"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"
)
librefs map[tileLibRef]bool
}
-type outputFormat struct {
- Filename string
- Head func(out io.Writer, cgs []CompactGenome)
- Print func(out io.Writer, seqname string, varslice []tvVariant)
- PadLeft bool
+type outputFormat interface {
+ Filename() string
+ PadLeft() bool
+ Head(out io.Writer, cgs []CompactGenome) error
+ Print(out io.Writer, seqname string, varslice []tvVariant) error
+ Finish(outdir string, out io.Writer, seqname string) error
}
-var (
- outputFormats = map[string]outputFormat{
- "hgvs-onehot": outputFormatHGVSOneHot,
- "hgvs": outputFormatHGVS,
- "pvcf": outputFormatPVCF,
- "vcf": outputFormatVCF,
- }
- outputFormatHGVS = outputFormat{Filename: "out.tsv", Head: headNone, Print: printHGVS}
- outputFormatHGVSOneHot = outputFormat{Filename: "out.tsv", Head: headNone, Print: printHGVSOneHot}
- outputFormatPVCF = outputFormat{Filename: "out.vcf", Head: headPVCF, Print: printPVCF, PadLeft: true}
- outputFormatVCF = outputFormat{Filename: "out.vcf", Head: headVCF, Print: printVCF, PadLeft: true}
- headNone = func(io.Writer, []CompactGenome) {}
-)
+var outputFormats = map[string]func() outputFormat{
+ "hgvs-numpy": func() outputFormat {
+ return &formatHGVSNumpy{alleles: map[string][][]bool{}, variants: map[string][]hgvs.Variant{}}
+ },
+ "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
err = fmt.Errorf("invalid output format %q", *outputFormatStr)
return 2
} else {
- cmd.outputFormat = f
+ cmd.outputFormat = f()
}
if *pprof != "" {
}
defer f.Close()
for i, name := range names {
- _, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), cmd.outputFormat.Filename)
+ _, 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
}
if cmd.outputPerChrom {
for i, seqname := range seqnames {
- fnm := filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename, ".", "."+seqname+".", 1))
+ fnm := filepath.Join(outdir, strings.Replace(cmd.outputFormat.Filename(), ".", "."+seqname+".", 1))
if cmd.compress {
fnm += ".gz"
}
defer z.Close()
outw[i] = z
}
- cmd.outputFormat.Head(outw[i], cgs)
+ err = cmd.outputFormat.Head(outw[i], cgs)
+ if err != nil {
+ return err
+ }
}
} else {
- fnm := filepath.Join(outdir, cmd.outputFormat.Filename)
+ fnm := filepath.Join(outdir, cmd.outputFormat.Filename())
if cmd.compress {
fnm += ".gz"
}
defer bedw.Close()
}
outwb := bufio.NewWriterSize(outw, 8*1024*1024)
- cmd.exportSeq(outwb, bedw, tilelib.taglib.keylen, seqname, refseq[seqname], tilelib, cgs)
- err := outwb.Flush()
+ 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)
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, tilelib *tileLibrary, 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()
// was false during import
continue
}
- if len(genomeseq) > cmd.maxTileSize {
+ if len(genomeseq) > maxTileSize {
continue
}
refSequence := refseq
// 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) <= cmd.maxTileSize {
+ 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...)
}
refstepend++
}
// (TODO: handle no-calls)
- if len(refSequence) <= cmd.maxTileSize {
+ if len(refSequence) <= maxTileSize {
refstr := strings.ToUpper(string(refSequence))
genomestr := strings.ToUpper(string(genomeseq))
vars, _ = hgvs.Diff(refstr, genomestr, time.Second)
diffs[glibref] = vars
}
for _, v := range vars {
- if cmd.outputFormat.PadLeft {
+ if padLeft {
v = v.PadLeft()
}
v.Position += refpos
go func() {
defer outmtx.Unlock()
for _, varslice := range flushvariants {
- cmd.outputFormat.Print(outw, seqname, varslice)
+ callback(varslice)
}
}()
if bedw != nil && len(refseq) > 0 {
return byref
}
-func headVCF(out io.Writer, cgs []CompactGenome) {
- fmt.Fprint(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
-}
+type formatVCF struct{}
-func printVCF(out io.Writer, seqname string, varslice []tvVariant) {
+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) 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 {
}
info += strconv.Itoa(alts[a])
}
- 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)
+ _, 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
}
-func headPVCF(out io.Writer, cgs []CompactGenome) {
+type formatPVCF struct{}
+
+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) 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)
}
- fmt.Fprintf(out, "\n")
+ _, err := fmt.Fprintf(out, "\n")
+ return err
}
-func printPVCF(out io.Writer, seqname string, varslice []tvVariant) {
+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 {
for i, a := range altslice {
alts[a] = i + 1
}
- fmt.Fprintf(out, "%s\t%d\t.\t%s\t%s\t.\t.\t.\tGT", 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 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 []tvVariant) {
+type formatHGVS struct{}
+
+func (formatHGVS) Filename() string { return "out.tsv" }
+func (formatHGVS) PadLeft() bool { return false }
+func (formatHGVS) Head(out io.Writer, cgs []CompactGenome) 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.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 []tvVariant) {
+type formatHGVSOneHot struct{}
+
+func (formatHGVSOneHot) Filename() string { return "out.tsv" }
+func (formatHGVSOneHot) PadLeft() bool { return false }
+func (formatHGVSOneHot) Head(out io.Writer, cgs []CompactGenome) 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 {
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
+ variants map[string][]hgvs.Variant // variants[seqname][variantidx]
+ alleles map[string][][]bool // alleles[seqname][variantidx][genomeidx*2+phase]
+}
+
+func (*formatHGVSNumpy) Filename() string { return "matrix.npy" }
+func (*formatHGVSNumpy) PadLeft() bool { return false }
+func (*formatHGVSNumpy) Head(out io.Writer, cgs []CompactGenome) error { return nil }
+func (f *formatHGVSNumpy) Print(_ 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()
+ defer f.Unlock()
+
+ seqvariants := f.variants[seqname]
+ seqalleles := f.alleles[seqname]
+
+ // append a row to seqvariants and seqalleles for each unique
+ // non-ref variant in varslice.
