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