+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
package lightning
import (
"net/http"
_ "net/http/pprof"
"os"
- "path"
+ "path/filepath"
+ "runtime"
"sort"
+ "strconv"
"strings"
"sync"
"time"
"git.arvados.org/arvados.git/sdk/go/arvados"
"github.com/arvados/lightning/hgvs"
+ "github.com/klauspost/pgzip"
+ "github.com/kshedden/gonpy"
+ "github.com/sirupsen/logrus"
log "github.com/sirupsen/logrus"
)
-type outputFormat struct {
- Print func(out io.Writer, seqname string, varslice []hgvs.Variant)
- PadLeft bool
+type tvVariant struct {
+ hgvs.Variant
+ librefs map[tileLibRef]bool
}
-var (
- outputFormats = map[string]outputFormat{
- "hgvs-onehot": outputFormatHGVSOneHot,
- "hgvs": outputFormatHGVS,
- "vcf": outputFormatVCF,
- }
- outputFormatHGVS = outputFormat{Print: printHGVS}
- outputFormatHGVSOneHot = outputFormat{Print: printHGVSOneHot}
- outputFormatVCF = outputFormat{Print: printVCF, PadLeft: true}
-)
+type outputFormat interface {
+ Filename() string
+ PadLeft() bool
+ Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error
+ Print(out io.Writer, seqname string, varslice []tvVariant) error
+ Finish(outdir string, out io.Writer, seqname string) error
+ MaxGoroutines() int
+}
+
+var outputFormats = map[string]func() outputFormat{
+ "hgvs-numpy": func() outputFormat {
+ return &formatHGVSNumpy{alleles: map[string][][]int8{}}
+ },
+ "hgvs-onehot": func() outputFormat { return formatHGVSOneHot{} },
+ "hgvs": func() outputFormat { return formatHGVS{} },
+ "pvcf": func() outputFormat { return formatPVCF{} },
+ "vcf": func() outputFormat { return formatVCF{} },
+}
type exporter struct {
- outputFormat outputFormat
+ outputFormat outputFormat
+ outputPerChrom bool
+ compress bool
+ maxTileSize int
+ filter filter
+ maxPValue float64
+ cases []bool
}
func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
projectUUID := flags.String("project", "", "project `UUID` for output data")
priority := flags.Int("priority", 500, "container request priority")
refname := flags.String("ref", "", "reference genome `name`")
- inputFilename := flags.String("i", "-", "input `file` (library)")
- outputFilename := flags.String("o", "-", "output `file`")
- outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs or vcf")
+ inputDir := flags.String("input-dir", ".", "input `directory`")
+ cases := flags.String("cases", "", "file indicating which genomes are positive cases (for computing p-values)")
+ flags.Float64Var(&cmd.maxPValue, "p-value", 1, "do chi square test and omit columns with p-value above this threshold")
+ outputDir := flags.String("output-dir", ".", "output `directory`")
+ outputFormatStr := flags.String("output-format", "hgvs", "output `format`: hgvs, pvcf, or vcf")
outputBed := flags.String("output-bed", "", "also output bed `file`")
+ flags.BoolVar(&cmd.outputPerChrom, "output-per-chromosome", true, "output one file per chromosome")
+ flags.BoolVar(&cmd.compress, "z", false, "write gzip-compressed output files")
labelsFilename := flags.String("output-labels", "", "also output genome labels csv `file`")
+ flags.IntVar(&cmd.maxTileSize, "max-tile-size", 50000, "don't try to make annotations for tiles bigger than given `size`")
+ cmd.filter.Flags(flags)
err = flags.Parse(args)
if err == flag.ErrHelp {
err = nil
return 0
} else if err != nil {
return 2
+ } else if flags.NArg() > 0 {
+ err = fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
+ return 2
}
if f, ok := outputFormats[*outputFormatStr]; !ok {
err = fmt.Errorf("invalid output format %q", *outputFormatStr)
return 2
} else {
- cmd.outputFormat = f
+ cmd.outputFormat = f()
}
if *pprof != "" {
}
if !*runlocal {
- if *outputFilename != "-" {
- err = errors.New("cannot specify output file in container mode: not implemented")
+ if *outputDir != "." {
+ err = errors.New("cannot specify output directory in container mode: not implemented")
return 1
}
runner := arvadosContainerRunner{
Name: "lightning export",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
- RAM: 1600000000000,
- VCPUs: 64,
+ RAM: 750000000000,
+ VCPUs: 96,
Priority: *priority,
+ APIAccess: true,
}
- err = runner.TranslatePaths(inputFilename)
+ err = runner.TranslatePaths(inputDir, cases)
if err != nil {
return 1
}
"-pprof", ":6000",
"-pprof-dir", "/mnt/output",
"-ref", *refname,
+ "-cases", *cases,
+ "-p-value", fmt.Sprintf("%f", cmd.maxPValue),
"-output-format", *outputFormatStr,
"-output-bed", *outputBed,
"-output-labels", "/mnt/output/labels.csv",
- "-i", *inputFilename,
- "-o", "/mnt/output/export.csv",
+ "-output-per-chromosome=" + fmt.Sprintf("%v", cmd.outputPerChrom),
+ "-max-tile-size", fmt.Sprintf("%d", cmd.maxTileSize),
+ "-input-dir", *inputDir,
+ "-output-dir", "/mnt/output",
+ "-z=" + fmt.Sprintf("%v", cmd.compress),
}
+ runner.Args = append(runner.Args, cmd.filter.Args()...)
