.Scan() {
 327                         var chr string
 328                         var size int
 329                         _, err := fmt.Sscanf(scanner.Text(), "%s\t%d", &chr, &size)
 330                         if err != nil {
 331                                 return fmt.Errorf("error parsing gvcf_regions output: %s", err)
 332                         }
 333                         if size, ok := chrSize[chr]; ok {
 334                                 fmt.Fprintf(&sortedGenomeFile, "%s\t%d\n", chr, size)
 335                                 delete(chrSize, chr)
 336                         }
 337                 }
 338
 339                 // The bcftools --mask argument needs to end in ".bed"
 340                 // in order to be parsed as a BED file, so we need to
 341                 // use a named pipe instead of stdin.
 342                 tempdir, err := ioutil.TempDir("", "")
 343                 if err != nil {
 344                         return fmt.Errorf("TempDir: %s", err)
 345                 }
 346                 defer os.RemoveAll(tempdir)
 347                 maskfifo = filepath.Join(tempdir, "fifo.bed")
 348                 err = syscall.Mkfifo(maskfifo, 0600)
 349                 if err != nil {
 350                         return fmt.Errorf("mkfifo: %s", err)
 351                 }
 352
 353                 // bedtools complement can't seem to read from a pipe
 354                 // reliably -- "Error: line number 1 of file
 355                 // /dev/stdin has 1 fields, but 3 were expected." --
 356                 // so we stage to a temp file.
 357                 regionsFile := filepath.Join(tempdir, "gvcf_regions.bed")
 358                 err = ioutil.WriteFile(regionsFile, regions.Bytes(), 0644)
 359                 if err != nil {
 360                         return err
 361                 }
 362
 363                 wg.Add(1)
 364                 go func() {
 365                         defer wg.Done()
 366
 367                         maskfifow, err := os.OpenFile(maskfifo, os.O_WRONLY, 0)
 368                         if err != nil {
 369                                 errs <- err
 370                                 return
 371                         }
 372                         defer maskfifow.Close()
 373
 374                         bedcompargs := []string{"bedtools", "complement", "-i", regionsFile, "-g", "/dev/stdin"}
 375                         bedcompargs = maybeInDocker(bedcompargs, []string{cmd.genomeFile})
 376                         bedcomp := exec.CommandContext(ctx, bedcompargs[0], bedcompargs[1:]...)
 377                         bedcomp.Stdin = &sortedGenomeFile
 378                         bedcomp.Stdout = maskfifow
 379                         bedcomp.Stderr = cmd.stderr
 380                         log.Printf("running %v", bedcomp.Args)
 381                         err = bedcomp.Run()
 382                         log.Printf("exited %v", bedcomp.Args)
 383                         if err != nil {
 384                                 errs <- fmt.Errorf("bedtools complement: %s", err)
 385                                 return
 386                         }
 387                         err = maskfifow.Close()
 388                         if err != nil {
 389                                 errs <- err
 390                                 return
 391                         }
 392                 }()
 393         }
 394
 395         wg.Add(1)
 396         go func() {
 397                 defer wg.Done()
 398                 consargs := []string{"bcftools", "consensus", "--fasta-ref", cmd.refFile, "-H", fmt.Sprint(phase)}
 399                 if maskfifo != "" {
 400                         consargs = append(consargs, "--mask", maskfifo)
 401                 }
 402                 consargs = append(consargs, infile)
 403                 indexsuffix := ".tbi"
 404                 if _, err := os.Stat(infile + ".csi"); err == nil {
 405                         indexsuffix = ".csi"
 406                 }
 407                 mounts := []string{infile, infile + indexsuffix, cmd.refFile}
 408                 if maskfifo != "" {
 409                         mounts = append(mounts, maskfifo)
 410                 }
 411                 consargs = maybeInDocker(consargs, mounts)
 412
 413                 consensus := exec.CommandContext(ctx, consargs[0], consargs[1:]...)
 414                 consensus.Stderr = os.Stderr
 415                 consensus.Stdout = gzipw
 416                 consensus.Stderr = cmd.stderr
 417                 log.Printf("running %v", consensus.Args)
 418                 err = consensus.Run()
 419                 if err != nil {
 420                         errs <- fmt.Errorf("bcftools consensus: %s", err)
 421                         return
 422                 }
 423                 log.Printf("exited %v", consensus.Args)
 424                 err = gzipw.Close()
 425                 if err != nil {
 426                         errs <- err
 427                         return
 428                 }
 429                 err = bufw.Flush()
 430                 if err != nil {
 431                         errs <- err
 432                         return
 433                 }
 434                 errs <- outf.Close()
 435         }()
 436
 437         go func() {
 438                 wg.Wait()
 439                 close(errs)
 440         }()
 441
 442         for err := range errs {
 443                 if err != nil {
 444                         cancel()
 445                         wg.Wait()
 446                         return err
 447                 }
 448         }
 449         return nil
 450 }
 451
 452 func (cmd *vcf2fasta) loadRegionsPy() error {
 453         if strings.HasPrefix(cmd.gvcfRegionsPy, "http") {
 454                 resp, err := http.Get(cmd.gvcfRegionsPy)
 455                 if err != nil {
 456                         return err
 457                 }
 458                 if resp.StatusCode != http.StatusOK {
 459                         return fmt.Errorf("get %q: http status %d", cmd.gvcfRegionsPy, resp.StatusCode)
 460                 }
 461                 buf, err := ioutil.ReadAll(resp.Body)
 462                 if err != nil {
 463                         return fmt.Errorf("get %q: read body: %s", cmd.gvcfRegionsPy, err)
 464                 }
 465                 cmd.gvcfRegionsPyData = buf
 466                 return nil
 467         } else {
 468                 buf, err := ioutil.ReadFile(cmd.gvcfRegionsPy)
 469                 if err != nil {
 470                         return err
 471                 }
 472                 cmd.gvcfRegionsPyData = buf
 473                 return nil
 474         }
 475 }