import (
"bufio"
+ "bytes"
+ "encoding/gob"
"flag"
"fmt"
"io"
+ "io/ioutil"
"net/http"
_ "net/http/pprof"
"os"
+ "regexp"
"runtime"
+ "runtime/debug"
"sort"
+ "strconv"
"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`")
+ mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
+ hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
+ hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
+ 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: 750000000000,
+ VCPUs: 96,
Priority: *priority,
- KeepCache: 1,
+ KeepCache: 2,
APIAccess: true,
}
err = runner.TranslatePaths(inputDir, regionsFilename)
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),
+ "-pprof=:6060",
+ "-input-dir=" + *inputDir,
+ "-output-dir=/mnt/output",
+ "-threads=" + fmt.Sprintf("%d", cmd.threads),
+ "-regions=" + *regionsFilename,
+ "-expand-regions=" + fmt.Sprintf("%d", *expandRegions),
+ "-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
+ "-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
+ "-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
}
runner.Args = append(runner.Args, cmd.filter.Args()...)
var output string
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 chromosome to starttag
+ tiledata []byte // acgtggcaa...
+ }
+ isdup := map[tagID]bool{}
+ reftile := map[tagID]*reftileinfo{}
+ for seqname, cseq := range refseq {
+ pos := 0
+ for _, libref := range cseq {
+ tiledata := reftiledata[libref]
+ if len(tiledata) == 0 {
+ err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
+ return 1
}
+ if isdup[libref.Tag] {
+ log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
+ } else if reftile[libref.Tag] != nil {
+ log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", tileLibRef{Tag: libref.Tag, Variant: reftile[libref.Tag].variant}, reftile[libref.Tag].seqname, reftile[libref.Tag].pos)
+ delete(reftile, libref.Tag)
+ log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
+ isdup[libref.Tag] = true
+ } else {
+ reftile[libref.Tag] = &reftileinfo{
+ seqname: seqname,
+ variant: libref.Variant,
+ tiledata: tiledata,
+ pos: pos,
+ }
+ }
+ pos += len(tiledata) - taglen
}
+ log.Printf("... %s done, len %d", seqname, pos+taglen)
}
- 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)
+
+ var mask *mask
+ if *regionsFilename != "" {
+ log.Printf("loading regions from %s", *regionsFilename)
+ mask, err = makeMask(*regionsFilename, *expandRegions)
+ if err != nil {
+ return 1
+ }
+ log.Printf("before applying mask, len(reftile) == %d", len(reftile))
+ log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
+ for tag, rt := range reftile {
+ if !mask.Check(strings.TrimPrefix(rt.seqname, "chr"), rt.pos, rt.pos+len(rt.tiledata)) {
+ delete(reftile, tag)
+ }
+ }
+ log.Printf("after applying mask, len(reftile) == %d", len(reftile))
+ }
+
+ type hgvsColSet map[hgvs.Variant][2][]int8
+ encodeHGVS := throttle{Max: len(refseq)}
+ encodeHGVSTodo := map[string]chan hgvsColSet{}
+ tmpHGVSCols := map[string]*os.File{}
+ if *hgvsChunked {
+ for seqname := range refseq {
+ var f *os.File
+ f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
if err != nil {
- return err
+ return 1
}
- 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
+ defer os.Remove(f.Name())
+ bufw := bufio.NewWriterSize(f, 1<<24)
+ enc := gob.NewEncoder(bufw)
+ tmpHGVSCols[seqname] = f
+ todo := make(chan hgvsColSet, 128)
+ encodeHGVSTodo[seqname] = todo
+ encodeHGVS.Go(func() error {
+ for colset := range todo {
+ err := enc.Encode(colset)
+ if err != nil {
+ encodeHGVS.Report(err)
+ for range todo {
+ }
+ return err
}
}
- return nil
+ return bufw.Flush()
})
- })
+ }
}
- throttle.Wait()
- log.Info("TODO: determining which tiles intersect given regions")
+ var toMerge [][]int16
+ if *mergeOutput || *hgvsSingle {
+ toMerge = make([][]int16, len(infiles))
+ }
+ 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
+ }
+ if mask != nil && reftile[tv.Tag] == nil {
+ // Don't waste
+ // time/memory on
+ // masked-out tiles.
+ 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) {
+ continue
+ }
+ // pad to full slice size
+ // to avoid out-of-bounds
+ // checks later
+ if sliceSize := 2 * int(cg.EndTag-cg.StartTag); len(cg.Variants) < sliceSize {
+ cg.Variants = append(cg.Variants, make([]tileVariantID, sliceSize-len(cg.Variants))...)