var output string
output, err = runner.Run()
if err != nil {
return 1
}
- fmt.Fprintln(stdout, output+"/export.csv")
+ fmt.Fprintln(stdout, output)
return 0
}
- in, err := open(*inputFilename)
- if err != nil {
- return 1
- }
- defer in.Close()
- input, ok := in.(io.ReadSeeker)
- if !ok {
- err = fmt.Errorf("%s: %T cannot seek", *inputFilename, in)
- return 1
- }
-
- // Error out early if seeking doesn't work on the input file.
- _, err = input.Seek(0, io.SeekEnd)
- if err != nil {
- return 1
- }
- _, err = input.Seek(0, io.SeekStart)
- if err != nil {
- return 1
- }
-
var cgs []CompactGenome
tilelib := &tileLibrary{
- retainNoCalls: true,
- compactGenomes: map[string][]tileVariantID{},
+ retainNoCalls: true,
+ retainTileSequences: true,
+ compactGenomes: map[string][]tileVariantID{},
}
- err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), nil)
+ err = tilelib.LoadDir(context.Background(), *inputDir)
if err != nil {
return 1
}
return 1
}
+ log.Infof("filtering: %+v", cmd.filter)
+ cmd.filter.Apply(tilelib)
+
names := cgnames(tilelib)
for _, name := range names {
cgs = append(cgs, CompactGenome{Name: name, Variants: tilelib.compactGenomes[name]})
return 1
}
defer f.Close()
- _, outBasename := path.Split(*outputFilename)
for i, name := range names {
- _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), outBasename)
+ _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), cmd.outputFormat.Filename())
if err != nil {
err = fmt.Errorf("write %s: %w", *labelsFilename, err)
return 1
}
}
- _, err = input.Seek(0, io.SeekStart)
- if err != nil {
- return 1
- }
-
- var output io.WriteCloser
- if *outputFilename == "-" {
- output = nopCloser{stdout}
- } else {
- output, err = os.OpenFile(*outputFilename, os.O_CREATE|os.O_WRONLY, 0666)
+ cmd.cases = make([]bool, len(names))
+ if *cases != "" {
+ log.Infof("reading cases file: %s", *cases)
+ var f io.ReadCloser
+ f, err = open(*cases)
+ if err != nil {
+ return 1
+ }
+ defer f.Close()
+ var buf []byte
+ buf, err = io.ReadAll(f)
if err != nil {
return 1
}
- defer output.Close()
+ for _, pattern := range bytes.Split(buf, []byte("\n")) {
+ if len(pattern) == 0 {
+ continue
+ }
+ pattern := string(pattern)
+ idx := -1
+ for i, name := range names {
+ if !strings.Contains(name, pattern) {
+ continue
+ } else if idx >= 0 {
+ err = fmt.Errorf("pattern %q in cases file matches multiple genome IDs: %q, %q", pattern, names[idx], name)
+ return 1
+ } else {
+ idx = i
+ }
+ }
+ if idx < 0 {
+ log.Warnf("pattern %q in cases file does not match any genome IDs", pattern)
+ continue
+ }
+ cmd.cases[idx] = true
+ }
}
- bufw := bufio.NewWriter(output)
- var bedout *os.File
+ var bedout io.Writer
+ var bedfile *os.File
var bedbufw *bufio.Writer
if *outputBed != "" {
- bedout, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
+ bedfile, err = os.OpenFile(*outputBed, os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return 1
}
- defer bedout.Close()
- bedbufw = bufio.NewWriter(bedout)
+ defer bedfile.Close()
+ bedbufw = bufio.NewWriterSize(bedfile, 16*1024*1024)
+ bedout = bedbufw
}
- err = cmd.export(bufw, bedout, input, strings.HasSuffix(*inputFilename, ".gz"), tilelib, refseq, cgs)
- if err != nil {
- return 1
- }
- err = bufw.Flush()
