+++ /dev/null
-// Copyright (C) The Lightning Authors. All rights reserved.
-//
-// SPDX-License-Identifier: AGPL-3.0
-
-package lightning
-
-import (
- "bufio"
- "bytes"
- "flag"
- "fmt"
- "io"
- "net/http"
- _ "net/http/pprof"
- "os"
- "regexp"
- "runtime"
- "sort"
- "strings"
- "sync/atomic"
-
- "git.arvados.org/arvados.git/sdk/go/arvados"
- "github.com/arvados/lightning/hgvs"
- "github.com/kshedden/gonpy"
- log "github.com/sirupsen/logrus"
- "golang.org/x/crypto/blake2b"
-)
-
-type sliceNumpy struct {
- filter filter
- threads int
-}
-
-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`")
- ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
- 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`")
- flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
- 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: 650000000000,
- VCPUs: 96,
- Priority: *priority,
- KeepCache: 2,
- 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",
- "-threads", fmt.Sprintf("%d", cmd.threads),
- "-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
- var refseq map[string][]tileLibRef
- var reftiledata = make(map[tileLibRef][]byte, 11000000)
- in0, err := open(infiles[0])
- if err != nil {
- return 1
- }
-
- matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
- if err != nil {
- err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
- return 1
- }
-
- taglen := -1
- DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
- if len(ent.TagSet) > 0 {
- taglen = len(ent.TagSet[0])
- }
- for _, cseq := range ent.CompactSequences {
- if cseq.Name == *ref || *ref == "" {
- refseq = cseq.TileSequences
- }
- }
- for _, cg := range ent.CompactGenomes {
- if matchGenome.MatchString(cg.Name) {
- cgnames = append(cgnames, cg.Name)
- }
- }
- for _, tv := range ent.TileVariants {
- if tv.Ref {
- reftiledata[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
- }
- }
- return nil
- })
- if err != nil {
- return 1
- }
- in0.Close()
- if refseq == nil {
- err = fmt.Errorf("%s: reference sequence not found", infiles[0])
- return 1
- }
- if taglen < 0 {
- err = fmt.Errorf("tagset not found")
- return 1
- }
- if len(cgnames) == 0 {
- err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
- return 1
- }
- 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("indexing reference tiles")
- type reftileinfo struct {
- variant tileVariantID
- seqname string // chr1
- pos int // distance from start of chr1 to start of tile
- tiledata []byte // acgtggcaa...
- }
- reftile := map[tagID]*reftileinfo{}
- for seqname, cseq := range refseq {
- for _, libref := range cseq {
- reftile[libref.Tag] = &reftileinfo{
- seqname: seqname,
- variant: libref.Variant,
- tiledata: reftiledata[libref],
- }
- }
- }
-
- throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
- log.Info("reconstructing reference sequences")
- for seqname, cseq := range refseq {
- seqname, cseq := seqname, cseq
- throttleCPU.Go(func() error {
- defer log.Printf("... %s done", seqname)
- pos := 0
- for _, libref := range cseq {
- rt := reftile[libref.Tag]
- rt.pos = pos
- if len(rt.tiledata) == 0 {
- return fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
- }
- pos += len(rt.tiledata) - taglen
- }
- return nil
- })
- }
- throttleCPU.Wait()
-
- log.Info("TODO: determining which tiles intersect given regions")
-
- throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
- throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
- log.Info("generating annotations and numpy matrix for each slice")
- var done int64
- for infileIdx, infile := range infiles {
- infileIdx, infile := infileIdx, infile
- throttleMem.Go(func() error {
- seq := make(map[tagID][]TileVariant, 50000)
- cgs := make(map[string]CompactGenome, len(cgnames))
- f, err := open(infile)
- if err != nil {
- return err
- }
- defer f.Close()
- log.Infof("%04d: reading %s", infileIdx, infile)
- err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
- for _, tv := range ent.TileVariants {
- if tv.Ref {
- continue
- }
- variants := seq[tv.Tag]
- if len(variants) == 0 {
- variants = make([]TileVariant, 100)
- }
- for len(variants) <= int(tv.Variant) {
- variants = append(variants, TileVariant{})
- }
- variants[int(tv.Variant)] = tv
- seq[tv.Tag] = variants
- }
- for _, cg := range ent.CompactGenomes {
- if matchGenome.MatchString(cg.Name) {
- cgs[cg.Name] = cg
- }
- }
- return nil
- })
- if err != nil {
- return err
- }
- tagstart := cgs[cgnames[0]].StartTag
- tagend := cgs[cgnames[0]].EndTag
-
- // TODO: filters
-
- log.Infof("%04d: renumber/dedup variants for tags %d-%d", infileIdx, tagstart, tagend)
- variantRemap := make([][]tileVariantID, tagend-tagstart)
- throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
- for tag, variants := range seq {
- tag, variants := tag, variants
- throttleCPU.Acquire()
- go func() {
- defer throttleCPU.Release()
- count := make(map[[blake2b.Size256]byte]int, len(variants))
- for _, cg := range cgs {
- idx := (tag - tagstart) * 2
- if int(idx) < len(cg.Variants) {
- count[variants[cg.Variants[idx]].Blake2b]++
- count[variants[cg.Variants[idx+1]].Blake2b]++
- }
- }
- // hash[i] will be the hash of
- // the variant(s) that should
- // be at rank i (0-based).
