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"
- "github.com/sirupsen/logrus"
log "github.com/sirupsen/logrus"
+ "golang.org/x/crypto/blake2b"
)
type sliceNumpy struct {
- filter filter
+ filter filter
+ threads int
}
func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
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 {
Name: "lightning slice-numpy",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
- RAM: 150000000000,
- VCPUs: 32,
+ RAM: 650000000000,
+ VCPUs: 96,
Priority: *priority,
- KeepCache: 1,
+ KeepCache: 2,
APIAccess: true,
}
err = runner.TranslatePaths(inputDir, regionsFilename)
"-pprof", ":6060",
"-input-dir", *inputDir,
"-output-dir", "/mnt/output",
+ "-threads", fmt.Sprintf("%d", cmd.threads),
"-regions", *regionsFilename,
"-expand-regions", fmt.Sprintf("%d", *expandRegions),
}
sort.Strings(infiles)
var cgnames []string
- refseqs := map[string]map[string][]tileLibRef{}
+ 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 {
- refseqs[cseq.Name] = cseq.TileSequences
+ if cseq.Name == *ref || *ref == "" {
+ refseq = cseq.TileSequences
+ }
}
for _, cg := range ent.CompactGenomes {
- cgnames = append(cgnames, cg.Name)
+ 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
})
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)
{
}
}
- 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("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],
}
}
}
- 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
- }
+
+ 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)
}
- return nil
- })
+ pos += len(rt.tiledata) - taglen
+ }
+ return nil
})
}
- throttle.Wait()
+ 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
- throttle.Go(func() error {
- defer log.Infof("%s: done", infile)
- seq := map[tileLibRef][]byte{}
+ 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 {
- seq[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
+ 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 {
- cgs[cg.Name] = cg
+ 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("TODO: %s: filtering", infile)
- log.Infof("TODO: %s: tidying", infile)
- log.Infof("TODO: %s: lowqual to -1", infile)
+ 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 := int(tag-tagstart) * 2
+ if idx < len(cg.Variants) {
+ for allele := 0; allele < 2; allele++ {
+ v := cg.Variants[idx+allele]
+ if v > 0 && len(variants[v].Sequence) > 0 {
+ count[variants[v].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("%s: writing annotations to %s", infile, annotationsFilename)
- annow, err := os.Create(annotationsFilename)
+ log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
+ annof, err := os.Create(annotationsFilename)
if err != nil {
return err
}
- // for libref, seq := range seq {
- // // TODO: diff from ref.
- // }
- err = annow.Close()
+ 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]
+ done := make([]bool, len(variants))
+ for v, tv := range variants {
+ v := remap[v]
+ if done[v] {
+ continue
+ } else {
+ done[v] = true
+ }
+ 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,%s\n", tag, outcol, v, rt.seqname, diff.String(), rt.seqname, diff.Position, diff.Ref, diff.New, diff.Left)
+ }
+ }
+ }
+ err = annow.Flush()
+ if err != nil {
+ return err
+ }
+ err = annof.Close()
if err != nil {
return err
}
- log.Infof("%s: preparing numpy", infile)
- tagstart := cgs[cgnames[0]].StartTag
- tagend := cgs[cgnames[0]].EndTag
+ 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 v == 0 {
- // out[col] = 0
- } else if _, ok := seq[tileLibRef{tagstart + tagID(col/2), v}]; ok {
- out[col] = int16(v)
+ 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)
return err
}
defer output.Close()
- bufw := bufio.NewWriter(output)
+ bufw := bufio.NewWriterSize(output, 1<<26)
npw, err := gonpy.NewWriter(nopCloser{bufw})
if err != nil {
return err
}
- log.WithFields(logrus.Fields{
+ log.WithFields(log.Fields{
"filename": fnm,
"rows": rows,
"cols": cols,
- }).Info("writing numpy")
+ }).Infof("%04d: writing numpy", infileIdx)
npw.Shape = []int{rows, cols}
npw.WriteInt16(out)
err = bufw.Flush()
if err != nil {
return err
}
+ log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
return nil
})
}
- if err = throttle.Wait(); err != nil {
+ if err = throttleMem.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 / blobdiff