- if err != nil {
- return 1
- }
- err = output.Close()
+ err = cmd.export(*outputDir, bedout, tilelib, refseq, cgs)
if err != nil {
return 1
}
if err != nil {
return 1
}
- err = bedout.Close()
+ err = bedfile.Close()
if err != nil {
return 1
}
}
- err = in.Close()
- if err != nil {
- return 1
- }
return 0
}
-func (cmd *exporter) export(out, bedout io.Writer, librdr io.Reader, gz bool, tilelib *tileLibrary, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
- need := map[tileLibRef]bool{}
+func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrary, refseq map[string][]tileLibRef, cgs []CompactGenome) error {
var seqnames []string
+ var missing []tileLibRef
for seqname, librefs := range refseq {
seqnames = append(seqnames, seqname)
for _, libref := range librefs {
- if libref.Variant != 0 {
- need[libref] = true
+ if libref.Variant != 0 && tilelib.TileVariantSequence(libref) == nil {
+ missing = append(missing, libref)
}
}
}
sort.Strings(seqnames)
- for _, cg := range cgs {
- for i, variant := range cg.Variants {
- if variant == 0 {
- continue
- }
- libref := tileLibRef{Tag: tagID(i / 2), Variant: variant}
- need[libref] = true
- }
- }
-
- log.Infof("export: loading %d tile variants", len(need))
- tileVariant := map[tileLibRef]TileVariant{}
- err := DecodeLibrary(librdr, gz, func(ent *LibraryEntry) error {
- for _, tv := range ent.TileVariants {
- libref := tilelib.getRef(tv.Tag, tv.Sequence)
- if need[libref] {
- tileVariant[libref] = tv
- }
- }
- return nil
- })
- if err != nil {
- return err
- }
-
- log.Infof("export: loaded %d tile variants", len(tileVariant))
- var missing []tileLibRef
- for libref := range need {
- if _, ok := tileVariant[libref]; !ok {
- missing = append(missing, libref)
- }
- }
if len(missing) > 0 {
if limit := 100; len(missing) > limit {
log.Warnf("first %d missing tiles: %v", limit, missing[:limit])
}()
}
}
- merge(out, outw, "output")
+ if cmd.outputPerChrom {
+ for i, seqname := range seqnames {
+ fnm := filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename(), ".", "."+seqname+".", 1))
+ if cmd.compress {
+ fnm += ".gz"
+ }
+ f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ log.Infof("writing %q", f.Name())
+ outw[i] = f
+ if cmd.compress {
+ z := pgzip.NewWriter(f)
+ defer z.Close()
+ outw[i] = z
+ }
+ err = cmd.outputFormat.Head(outw[i], cgs, cmd.cases, cmd.maxPValue)
+ if err != nil {
+ return err
+ }
+ }
+ } else {
+ fnm := filepath.Join(outdir, cmd.outputFormat.Filename())
+ if cmd.compress {
+ fnm += ".gz"
+ }
+ f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY|os.O_TRUNC, 0666)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ log.Infof("writing %q", fnm)
+ var out io.Writer = f
+ if cmd.compress {
+ z := pgzip.NewWriter(out)
+ defer z.Close()
+ out = z
+ }
+ cmd.outputFormat.Head(out, cgs, cmd.cases, cmd.maxPValue)
+ merge(out, outw, "output")
+ }
if bedout != nil {
merge(bedout, bedw, "bed")
}
- throttle := throttle{Max: 8}
+ throttle := throttle{Max: runtime.NumCPU()}
+ if max := cmd.outputFormat.MaxGoroutines(); max > 0 {
+ throttle.Max = max
+ }
log.Infof("assembling %d sequences in %d goroutines", len(seqnames), throttle.Max)
for seqidx, seqname := range seqnames {
seqidx, seqname := seqidx, seqname