+ }
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))
+
+ rt := reftile[tag]
+ if rt != nil {
+ count[blake2b.Sum256(rt.tiledata)] = 0
+ }
+
+ for _, cg := range cgs {
+ idx := int(tag-tagstart) * 2
+ 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
+ if rt != nil {
+ rt.variant = rank[blake2b.Sum256(rt.tiledata)]
+ }
+ }()
+ }
+ 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
+ }
+ annow := bufio.NewWriterSize(annof, 1<<20)
+ outcol := 0
+ for tag := tagstart; tag < tagend; tag++ {
+ rt, ok := reftile[tag]
+ if !ok {
+ if mask == nil {
+ outcol++
+ }
+ // Excluded by specified
+ // regions, or reference does
+ // not use any variant of this
+ // tile. (TODO: log this?
+ // mention it in annotations?)
+ continue
+ }
+ fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
+ variants := seq[tag]
+ reftilestr := strings.ToUpper(string(rt.tiledata))
+ remap := variantRemap[tag-tagstart]
+ maxv := tileVariantID(0)
+ for _, v := range remap {
+ if maxv < v {
+ maxv = v
+ }
+ }
+ done := make([]bool, maxv+1)
+ variantDiffs := make([][]hgvs.Variant, maxv+1)
+ for v, tv := range variants {
+ v := remap[v]
+ if v == rt.variant || done[v] {
+ continue
+ } else {
+ done[v] = true
+ }
+ if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
+ fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
+ continue
+ }
+ if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
+ fmt.Fprintf(annow, "%d,%d,%d,,%s,%d,,,\n", tag, outcol, v, rt.seqname, rt.pos)
+ continue
+ }
+ diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
+ for i := range diffs {
+ diffs[i].Position += rt.pos
+ }
+ for _, diff := range diffs {
+ 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)
+ }
+ if *hgvsChunked {
+ variantDiffs[v] = diffs
+ }
+ }
+ if *hgvsChunked {
+ // We can now determine, for each HGVS
+ // variant (diff) in this reftile
+ // region, whether a given genome
+ // phase/allele (1) has the variant, (0) has
+ // =ref or a different variant in that
+ // position, or (-1) is lacking
+ // coverage / couldn't be diffed.
+ hgvsCol := hgvsColSet{}
+ for _, diffs := range variantDiffs {
+ for _, diff := range diffs {
+ if _, ok := hgvsCol[diff]; ok {
+ continue
+ }
+ hgvsCol[diff] = [2][]int8{
+ make([]int8, len(cgnames)),
+ make([]int8, len(cgnames)),
+ }
+ }
+ }
+ for row, name := range cgnames {
+ variants := cgs[name].Variants[(tag-tagstart)*2:]
+ for ph := 0; ph < 2; ph++ {
+ v := variants[ph]
+ if int(v) >= len(remap) {
+ v = 0
+ } else {
+ v = remap[v]
+ }
+ if v == rt.variant {
+ // hgvsCol[*][ph][row] is already 0
+ } else if len(variantDiffs[v]) == 0 {
+ // lacking coverage / couldn't be diffed
+ for _, col := range hgvsCol {
+ col[ph][row] = -1
+ }
+ } else {
+ for _, diff := range variantDiffs[v] {
+ hgvsCol[diff][ph][row] = 1
+ }
+ }
+ }
+ }
+ encodeHGVSTodo[rt.seqname] <- hgvsCol
+ }
+ outcol++
+ }
+ err = annow.Flush()
if err != nil {
return err
}
- // for libref, seq := range seq {
- // // TODO: diff from ref.
