--- /dev/null
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
+
+import (
+ "bufio"
+ "flag"
+ "fmt"
+ "io"
+ "net/http"
+ _ "net/http/pprof"
+ "os"
+ "runtime"
+ "sort"
+ "strings"
+
+ "git.arvados.org/arvados.git/sdk/go/arvados"
+ "github.com/kshedden/gonpy"
+ "github.com/sirupsen/logrus"
+ log "github.com/sirupsen/logrus"
+)
+
+type sliceNumpy struct {
+ filter filter
+}
+
+func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
+ var err error
+ defer func() {
+ if err != nil {
+ fmt.Fprintf(stderr, "%s\n", err)
+ }
+ }()
+ flags := flag.NewFlagSet("", flag.ContinueOnError)
+ flags.SetOutput(stderr)
+ pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
+ runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
+ projectUUID := flags.String("project", "", "project `UUID` for output data")
+ priority := flags.Int("priority", 500, "container request priority")
+ inputDir := flags.String("input-dir", "./in", "input `directory`")
+ outputDir := flags.String("output-dir", "./out", "output `directory`")
+ regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
+ expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
+ cmd.filter.Flags(flags)
+ err = flags.Parse(args)
+ if err == flag.ErrHelp {
+ err = nil
+ return 0
+ } else if err != nil {
+ return 2
+ }
+
+ if *pprof != "" {
+ go func() {
+ log.Println(http.ListenAndServe(*pprof, nil))
+ }()
+ }
+
+ if !*runlocal {
+ runner := arvadosContainerRunner{
+ Name: "lightning slice-numpy",
+ Client: arvados.NewClientFromEnv(),
+ ProjectUUID: *projectUUID,
+ RAM: 150000000000,
+ VCPUs: 32,
+ Priority: *priority,
+ KeepCache: 1,
+ APIAccess: true,
+ }
+ err = runner.TranslatePaths(inputDir, regionsFilename)
+ if err != nil {
+ return 1
+ }
+ runner.Args = []string{"slice-numpy", "-local=true",
+ "-pprof", ":6060",
+ "-input-dir", *inputDir,
+ "-output-dir", "/mnt/output",
+ "-regions", *regionsFilename,
+ "-expand-regions", fmt.Sprintf("%d", *expandRegions),
+ }
+ runner.Args = append(runner.Args, cmd.filter.Args()...)
+ var output string
+ output, err = runner.Run()
+ if err != nil {
+ return 1
+ }
+ fmt.Fprintln(stdout, output)
+ return 0
+ }
+
+ infiles, err := allGobFiles(*inputDir)
+ if err != nil {
+ return 1
+ }
+ if len(infiles) == 0 {
+ err = fmt.Errorf("no input files found in %s", *inputDir)
+ return 1
+ }
+ sort.Strings(infiles)
+
+ var cgnames []string
+ refseqs := map[string]map[string][]tileLibRef{}
+ in0, err := open(infiles[0])
+ if err != nil {
+ return 1
+ }
+ DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
+ for _, cseq := range ent.CompactSequences {
+ refseqs[cseq.Name] = cseq.TileSequences
+ }
+ for _, cg := range ent.CompactGenomes {
+ cgnames = append(cgnames, cg.Name)
+ }
+ return nil
+ })
+ if err != nil {
+ return 1
+ }
+ in0.Close()
+ sort.Strings(cgnames)
+
+ {
+ labelsFilename := *outputDir + "/labels.csv"
+ log.Infof("writing labels to %s", labelsFilename)
+ var f *os.File
+ f, err = os.Create(labelsFilename)
+ if err != nil {
+ return 1
+ }
+ defer f.Close()
+ for i, name := range cgnames {
+ _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
+ if err != nil {
+ err = fmt.Errorf("write %s: %w", labelsFilename, err)
+ return 1
+ }
+ }
+ err = f.Close()
+ if err != nil {
+ err = fmt.Errorf("close %s: %w", labelsFilename, err)
+ return 1
+ }
+ }
+
+ log.Info("building list of reference tiles to load") // TODO: more efficient if we had saved all ref tiles in slice0