if bedw != nil {
defer bedw.Close()
}
- defer outw.Close()
- outwb := bufio.NewWriter(outw)
- defer outwb.Flush()
- cmd.exportSeq(outwb, bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tileVariant, cgs)
+ outwb := bufio.NewWriterSize(outw, 8*1024*1024)
+ eachVariant(bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tilelib, cgs, cmd.outputFormat.PadLeft(), cmd.maxTileSize, func(varslice []tvVariant) {
+ err := cmd.outputFormat.Print(outwb, seqname, varslice)
+ throttle.Report(err)
+ })
+ err := cmd.outputFormat.Finish(outdir, outwb, seqname)
+ throttle.Report(err)
+ err = outwb.Flush()
+ throttle.Report(err)
+ err = outw.Close()
+ throttle.Report(err)
}()
}
merges.Wait()
- return nil
+ throttle.Wait()
+ return throttle.Err()
}
-// Align genome tiles to reference tiles, write diffs to outw, and (if
-// bedw is not nil) write tile coverage to bedw.
-func (cmd *exporter) exportSeq(outw, bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tileVariant map[tileLibRef]TileVariant, cgs []CompactGenome) {
+// Align genome tiles to reference tiles, call callback func on each
+// variant, and (if bedw is not nil) write tile coverage to bedw.
+func eachVariant(bedw io.Writer, taglen int, seqname string, reftiles []tileLibRef, tilelib *tileLibrary, cgs []CompactGenome, padLeft bool, maxTileSize int, callback func(varslice []tvVariant)) {
+ t0 := time.Now()
+ progressbar := time.NewTicker(time.Minute)
+ defer progressbar.Stop()
+ var outmtx sync.Mutex
+ defer outmtx.Lock()
refpos := 0
- variantAt := map[int][]hgvs.Variant{} // variantAt[chromOffset][genomeIndex*2+phase]
+ variantAt := map[int][]tvVariant{} // variantAt[chromOffset][genomeIndex*2+phase]
for refstep, libref := range reftiles {
- reftile := tileVariant[libref]
+ select {
+ case <-progressbar.C:
+ var eta interface{}
+ if refstep > 0 {
+ fin := t0.Add(time.Duration(float64(time.Now().Sub(t0)) * float64(len(reftiles)) / float64(refstep)))
+ eta = fmt.Sprintf("%v (%v)", fin.Format(time.RFC3339), fin.Sub(time.Now()))
+ } else {
+ eta = "N/A"
+ }
+ log.Printf("exportSeq: %s: refstep %d of %d, %.0f/s, ETA %v", seqname, refstep, len(reftiles), float64(refstep)/time.Now().Sub(t0).Seconds(), eta)
+ default:
+ }
+ diffs := map[tileLibRef][]hgvs.Variant{}
+ refseq := tilelib.TileVariantSequence(libref)
tagcoverage := 0 // number of times the start tag was found in genomes -- max is len(cgs)*2
for cgidx, cg := range cgs {
for phase := 0; phase < 2; phase++ {
- if len(cg.Variants) <= int(libref.Tag)*2+phase {
- continue
- }
- variant := cg.Variants[int(libref.Tag)*2+phase]
- if variant == 0 {
- continue
+ var variant tileVariantID
+ if i := int(libref.Tag)*2 + phase; len(cg.Variants) > i {
+ variant = cg.Variants[i]
}
- tagcoverage++
- if variant == libref.Variant {
- continue
+ if variant > 0 {
+ tagcoverage++
}
- genometile := tileVariant[tileLibRef{Tag: libref.Tag, Variant: variant}]
- if len(genometile.Sequence) == 0 {
- // Hash is known but sequence
- // is not, e.g., retainNoCalls
- // was false during import
+ if variant == libref.Variant || variant == 0 {
continue
}
- refSequence := reftile.Sequence
- // If needed, extend the reference
- // sequence up to the tag at the end
- // of the genometile sequence.
