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