+ reftiledata := map[tileLibRef]*[]byte{}
+ for _, ref := range refseqs {
+ for _, cseq := range ref {
+ for _, libref := range cseq {
+ reftiledata[libref] = new([]byte)
+ }
+ }
+ }
+ log.Info("loading reference tiles from all slices")
+ throttle := throttle{Max: runtime.NumCPU()}
+ for _, infile := range infiles {
+ infile := infile
+ throttle.Go(func() error {
+ defer log.Infof("%s: done", infile)
+ f, err := open(infile)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
+ for _, tv := range ent.TileVariants {
+ libref := tileLibRef{tv.Tag, tv.Variant}
+ if dst, ok := reftiledata[libref]; ok {
+ *dst = tv.Sequence
+ }
+ }
+ return nil
+ })
+ })
+ }
+ throttle.Wait()
+
+ log.Info("TODO: determining which tiles intersect given regions")
+
+ log.Info("generating annotations and numpy matrix for each slice")
+ for infileIdx, infile := range infiles {
+ infileIdx, infile := infileIdx, infile
+ throttle.Go(func() error {
+ defer log.Infof("%s: done", infile)
+ seq := map[tileLibRef][]byte{}
+ cgs := make(map[string]CompactGenome, len(cgnames))
+ f, err := open(infile)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
+ for _, tv := range ent.TileVariants {
+ seq[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
+ }
+ for _, cg := range ent.CompactGenomes {
+ cgs[cg.Name] = cg
+ }
+ return nil
+ })
+ if err != nil {
+ return err
+ }
+
+ log.Infof("TODO: %s: filtering", infile)
+ log.Infof("TODO: %s: tidying", infile)
+ log.Infof("TODO: %s: lowqual to -1", infile)
+
+ annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
+ log.Infof("%s: writing annotations to %s", infile, annotationsFilename)
+ annow, err := os.Create(annotationsFilename)
+ if err != nil {
+ return err
+ }
+ // for libref, seq := range seq {
+ // // TODO: diff from ref.
+ // }
+ err = annow.Close()
+ if err != nil {
+ return err
+ }
+
+ log.Infof("%s: preparing numpy", infile)
+ tagstart := cgs[cgnames[0]].StartTag
+ tagend := cgs[cgnames[0]].EndTag
+ rows := len(cgnames)
+ cols := 2 * int(tagend-tagstart)
+ out := make([]int16, rows*cols)
+ for row, name := range cgnames {
+ out := out[row*cols:]
+ for col, v := range cgs[name].Variants {
+ if v == 0 {
+ // out[col] = 0
+ } else if _, ok := seq[tileLibRef{tagstart + tagID(col/2), v}]; ok {
+ out[col] = int16(v)
+ } else {
+ out[col] = -1
+ }
+ }
+ }
+
+ fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
+ output, err := os.Create(fnm)
+ if err != nil {
+ return err
+ }
+ defer output.Close()
+ bufw := bufio.NewWriter(output)
+ npw, err := gonpy.NewWriter(nopCloser{bufw})
+ if err != nil {
+ return err
+ }
+ log.WithFields(logrus.Fields{
+ "filename": fnm,
+ "rows": rows,
+ "cols": cols,
+ }).Info("writing numpy")
+ npw.Shape = []int{rows, cols}
+ npw.WriteInt16(out)
+ err = bufw.Flush()
+ if err != nil {
+ return err
+ }
+ err = output.Close()
+ if err != nil {
+ return err
+ }
+ return nil
+ })
+ }
+ if err = throttle.Wait(); err != nil {
+ return 1
+ }
+ return 0
+}
+
+func (*sliceNumpy) writeLibRefs(fnm string, tilelib *tileLibrary, librefs []tileLibRef) error {
+ f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY, 0666)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ for i, libref := range librefs {
+ _, err = fmt.Fprintf(f, "%d,%d,%d\n", i, libref.Tag, libref.Variant)
+ if err != nil {
+ return err
+ }
+ }
+ return f.Close()
+}
projects / lightning.git / commitdiff