- refstepend := refstep + 1
- for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genometile.Sequence[len(genometile.Sequence)-taglen:]) {
- if &refSequence[0] == &reftile.Sequence[0] {
- refSequence = append([]byte(nil), refSequence...)
+ glibref := tileLibRef{Tag: libref.Tag, Variant: variant}
+ vars, ok := diffs[glibref]
+ if !ok {
+ genomeseq := tilelib.TileVariantSequence(glibref)
+ if len(genomeseq) == 0 {
+ // Hash is known but sequence
+ // is not, e.g., retainNoCalls
+ // was false during import
+ continue
+ }
+ if len(genomeseq) > maxTileSize {
+ continue
+ }
+ refSequence := refseq
+ // If needed, extend the
+ // reference sequence up to
+ // the tag at the end of the
+ // genomeseq sequence.
+ refstepend := refstep + 1
+ for refstepend < len(reftiles) && len(refSequence) >= taglen && !bytes.EqualFold(refSequence[len(refSequence)-taglen:], genomeseq[len(genomeseq)-taglen:]) && len(refSequence) <= maxTileSize {
+ if &refSequence[0] == &refseq[0] {
+ refSequence = append([]byte(nil), refSequence...)
+ }
+ refSequence = append(refSequence, tilelib.TileVariantSequence(reftiles[refstepend])...)
+ refstepend++
}
- refSequence = append(refSequence, tileVariant[reftiles[refstepend]].Sequence...)
- refstepend++
+ // (TODO: handle no-calls)
+ if len(refSequence) <= maxTileSize {
+ refstr := strings.ToUpper(string(refSequence))
+ genomestr := strings.ToUpper(string(genomeseq))
+ vars, _ = hgvs.Diff(refstr, genomestr, time.Second)
+ }
+ diffs[glibref] = vars
}
- // (TODO: handle no-calls)
- vars, _ := hgvs.Diff(strings.ToUpper(string(refSequence)), strings.ToUpper(string(genometile.Sequence)), time.Second)
for _, v := range vars {
- if cmd.outputFormat.PadLeft {
+ if padLeft {
v = v.PadLeft()
}
v.Position += refpos
varslice := variantAt[v.Position]
if varslice == nil {
- varslice = make([]hgvs.Variant, len(cgs)*2)
+ varslice = make([]tvVariant, len(cgs)*2)
variantAt[v.Position] = varslice
}
- varslice[cgidx*2+phase] = v
+ varslice[cgidx*2+phase].Variant = v
+ if varslice[cgidx*2+phase].librefs == nil {
+ varslice[cgidx*2+phase].librefs = map[tileLibRef]bool{glibref: true}
+ } else {
+ varslice[cgidx*2+phase].librefs[glibref] = true
+ }
}
}
}
- refpos += len(reftile.Sequence) - taglen
+ refpos += len(refseq) - taglen
// Flush entries from variantAt that are behind
// refpos. Flush all entries if this is the last
// reftile of the path/chromosome.
- var flushpos []int
+ flushpos := make([]int, 0, len(variantAt))
lastrefstep := refstep == len(reftiles)-1
for pos := range variantAt {
if lastrefstep || pos <= refpos {
}
}
sort.Slice(flushpos, func(i, j int) bool { return flushpos[i] < flushpos[j] })
- for _, pos := range flushpos {
+ flushvariants := make([][]tvVariant, len(flushpos))
+ for i, pos := range flushpos {
varslice := variantAt[pos]
delete(variantAt, pos)
+ // Check for uninitialized (zero-value)
+ // elements in varslice
for i := range varslice {
- if varslice[i].Position == 0 {
- varslice[i].Position = pos
+ if varslice[i].Position != 0 {
+ // Not a zero-value element
+ continue
+ }
+ // Set the position so
+ // varslice[*].Position are all equal
+ varslice[i].Position = pos
+ // This could be either =ref or a
+ // missing/low-quality tile. Figure
+ // out which.
+ vidx := int(libref.Tag)*2 + i%2
+ if vidx >= len(cgs[i/2].Variants) {
+ // Missing tile.