- // }
- err = annow.Close()
+ err = annof.Close()
if err != nil {
return err
}
- log.Infof("%s: preparing numpy", infile)
- tagstart := cgs[cgnames[0]].StartTag
- tagend := cgs[cgnames[0]].EndTag
+ log.Infof("%04d: preparing numpy", infileIdx)
+ throttleNumpyMem.Acquire()
rows := len(cgnames)
- cols := 2 * int(tagend-tagstart)
+ cols := 2 * outcol
out := make([]int16, rows*cols)
for row, name := range cgnames {
out := out[row*cols:]
+ outcol := 0
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)
+ tag := tagstart + tagID(col/2)
+ if mask != nil && reftile[tag] == nil {
+ continue
+ }
+ if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
+ out[outcol] = int16(variantRemap[tag-tagstart][v])
} else {
- out[col] = -1
+ out[outcol] = -1
}
+ outcol++
}
}
+ seq = nil
+ cgs = nil
+ debug.FreeOSMemory()
+ throttleNumpyMem.Release()
- fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
- output, err := os.Create(fnm)
- if err != nil {
- return err
+ if *mergeOutput || *hgvsSingle {
+ log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
+ toMerge[infileIdx] = out
+ }
+ if !*mergeOutput {
+ fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
+ err = writeNumpyInt16(fnm, out, rows, cols)
+ if err != nil {
+ return err
+ }
+ debug.FreeOSMemory()
}
- defer output.Close()
- bufw := bufio.NewWriter(output)
- npw, err := gonpy.NewWriter(nopCloser{bufw})
+ log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
+ return nil
+ })
+ }
+ if err = throttleMem.Wait(); err != nil {
+ return 1
+ }
+
+ if *hgvsChunked {
+ log.Info("flushing hgvsCols temp files")
+ for seqname := range refseq {
+ close(encodeHGVSTodo[seqname])
+ }
+ err = encodeHGVS.Wait()
+ if err != nil {
+ return 1
+ }
+ for seqname := range refseq {
+ log.Infof("%s: reading hgvsCols from temp file", seqname)
+ f := tmpHGVSCols[seqname]
+ _, err = f.Seek(0, io.SeekStart)
if err != nil {
- return err
+ return 1
+ }
+ var hgvsCols hgvsColSet
+ dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
+ for err == nil {
+ err = dec.Decode(&hgvsCols)
+ }
+ if err != io.EOF {
+ return 1
+ }
+ log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
+ variants := make([]hgvs.Variant, 0, len(hgvsCols))
+ for v := range hgvsCols {
+ variants = append(variants, v)
+ }
+ sort.Slice(variants, func(i, j int) bool {
+ vi, vj := &variants[i], &variants[j]
+ if vi.Position != vj.Position {
+ return vi.Position < vj.Position
+ } else if vi.Ref != vj.Ref {
+ return vi.Ref < vj.Ref
+ } else {
+ return vi.New < vj.New
+ }
+ })
+ rows := len(cgnames)
+ cols := len(variants) * 2
+ log.Infof("%s: building hgvs matrix (rows=%d, cols=%d, mem=%d)", seqname, rows, cols, rows*cols)
+ out := make([]int8, rows*cols)
+ for varIdx, variant := range variants {
+ hgvsCols := hgvsCols[variant]
+ for row := range cgnames {
+ for ph := 0; ph < 2; ph++ {
+ out[row*cols+varIdx+ph] = hgvsCols[ph][row]
+ }
+ }
}
- log.WithFields(logrus.Fields{
- "filename": fnm,
- "rows": rows,
- "cols": cols,
- }).Info("writing numpy")
- npw.Shape = []int{rows, cols}
- npw.WriteInt16(out)
- err = bufw.Flush()
+ err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
if err != nil {
- return err
+ return 1
+ }
+ out = nil
+
+ fnm := fmt.Sprintf("%s/hgvs.%s.annotations.csv", *outputDir, seqname)
+ log.Infof("%s: writing hgvs column labels to %s", seqname, fnm)
+ var hgvsLabels bytes.Buffer
+ for varIdx, variant := range variants {
+ fmt.Fprintf(&hgvsLabels, "%d,%s:g.%s\n", varIdx, seqname, variant.String())
}
- err = output.Close()
+ err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
if err != nil {
- return err
+ return 1
}
- return nil
- })
+ }
}
- if err = throttle.Wait(); err != nil {
- return 1
+
+ if *mergeOutput || *hgvsSingle {
+ var annow *bufio.Writer
+ var annof *os.File
+ if *mergeOutput {
+ annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
+ annof, err = os.Create(annoFilename)
+ if err != nil {
+ return 1
+ }
+ annow = bufio.NewWriterSize(annof, 1<<20)
+ }
+
+ rows := len(cgnames)
+ cols := 0
+ for _, chunk := range toMerge {
+ cols += len(chunk) / rows
+ }
+ log.Infof("merging output matrix (rows=%d, cols=%d, mem=%d) and annotations", rows, cols, rows*cols*2)
+ var out []int16
+ if *mergeOutput {
+ out = make([]int16, rows*cols)
+ }
+ hgvsCols := map[string][2][]int16{} // hgvs -> [[g0,g1,g2,...], [g0,g1,g2,...]] (slice of genomes for each phase)
+ startcol := 0
+ for outIdx, chunk := range toMerge {
+ chunkcols := len(chunk) / rows
+ if *mergeOutput {
+ for row := 0; row < rows; row++ {
+ copy(out[row*cols+startcol:], chunk[row*chunkcols:(row+1)*chunkcols])
+ }
+ }
+ toMerge[outIdx] = nil
+
+ annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, outIdx)
+ log.Infof("reading %s", annotationsFilename)
+ buf, err := os.ReadFile(annotationsFilename)
+ if err != nil {
+ return 1
+ }
+ if *mergeOutput {
+ err = os.Remove(annotationsFilename)
+ if err != nil {
+ return 1
+ }
+ }
+ for _, line := range bytes.Split(buf, []byte{'\n'}) {
+ if len(line) == 0 {
+ continue
+ }
+ fields := bytes.SplitN(line, []byte{','}, 9)
+ tag, _ := strconv.Atoi(string(fields[0]))
+ incol, _ := strconv.Atoi(string(fields[1]))
+ tileVariant, _ := strconv.Atoi(string(fields[2]))
+ hgvsID := string(fields[3])
+ seqname := string(fields[4])
+ pos, _ := strconv.Atoi(string(fields[5]))
+ refseq := fields[6]
+ if hgvsID == "" {
+ // Null entry for un-diffable
+ // tile variant
+ continue
+ }
+ if hgvsID == "=" {
+ // Null entry for ref tile
+ continue
+ }
+ if mask != nil && !mask.Check(strings.TrimPrefix(seqname, "chr"), pos, pos+len(refseq)) {
+ // The tile intersects one of
+ // the selected regions, but
+ // this particular HGVS
+ // variant does not.
