vcf2fasta.go

   1 package main
   2
   3 import (
   4         "bytes"
   5         "compress/gzip"
   6         "errors"
   7         "flag"
   8         "fmt"
   9         "io"
  10         "io/ioutil"
  11         "net/http"
  12         _ "net/http/pprof"
  13         "os"
  14         "os/exec"
  15         "path/filepath"
  16         "runtime"
  17         "strings"
  18         "sync"
  19
  20         "git.arvados.org/arvados.git/sdk/go/arvados"
  21         log "github.com/sirupsen/logrus"
  22 )
  23
  24 type vcf2fasta struct {
  25         refFile           string
  26         mask              bool
  27         gvcfRegionsPy     string
  28         gvcfRegionsPyData []byte
  29         projectUUID       string
  30         outputDir         string
  31         runLocal          bool
  32         vcpus             int
  33
  34         stderr io.Writer
  35 }
  36
  37 func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
  38         var err error
  39         defer func() {
  40                 if err != nil {
  41                         fmt.Fprintf(stderr, "%s\n", err)
  42                 }
  43         }()
  44         flags := flag.NewFlagSet("", flag.ContinueOnError)
  45         flags.SetOutput(stderr)
  46         flags.StringVar(&cmd.refFile, "ref", "", "reference fasta `file`")
  47         flags.BoolVar(&cmd.mask, "mask", false, "mask uncalled regions (default: output hom ref)")
  48         flags.StringVar(&cmd.gvcfRegionsPy, "gvcf-regions.py", "https://raw.githubusercontent.com/lijiayong/gvcf_regions/master/gvcf_regions.py", "source of gvcf_regions.py")
  49         flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for containers and output data")
  50         flags.StringVar(&cmd.outputDir, "output-dir", "", "output directory")
  51         flags.IntVar(&cmd.vcpus, "vcpus", 0, "number of VCPUs to request for arvados container (default: 2*number of input files, max 32)")
  52         flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)")
  53         priority := flags.Int("priority", 500, "container request priority")
  54         pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
  55         err = flags.Parse(args)
  56         if err == flag.ErrHelp {
  57                 err = nil
  58                 return 0
  59         } else if err != nil {
  60                 return 2
  61         } else if cmd.refFile == "" {
  62                 err = errors.New("reference data (-ref) not specified")
  63                 return 2
  64         } else if flags.NArg() == 0 {
  65                 flags.Usage()
  66                 return 2
  67         }
  68         cmd.stderr = stderr
  69
  70         if *pprof != "" {
  71                 go func() {
  72                         log.Println(http.ListenAndServe(*pprof, nil))
  73                 }()
  74         }
  75
  76         if cmd.mask {
  77                 err = cmd.loadRegionsPy()
  78                 if err != nil {
  79                         return 1
  80                 }
  81         }
  82
  83         if !cmd.runLocal {
  84                 if cmd.outputDir != "" {
  85                         err = errors.New("cannot specify output dir in non-local mode")
  86                         return 2
  87                 }
  88                 if cmd.vcpus < 1 {
  89                         var infiles []string
  90                         infiles, err = listInputFiles(flags.Args())
  91                         if err != nil {
  92                                 return 1
  93                         }
  94                         if cmd.vcpus = len(infiles) * 2; cmd.vcpus > 32 {
  95                                 cmd.vcpus = 32
  96                         }
  97                 }
  98                 runner := arvadosContainerRunner{
  99                         Name:        "lightning vcf2fasta",
 100                         Client:      arvados.NewClientFromEnv(),
 101                         ProjectUUID: cmd.projectUUID,
 102                         RAM:         2<<30 + int64(cmd.vcpus)<<28,
 103                         VCPUs:       cmd.vcpus,
 104                         Priority:    *priority,
 105                         Mounts: map[string]map[string]interface{}{
 106                                 "/gvcf_regions.py": map[string]interface{}{
 107                                         "kind":    "text",
 108                                         "content": string(cmd.gvcfRegionsPyData),
 109                                 },
 110                         },
 111                 }
 112                 err = runner.TranslatePaths(&cmd.refFile)
 113                 if err != nil {
 114                         return 1
 115                 }
 116                 inputs := flags.Args()
 117                 for i := range inputs {
 118                         err = runner.TranslatePaths(&inputs[i])
 119                         if err != nil {
 120                                 return 1
 121                         }
 122                 }
 123                 runner.Args = append([]string{"vcf2fasta", "-local=true", "-ref", cmd.refFile, fmt.Sprintf("-mask=%v", cmd.mask), "-gvcf-regions.py", "/gvcf_regions.py", "-output-dir", "/mnt/output"}, inputs...)