+ varslice[i].New = "-"
+ continue
+ }
+ v := cgs[i/2].Variants[vidx]
+ if v < 1 || len(tilelib.TileVariantSequence(tileLibRef{Tag: libref.Tag, Variant: v})) == 0 {
+ // Missing/low-quality tile.
+ varslice[i].New = "-" // fasta "gap of indeterminate length"
}
}
- cmd.outputFormat.Print(outw, seqname, varslice)
+ flushvariants[i] = varslice
}
- if bedw != nil && len(reftile.Sequence) > 0 {
- tilestart := refpos - len(reftile.Sequence) + taglen
+ outmtx.Lock()
+ go func() {
+ defer outmtx.Unlock()
+ for _, varslice := range flushvariants {
+ callback(varslice)
+ }
+ }()
+ if bedw != nil && len(refseq) > 0 {
+ tilestart := refpos - len(refseq) + taglen
tileend := refpos
if !lastrefstep {
tileend += taglen
}
}
-func printVCF(out io.Writer, seqname string, varslice []hgvs.Variant) {
- refs := map[string]map[string]int{}
+func bucketVarsliceByRef(varslice []tvVariant) map[string]map[string]int {
+ byref := map[string]map[string]int{}
for _, v := range varslice {
if v.Ref == "" && v.New == "" {
+ // =ref
continue
}
- alts := refs[v.Ref]
+ if v.New == "-" {
+ // no-call
+ continue
+ }
+ alts := byref[v.Ref]
if alts == nil {
alts = map[string]int{}
- refs[v.Ref] = alts
+ byref[v.Ref] = alts
}
- alts[v.New] = 0
+ alts[v.New]++
}
- for ref, alts := range refs {
- var altslice []string
+ return byref
+}
+
+type formatVCF struct{}
+
+func (formatVCF) MaxGoroutines() int { return 0 }
+func (formatVCF) Filename() string { return "out.vcf" }
+func (formatVCF) PadLeft() bool { return true }
+func (formatVCF) Finish(string, io.Writer, string) error { return nil }
+func (formatVCF) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error {
+ _, err := fmt.Fprint(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
+ return err
+}
+func (formatVCF) Print(out io.Writer, seqname string, varslice []tvVariant) error {
+ for ref, alts := range bucketVarsliceByRef(varslice) {
+ altslice := make([]string, 0, len(alts))
+ for alt := range alts {
+ altslice = append(altslice, alt)
+ }
+ sort.Strings(altslice)
+
+ info := "AC="
+ for i, a := range altslice {
+ if i > 0 {
+ info += ","
+ }
+ info += strconv.Itoa(alts[a])
+ }
+ _, err := fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t%s\n", seqname, varslice[0].Position, ref, strings.Join(altslice, ","), info)
+ if err != nil {
+ return err
+ }
+ }
+ return nil
+}
+
+type formatPVCF struct{}
+
+func (formatPVCF) MaxGoroutines() int { return 0 }
+func (formatPVCF) Filename() string { return "out.vcf" }
+func (formatPVCF) PadLeft() bool { return true }
+func (formatPVCF) Finish(string, io.Writer, string) error { return nil }
+func (formatPVCF) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error {
+ fmt.Fprintln(out, `##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">`)
+ fmt.Fprintf(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT")
+ for _, cg := range cgs {
+ fmt.Fprintf(out, "\t%s", cg.Name)
+ }
+ _, err := fmt.Fprintf(out, "\n")
+ return err
+}
+
+func (formatPVCF) Print(out io.Writer, seqname string, varslice []tvVariant) error {
+ for ref, alts := range bucketVarsliceByRef(varslice) {
+ altslice := make([]string, 0, len(alts))
for alt := range alts {
altslice = append(altslice, alt)
}
for i, a := range altslice {
alts[a] = i + 1
}
- fmt.Fprintf(out, "%s\t%d\t%s\t%s", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
+ _, err := fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t.\tGT", seqname, varslice[0].Position, ref, strings.Join(altslice, ","))
+ if err != nil {
+ return err
+ }
for i := 0; i < len(varslice); i += 2 {
v1, v2 := varslice[i], varslice[i+1]
a1, a2 := alts[v1.New], alts[v2.New]
if v1.Ref != ref {
+ // variant on allele 0 belongs on a
+ // different output line -- same
+ // chr,pos but different "ref" length
a1 = 0
}
if v2.Ref != ref {
a2 = 0
}
- fmt.Fprintf(out, "\t%d/%d", a1, a2)
+ _, err := fmt.Fprintf(out, "\t%d/%d", a1, a2)