- hash := make([][blake2b.Size256]byte, 0, len(count))
- for b := range count {
- hash = append(hash, b)
- }
- sort.Slice(hash, func(i, j int) bool {
- bi, bj := &hash[i], &hash[j]
- if ci, cj := count[*bi], count[*bj]; ci != cj {
- return ci > cj
- } else {
- return bytes.Compare((*bi)[:], (*bj)[:]) < 0
- }
- })
- // rank[b] will be the 1-based
- // new variant number for
- // variants whose hash is b.
- rank := make(map[[blake2b.Size256]byte]tileVariantID, len(hash))
- for i, h := range hash {
- rank[h] = tileVariantID(i + 1)
- }
- // remap[v] will be the new
- // variant number for original
- // variant number v.
- remap := make([]tileVariantID, len(variants))
- for i, tv := range variants {
- remap[i] = rank[tv.Blake2b]
- }
- variantRemap[tag-tagstart] = remap
- }()
- }
- throttleCPU.Wait()
-
- annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
- log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
- annof, err := os.Create(annotationsFilename)
- if err != nil {
- return err
- }
- annow := bufio.NewWriterSize(annof, 1<<20)
- for tag, variants := range seq {
- rt, ok := reftile[tag]
- if !ok {
- // Reference does not use any
- // variant of this tile.
- // TODO: log this? mention it
- // in annotations?
- continue
- }
- outcol := tag - tagID(tagstart)
- reftilestr := strings.ToUpper(string(rt.tiledata))
- remap := variantRemap[tag-tagstart]
- for v, tv := range variants {
- if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
- continue
- }
- if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
- continue
- }
- diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
- for _, diff := range diffs {
- diff.Position += rt.pos
- fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s\n", tag, outcol, remap[v], rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New)
- }
- }
- }
- err = annow.Flush()
- if err != nil {
- return err
- }
- err = annof.Close()
- if err != nil {
- return err
- }
-
- throttleNumpyMem.Acquire()
- log.Infof("%04d: preparing numpy", infileIdx)
- 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 variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
- out[col] = int16(variantRemap[col/2][v])
- } else {
- out[col] = -1
- }
- }
- }
- seq = nil
- throttleNumpyMem.Release()
-
- fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
- output, err := os.Create(fnm)
- if err != nil {
- return err
- }
- defer output.Close()
- bufw := bufio.NewWriterSize(output, 1<<26)
- npw, err := gonpy.NewWriter(nopCloser{bufw})
- if err != nil {
- return err
- }
- log.WithFields(log.Fields{
- "filename": fnm,
- "rows": rows,
- "cols": cols,
- }).Infof("%04d: writing numpy", infileIdx)
- npw.Shape = []int{rows, cols}
- npw.WriteInt16(out)
- err = bufw.Flush()
- if err != nil {
- return err
- }
- err = output.Close()
- if err != nil {
- return err
- }
- log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
- return nil
- })
- }
- if err = throttleMem.Wait(); err != nil {
- return 1
- }
- return 0
-}
projects / lightning.git / blobdiff