+ continue
+ }
+ hgvsColPair := hgvsCols[hgvsID]
+ if hgvsColPair[0] == nil {
+ // values in new columns start
+ // out as -1 ("no data yet")
+ // or 0 ("=ref") here, may
+ // change to 1 ("hgvs variant
+ // present") below, either on
+ // this line or a future line.
+ hgvsColPair = [2][]int16{make([]int16, len(cgnames)), make([]int16, len(cgnames))}
+ rt, ok := reftile[tagID(tag)]
+ if !ok {
+ err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
+ return 1
+ }
+ for ph := 0; ph < 2; ph++ {
+ for row := 0; row < rows; row++ {
+ v := chunk[row*chunkcols+incol*2+ph]
+ if tileVariantID(v) == rt.variant {
+ hgvsColPair[ph][row] = 0
+ } else {
+ hgvsColPair[ph][row] = -1
+ }
+ }
+ }
+ hgvsCols[hgvsID] = hgvsColPair
+ if annow != nil {
+ hgvsref := hgvs.Variant{
+ Position: pos,
+ Ref: string(refseq),
+ New: string(refseq),
+ }
+ fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, rt.variant, seqname, hgvsref.String(), seqname, pos, refseq, refseq, fields[8])
+ }
+ }
+ if annow != nil {
+ fmt.Fprintf(annow, "%d,%d,%d,%s,%s,%d,%s,%s,%s\n", tag, incol+startcol/2, tileVariant, hgvsID, seqname, pos, refseq, fields[7], fields[8])
+ }
+ for ph := 0; ph < 2; ph++ {
+ for row := 0; row < rows; row++ {
+ v := chunk[row*chunkcols+incol*2+ph]
+ if int(v) == tileVariant {
+ hgvsColPair[ph][row] = 1
+ }
+ }
+ }
+ }
+
+ startcol += chunkcols
+ }
+ if *mergeOutput {
+ err = annow.Flush()
+ if err != nil {
+ return 1
+ }
+ err = annof.Close()
+ if err != nil {
+ return 1
+ }
+ err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
+ if err != nil {
+ return 1
+ }
+ }
+ out = nil
+
+ if *hgvsSingle {
+ cols = len(hgvsCols) * 2
+ log.Printf("building hgvs-based matrix: %d rows x %d cols", rows, cols)
+ out = make([]int16, rows*cols)
+ hgvsIDs := make([]string, 0, cols/2)
+ for hgvsID := range hgvsCols {
+ hgvsIDs = append(hgvsIDs, hgvsID)
+ }
+ sort.Strings(hgvsIDs)
+ var hgvsLabels bytes.Buffer
+ for idx, hgvsID := range hgvsIDs {
+ fmt.Fprintf(&hgvsLabels, "%d,%s\n", idx, hgvsID)
+ for ph := 0; ph < 2; ph++ {
+ hgvscol := hgvsCols[hgvsID][ph]
+ for row, val := range hgvscol {
+ out[row*cols+idx*2+ph] = val
+ }
+ }
+ }
+ err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
+ if err != nil {
+ return 1
+ }
+
+ fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
+ log.Printf("writing hgvs labels: %s", fnm)
+ err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
+ if 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)
+func writeNumpyInt16(fnm string, out []int16, rows, cols int) error {
+ output, err := os.Create(fnm)
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
- }
+ 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("writing numpy: %s", fnm)
+ npw.Shape = []int{rows, cols}
+ npw.WriteInt16(out)
+ err = bufw.Flush()
+ if err != nil {
+ return err
+ }
+ return output.Close()
+}
+
+func writeNumpyInt8(fnm string, out []int8, rows, cols int) error {
+ 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("writing numpy: %s", fnm)
+ npw.Shape = []int{rows, cols}
+ npw.WriteInt8(out)
+ err = bufw.Flush()
+ if err != nil {
+ return err
}
- return f.Close()
+ return output.Close()
}
projects / lightning.git / blobdiff