+ if err != nil {
+ return err
+ }
+ }
+ _, err = out.Write([]byte{'\n'})
+ if err != nil {
+ return err
}
- out.Write([]byte{'\n'})
}
+ return nil
}
-func printHGVS(out io.Writer, seqname string, varslice []hgvs.Variant) {
+type formatHGVS struct{}
+
+func (formatHGVS) MaxGoroutines() int { return 0 }
+func (formatHGVS) Filename() string { return "out.tsv" }
+func (formatHGVS) PadLeft() bool { return false }
+func (formatHGVS) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error { return nil }
+func (formatHGVS) Finish(string, io.Writer, string) error { return nil }
+func (formatHGVS) Print(out io.Writer, seqname string, varslice []tvVariant) error {
for i := 0; i < len(varslice)/2; i++ {
if i > 0 {
out.Write([]byte{'\t'})
}
var1, var2 := varslice[i*2], varslice[i*2+1]
- if var1 == var2 {
+ if var1.New == "-" || var2.New == "-" {
+ _, err := out.Write([]byte{'N'})
+ if err != nil {
+ return err
+ }
+ continue
+ }
+ if var1.Variant == var2.Variant {
if var1.Ref == var1.New {
- out.Write([]byte{'.'})
+ _, err := out.Write([]byte{'.'})
+ if err != nil {
+ return err
+ }
} else {
- fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
+ _, err := fmt.Fprintf(out, "%s:g.%s", seqname, var1.String())
+ if err != nil {
+ return err
+ }
}
} else {
- fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
+ _, err := fmt.Fprintf(out, "%s:g.[%s];[%s]", seqname, var1.String(), var2.String())
+ if err != nil {
+ return err
+ }
}
}
- out.Write([]byte{'\n'})
+ _, err := out.Write([]byte{'\n'})
+ return err
}
-func printHGVSOneHot(out io.Writer, seqname string, varslice []hgvs.Variant) {
+type formatHGVSOneHot struct{}
+
+func (formatHGVSOneHot) MaxGoroutines() int { return 0 }
+func (formatHGVSOneHot) Filename() string { return "out.tsv" }
+func (formatHGVSOneHot) PadLeft() bool { return false }
+func (formatHGVSOneHot) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error {
+ return nil
+}
+func (formatHGVSOneHot) Finish(string, io.Writer, string) error { return nil }
+func (formatHGVSOneHot) Print(out io.Writer, seqname string, varslice []tvVariant) error {
vars := map[hgvs.Variant]bool{}
for _, v := range varslice {
if v.Ref != v.New {
- vars[v] = true
+ vars[v.Variant] = true
}
}
sort.Slice(sorted, func(a, b int) bool { return hgvs.Less(sorted[a], sorted[b]) })
for _, v := range sorted {
+ if v.New == "-" {
+ continue
+ }
fmt.Fprintf(out, "%s.%s", seqname, v.String())
for i := 0; i < len(varslice); i += 2 {
- if varslice[i] == v || varslice[i+1] == v {
+ if varslice[i].Variant == v || varslice[i+1].Variant == v {
out.Write([]byte("\t1"))
} else {
out.Write([]byte("\t0"))
}
}
- out.Write([]byte{'\n'})
+ _, err := out.Write([]byte{'\n'})
+ if err != nil {
+ return err
+ }
}
+ return nil
+}
+
+type formatHGVSNumpy struct {
+ sync.Mutex
+ writelock sync.Mutex
+ alleles map[string][][]int8 // alleles[seqname][variantidx][genomeidx*2+phase]
+ cases []bool
+ maxPValue float64
+}
+
+func (*formatHGVSNumpy) MaxGoroutines() int { return 4 }
+func (*formatHGVSNumpy) Filename() string { return "annotations.csv" }
+func (*formatHGVSNumpy) PadLeft() bool { return false }
+func (f *formatHGVSNumpy) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error {
+ f.cases = cases
+ f.maxPValue = p
+ return nil
+}
+func (f *formatHGVSNumpy) Print(outw io.Writer, seqname string, varslice []tvVariant) error {
+ // sort variants to ensure output is deterministic
+ sorted := make([]hgvs.Variant, 0, len(varslice))
+ for _, v := range varslice {
+ sorted = append(sorted, v.Variant)
+ }
+ sort.Slice(sorted, func(a, b int) bool { return hgvs.Less(sorted[a], sorted[b]) })
+
+ f.Lock()
+ seqalleles := f.alleles[seqname]
+ f.Unlock()
+
+ chi2x := make([]bool, 0, len(varslice))
+ chi2y := make([]bool, 0, len(varslice))
+
+ // append a row to seqalleles for each unique non-ref variant
+ // in varslice.