 124                 var output string
 125                 output, err = runner.Run()
 126                 if err != nil {
 127                         return 1
 128                 }
 129                 fmt.Fprintln(stdout, output)
 130                 return 0
 131         }
 132
 133         infiles, err := listInputFiles(flags.Args())
 134         if err != nil {
 135                 return 1
 136         }
 137
 138         type job struct {
 139                 vcffile string
 140                 phase   int
 141         }
 142         todo := make(chan job)
 143         go func() {
 144                 for _, infile := range infiles {
 145                         for phase := 1; phase <= 2; phase++ {
 146                                 todo <- job{vcffile: infile, phase: phase}
 147                         }
 148                 }
 149                 close(todo)
 150         }()
 151
 152         done := make(chan error, runtime.NumCPU()*2)
 153         var wg sync.WaitGroup
 154         for i := 0; i < runtime.NumCPU(); i++ {
 155                 wg.Add(1)
 156                 go func() {
 157                         defer wg.Done()
 158                         for job := range todo {
 159                                 if len(done) > 0 {
 160                                         // a different worker encountered an error
 161                                         return
 162                                 }
 163                                 err := cmd.vcf2fasta(job.vcffile, job.phase)
 164                                 if err != nil {
 165                                         done <- fmt.Errorf("%s phase %d: %s", job.vcffile, job.phase, err)
 166                                         return
 167                                 }
 168                         }
 169                 }()
 170         }
 171         go func() {
 172                 wg.Wait()
 173                 close(done)
 174         }()
 175
 176         err = <-done
 177         if err != nil {
 178                 return 1
 179         }
 180         return 0
 181 }
 182
 183 func maybeInDocker(args, mountfiles []string) []string {
 184         if out, err := exec.Command("docker", "image", "ls", "-q", "lightning-runtime").Output(); err != nil || len(out) == 0 {
 185                 return args
 186         }
 187         dockerrun := []string{
 188                 "docker", "run", "--rm",
 189                 "--log-driver=none",
 190         }
 191         for _, f := range mountfiles {
 192                 dockerrun = append(dockerrun, "--volume="+f+":"+f+":ro")
 193         }
 194         dockerrun = append(dockerrun, "lightning-runtime")
 195         dockerrun = append(dockerrun, args...)
 196         return dockerrun
 197 }
 198
 199 func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
 200         _, basename := filepath.Split(infile)
 201         outfile := filepath.Join(cmd.outputDir, fmt.Sprintf("%s.%d.fasta.gz", basename, phase))
 202         outf, err := os.OpenFile(outfile, os.O_CREATE|os.O_WRONLY|os.O_EXCL, 0777)
 203         if err != nil {
 204                 return fmt.Errorf("error opening output file: %s", err)
 205         }
 206         defer outf.Close()
 207         gzipw := gzip.NewWriter(outf)
 208         defer gzipw.Close()
 209
 210         var maskfile *os.File // reading side of a pipe if we're running bedtools, otherwise nil
 211
 212         var wg sync.WaitGroup
 213         errs := make(chan error, 3)
 214         if cmd.mask {
 215                 bedr, bedw, err := os.Pipe()
 216                 if err != nil {
 217                         return err
 218                 }
 219                 bedargs := []string{"python", "-", "--gvcf_type", "gatk", infile}
 220                 bed := exec.Command(bedargs[0], bedargs[1:]...)
