20 "git.arvados.org/arvados.git/sdk/go/arvados"
21 log "github.com/sirupsen/logrus"
24 type vcf2fasta struct {
29 gvcfRegionsPyData []byte
38 func (cmd *vcf2fasta) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
42 fmt.Fprintf(stderr, "%s\n", err)
45 flags := flag.NewFlagSet("", flag.ContinueOnError)
46 flags.SetOutput(stderr)
47 flags.StringVar(&cmd.refFile, "ref", "", "reference fasta `file`")
48 flags.StringVar(&cmd.genomeFile, "genome", "", "reference genome `file`")
49 flags.BoolVar(&cmd.mask, "mask", false, "mask uncalled regions (default: output hom ref)")
50 flags.StringVar(&cmd.gvcfRegionsPy, "gvcf-regions.py", "https://raw.githubusercontent.com/lijiayong/gvcf_regions/master/gvcf_regions.py", "source of gvcf_regions.py")
51 flags.StringVar(&cmd.projectUUID, "project", "", "project `UUID` for containers and output data")
52 flags.StringVar(&cmd.outputDir, "output-dir", "", "output directory")
53 flags.IntVar(&cmd.vcpus, "vcpus", 0, "number of VCPUs to request for arvados container (default: 2*number of input files, max 32)")
54 flags.BoolVar(&cmd.runLocal, "local", false, "run on local host (default: run in an arvados container)")
55 priority := flags.Int("priority", 500, "container request priority")
56 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
57 err = flags.Parse(args)
58 if err == flag.ErrHelp {
61 } else if err != nil {
63 } else if cmd.refFile == "" {
64 err = errors.New("reference data (-ref) not specified")
66 } else if flags.NArg() == 0 {
74 log.Println(http.ListenAndServe(*pprof, nil))
79 err = cmd.loadRegionsPy()
86 if cmd.outputDir != "" {
87 err = errors.New("cannot specify output dir in non-local mode")
92 infiles, err = listInputFiles(flags.Args())
96 if cmd.vcpus = len(infiles) * 2; cmd.vcpus > 32 {
100 runner := arvadosContainerRunner{
101 Name: "lightning vcf2fasta",
102 Client: arvados.NewClientFromEnv(),
103 ProjectUUID: cmd.projectUUID,
104 RAM: 2<<30 + int64(cmd.vcpus)<<28,
107 Mounts: map[string]map[string]interface{}{
108 "/gvcf_regions.py": map[string]interface{}{
110 "content": string(cmd.gvcfRegionsPyData),
114 err = runner.TranslatePaths(&cmd.refFile)
118 inputs := flags.Args()
119 for i := range inputs {
120 err = runner.TranslatePaths(&inputs[i])
125 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...)
127 output, err = runner.Run()
131 fmt.Fprintln(stdout, output)
135 infiles, err := listInputFiles(flags.Args())
144 todo := make(chan job)
146 for _, infile := range infiles {
147 for phase := 1; phase <= 2; phase++ {
148 todo <- job{vcffile: infile, phase: phase}
154 done := make(chan error, runtime.NumCPU()*2)
155 var wg sync.WaitGroup
156 for i := 0; i < runtime.NumCPU(); i++ {
160 for job := range todo {
162 // a different worker encountered an error
165 err := cmd.vcf2fasta(job.vcffile, job.phase)
167 done <- fmt.Errorf("%s phase %d: %s", job.vcffile, job.phase, err)
185 func maybeInDocker(args, mountfiles []string) []string {
186 if out, err := exec.Command("docker", "image", "ls", "-q", "lightning-runtime").Output(); err != nil || len(out) == 0 {
189 dockerrun := []string{
190 "docker", "run", "--rm",
193 for _, f := range mountfiles {
194 dockerrun = append(dockerrun, "--volume="+f+":"+f+":ro")
196 dockerrun = append(dockerrun, "lightning-runtime")
197 dockerrun = append(dockerrun, args...)
201 func (cmd *vcf2fasta) vcf2fasta(infile string, phase int) error {
202 _, basename := filepath.Split(infile)
203 outfile := filepath.Join(cmd.outputDir, fmt.Sprintf("%s.%d.fasta.gz", basename, phase))
204 outf, err := os.OpenFile(outfile, os.O_CREATE|os.O_WRONLY|os.O_EXCL, 0777)
206 return fmt.Errorf("error opening output file: %s", err)
209 gzipw := gzip.NewWriter(outf)
212 var maskfile *os.File // reading side of a pipe if we're running bedtools, otherwise nil
214 var wg sync.WaitGroup
215 errs := make(chan error, 3)
217 if cmd.genomeFile == "" {
218 return errors.New("cannot apply mask without -genome argument")
220 bedr, bedw, err := os.Pipe()
224 bedargs := []string{"python", "-", "--gvcf_type", "gatk", infile}
225 bed := exec.Command(bedargs[0], bedargs[1:]...)
226 bed.Stdin = bytes.NewBuffer(cmd.gvcfRegionsPyData)
228 bed.Stderr = cmd.stderr
232 log.Printf("running %v", bed.Args)
236 bedcompr, bedcompw, err := os.Pipe()
240 bedcompargs := []string{"bedtools", "complement", "-i", "/dev/stdin", "-g", cmd.genomeFile}
241 bedcompargs = maybeInDocker(bedcompargs, []string{cmd.refFile, infile})
242 bedcomp := exec.Command(bedcompargs[0], bedcompargs[1:]...)
244 bedcomp.Stdout = bedcompw
245 bedcomp.Stderr = cmd.stderr
249 log.Printf("running %v", bedcomp.Args)
250 errs <- bedcomp.Run()
258 consargs := []string{"bcftools", "consensus", "--fasta-ref", cmd.refFile, "-H", fmt.Sprint(phase)}
260 consargs = append(consargs, "--mask", "/dev/stdin")
262 consargs = append(consargs, infile)
263 indexsuffix := ".tbi"
264 if _, err := os.Stat(infile + ".csi"); err == nil {
267 consargs = maybeInDocker(consargs, []string{infile, infile + indexsuffix, cmd.refFile})
269 consensus := exec.Command(consargs[0], consargs[1:]...)
270 consensus.Stderr = os.Stderr
271 consensus.Stdout = gzipw
272 consensus.Stderr = cmd.stderr
274 consensus.Stdin = maskfile
276 log.Printf("running %v", consensus.Args)
277 err = consensus.Run()
295 for err := range errs {
304 func (cmd *vcf2fasta) loadRegionsPy() error {
305 if strings.HasPrefix(cmd.gvcfRegionsPy, "http") {
306 resp, err := http.Get(cmd.gvcfRegionsPy)
310 if resp.StatusCode != http.StatusOK {
311 return fmt.Errorf("get %q: http status %d", cmd.gvcfRegionsPy, resp.StatusCode)
313 buf, err := ioutil.ReadAll(resp.Body)
315 return fmt.Errorf("get %q: read body: %s", cmd.gvcfRegionsPy, err)
317 cmd.gvcfRegionsPyData = buf
320 buf, err := ioutil.ReadFile(cmd.gvcfRegionsPy)
324 cmd.gvcfRegionsPyData = buf