+ var previous hgvs.Variant
+ for _, v := range sorted {
+ if previous == v || v.Ref == v.New || v.New == "-" {
+ continue
+ }
+ previous = v
+ chi2x, chi2y := chi2x, chi2y
+ newrow := make([]int8, len(varslice))
+ for i, allele := range varslice {
+ if allele.Variant == v {
+ newrow[i] = 1
+ chi2x = append(chi2x, true)
+ chi2y = append(chi2y, f.cases[i/2])
+ } else if allele.Variant.New == "-" {
+ newrow[i] = -1
+ } else {
+ chi2x = append(chi2x, false)
+ chi2y = append(chi2y, f.cases[i/2])
+ }
+ }
+ if f.maxPValue < 1 && pvalue(chi2x, chi2y) > f.maxPValue {
+ continue
+ }
+ seqalleles = append(seqalleles, newrow)
+ _, err := fmt.Fprintf(outw, "%d,%q\n", len(seqalleles)-1, seqname+"."+v.String())
+ if err != nil {
+ return err
+ }
+ }
+
+ f.Lock()
+ f.alleles[seqname] = seqalleles
+ f.Unlock()
+ return nil
+}
+func (f *formatHGVSNumpy) Finish(outdir string, _ io.Writer, seqname string) error {
+ // Write seqname's data to a .npy matrix with one row per
+ // genome and 2 columns per variant.
+ f.Lock()
+ seqalleles := f.alleles[seqname]
+ delete(f.alleles, seqname)
+ f.Unlock()
+ if len(seqalleles) == 0 {
+ return nil
+ }
+ out := make([]int8, len(seqalleles)*len(seqalleles[0]))
+ rows := len(seqalleles[0]) / 2
+ cols := len(seqalleles) * 2
+ // copy seqalleles[varidx][genome*2+phase] to
+ // out[genome*nvars*2 + varidx*2 + phase]
+ for varidx, alleles := range seqalleles {
+ for g := 0; g < len(alleles)/2; g++ {
+ aa, ab := alleles[g*2], alleles[g*2+1]
+ if aa < 0 || ab < 0 {
+ // no-call
+ out[g*cols+varidx*2] = -1
+ out[g*cols+varidx*2+1] = -1
+ } else if aa > 0 && ab > 0 {
+ // hom
+ out[g*cols+varidx*2] = 1
+ } else if aa > 0 || ab > 0 {
+ // het
+ out[g*cols+varidx*2+1] = 1
+ }
+ }
+ }
+ outf, err := os.OpenFile(outdir+"/matrix."+seqname+".npy", os.O_CREATE|os.O_EXCL|os.O_WRONLY, 0777)
+ if err != nil {
+ return err
+ }
+ defer outf.Close()
+ bufw := bufio.NewWriter(outf)
+ npw, err := gonpy.NewWriter(nopCloser{bufw})
+ if err != nil {
+ return err
+ }
+ log.WithFields(logrus.Fields{
+ "seqname": seqname,
+ "rows": rows,
+ "cols": cols,
+ }).Info("writing numpy")
+ npw.Shape = []int{rows, cols}
+ f.writelock.Lock() // serialize because WriteInt8 uses lots of memory
+ npw.WriteInt8(out)
+ f.writelock.Unlock()
+ err = bufw.Flush()
+ if err != nil {
+ return err
+ }
+ err = outf.Close()
+ if err != nil {
+ return err
+ }
+ return nil
}
projects / lightning.git / blobdiff