+ var previous hgvs.Variant
+ for _, v := range sorted {
+ if previous == v || v.Ref == v.New {
+ continue
+ }
+ previous = v
+ newrow := make([]bool, len(varslice))
+ for i, allele := range varslice {
+ if allele.Variant == v {
+ newrow[i] = true
+ }
+ }
+ seqalleles = append(seqalleles, newrow)
+ seqvariants = append(seqvariants, v)
}
+ f.variants[seqname] = seqvariants
+ f.alleles[seqname] = seqalleles
+ return nil
+}
+func (f *formatHGVSNumpy) Finish(outdir string, outw io.Writer, seqname string) error {
+ // Write seqname's data to a .npy matrix with one row per
+ // genome and 2 columns per variant.
+ seqvariants := f.variants[seqname]
+ seqalleles := f.alleles[seqname]
+ 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 && ab {
+ // hom
+ out[g*cols+varidx*2] = 1
+ } else if aa || ab {
+ // het
+ out[g*cols+varidx*2+1] = 1
+ }
+ }
+ }
+ bufw := bufio.NewWriter(outw)
+ 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}
+ npw.WriteInt8(out)
+ err = bufw.Flush()
+ if err != nil {
+ return err
+ }
+
+ // Write annotations
+ csv, err := os.OpenFile(outdir+"/annotations."+seqname+".csv", os.O_CREATE|os.O_EXCL|os.O_WRONLY, 0777)
+ if err != nil {
+ return err
+ }
+ defer csv.Close()
+ for i, v := range seqvariants {
+ fmt.Fprintf(csv, "%d,%q\n", i, seqname+"."+v.String())
+ }
+ err = csv.Close()
+ if err != nil {
+ return err
+ }
+
+ return nil
}
"os"
"os/exec"
+ "github.com/kshedden/gonpy"
"gopkg.in/check.v1"
)
chr2 469 . GTGG G . . AC=1
chr2 471 . GG AA . . AC=1
`))
+
+ outdir := c.MkDir()
+ exited = (&exporter{}).RunCommand("export", []string{
+ "-local=true",
+ "-input-dir=" + tmpdir,
+ "-output-dir=" + outdir,
+ "-output-format=hgvs-numpy",
+ "-ref=testdata/ref.fasta",
+ }, &buffer, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+
+ f, err := os.Open(outdir + "/matrix.chr1.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err := gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ variants, err := npy.GetInt8()
+ c.Assert(err, check.IsNil)
+ c.Check(variants, check.HasLen, 6*2*2) // 6 variants * 2 alleles * 2 genomes
+ c.Check(variants, check.DeepEquals, []int8{
+ 1, 0, 0, 1, 0, 1, 0, 1, 1, 0, 0, 1, // input1.1.fasta
+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // input2.1.fasta
+ })
+
+ f, err = os.Open(outdir + "/matrix.chr2.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err = gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ variants, err = npy.GetInt8()
+ c.Assert(err, check.IsNil)
+ c.Check(variants, check.HasLen, 7*2*2) // 6 variants * 2 alleles * 2 genomes
+ c.Check(variants, check.DeepEquals, []int8{
+ 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, // input1.1.fasta
+ 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, // input2.1.fasta
+ })
+
+ annotations, err := ioutil.ReadFile(outdir + "/annotations.chr1.csv")
+ c.Check(err, check.IsNil)
+ c.Logf("%s", string(annotations))
+ c.Check(string(annotations), check.Equals, `0,"chr1.1_3delinsGGC"
+1,"chr1.41_42delinsAA"
+2,"chr1.161A>T"
+3,"chr1.178A>T"
+4,"chr1.222_224del"
+5,"chr1.302_305delinsAAAA"
+`)
+ annotations, err = ioutil.ReadFile(outdir + "/annotations.chr2.csv")
+ c.Check(err, check.IsNil)
+ c.Check(string(annotations), check.Equals, `0,"chr2.1_3delinsAAA"
+1,"chr2.125_127delinsAAA"
+2,"chr2.241_254del"
+3,"chr2.258_269delinsAA"
+4,"chr2.315C>A"
+5,"chr2.470_472del"
+6,"chr2.471_472delinsAA"
+`)
}
projects / lightning.git / commitdiff