 221                 bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
 222                 bed.Stdout = bedw
 223                 bed.Stderr = cmd.stderr
 224                 wg.Add(1)
 225                 go func() {
 226                         defer wg.Done()
 227                         log.Printf("running %v", bed.Args)
 228                         errs <- bed.Run()
 229                 }()
 230
 231                 bedcompr, bedcompw, err := os.Pipe()
 232                 if err != nil {
 233                         return err
 234                 }
 235                 bedcompargs := []string{"bedtools", "complement", "-i", "/dev/stdin", "-g", cmd.refFile}
 236                 bedcompargs = maybeInDocker(bedcompargs, []string{cmd.refFile, infile})
 237                 bedcomp := exec.Command(bedcompargs[0], bedcompargs[1:]...)
 238                 bedcomp.Stdin = bedr
 239                 bedcomp.Stdout = bedcompw
 240                 bedcomp.Stderr = cmd.stderr
 241                 wg.Add(1)
 242                 go func() {
 243                         defer wg.Done()
 244                         log.Printf("running %v", bedcomp.Args)
 245                         errs <- bedcomp.Run()
 246                 }()
 247                 maskfile = bedcompr
 248         }
 249
 250         wg.Add(1)
 251         go func() {
 252                 defer wg.Done()
 253                 consargs := []string{"bcftools", "consensus", "--fasta-ref", cmd.refFile, "-H", fmt.Sprint(phase)}
 254                 if maskfile != nil {
 255                         consargs = append(consargs, "--mask", "/dev/stdin")
 256                 }
 257                 consargs = append(consargs, infile)
 258                 indexsuffix := ".tbi"
 259                 if _, err := os.Stat(infile + ".csi"); err == nil {
 260                         indexsuffix = ".csi"
 261                 }
 262                 consargs = maybeInDocker(consargs, []string{infile, infile + indexsuffix, cmd.refFile})
 263
 264                 consensus := exec.Command(consargs[0], consargs[1:]...)
 265                 consensus.Stderr = os.Stderr
 266                 consensus.Stdout = gzipw
 267                 consensus.Stderr = cmd.stderr
 268                 if maskfile != nil {
 269                         consensus.Stdin = maskfile
 270                 }
 271                 log.Printf("running %v", consensus.Args)
 272                 err = consensus.Run()
 273                 if err != nil {
 274                         errs <- err
 275                         return
 276                 }
 277                 err = gzipw.Close()
 278                 if err != nil {
 279                         errs <- err
 280                         return
 281                 }
 282                 errs <- outf.Close()
 283         }()
 284
 285         go func() {
 286                 wg.Wait()
 287                 close(errs)
 288         }()
 289
 290         for err := range errs {
 291                 if err != nil {
 292                         return err
 293                 }
 294         }
 295         return nil
 296 }
 297
 298 func (cmd *vcf2fasta) loadRegionsPy() error {
 299         if strings.HasPrefix(cmd.gvcfRegionsPy, "http") {
 300                 resp, err := http.Get(cmd.gvcfRegionsPy)
 301                 if err != nil {
 302                         return err
 303                 }
 304                 if resp.StatusCode != http.StatusOK {
 305                         return fmt.Errorf("get %q: http status %d", cmd.gvcfRegionsPy, resp.StatusCode)
 306                 }
 307                 buf, err := ioutil.ReadAll(resp.Body)
 308                 if err != nil {
 309                         return fmt.Errorf("get %q: read body: %s", cmd.gvcfRegionsPy, err)
 310                 }
 311                 cmd.gvcfRegionsPyData = buf
 312                 return nil
 313         } else {
 314                 buf, err := ioutil.ReadFile(cmd.gvcfRegionsPy)
 315                 if err != nil {
 316                         return err
 317                 }
 318                 cmd.gvcfRegionsPyData = buf
 319                 return nil
 320         }
 321 }