X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/a70ac669647881534d00e333f23c5d99cf2eb771..8fc5d19688d99d1ebacb9671b85ba30bbf3c3d35:/export.go diff --git a/export.go b/export.go index 5b0910054c..1ea08fe757 100644 --- a/export.go +++ b/export.go @@ -1,3 +1,7 @@ +// Copyright (C) The Lightning Authors. All rights reserved. +// +// SPDX-License-Identifier: AGPL-3.0 + package lightning import ( @@ -35,14 +39,15 @@ type tvVariant struct { type outputFormat interface { Filename() string PadLeft() bool - Head(out io.Writer, cgs []CompactGenome) error + 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][][]bool{}, variants: map[string][]hgvs.Variant{}} + return &formatHGVSNumpy{alleles: map[string][][]int8{}} }, "hgvs-onehot": func() outputFormat { return formatHGVSOneHot{} }, "hgvs": func() outputFormat { return formatHGVS{} }, @@ -55,6 +60,9 @@ type exporter struct { 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 { @@ -73,6 +81,8 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std priority := flags.Int("priority", 500, "container request priority") refname := flags.String("ref", "", "reference genome `name`") 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`") @@ -80,6 +90,7 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std 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 @@ -117,12 +128,12 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std Name: "lightning export", Client: arvados.NewClientFromEnv(), ProjectUUID: *projectUUID, - RAM: 700000000000, + RAM: 750000000000, VCPUs: 96, Priority: *priority, APIAccess: true, } - err = runner.TranslatePaths(inputDir) + err = runner.TranslatePaths(inputDir, cases) if err != nil { return 1 } @@ -137,6 +148,8 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std "-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", @@ -146,6 +159,7 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std "-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 { @@ -161,7 +175,7 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std retainTileSequences: true, compactGenomes: map[string][]tileVariantID{}, } - err = tilelib.LoadDir(context.Background(), *inputDir, nil) + err = tilelib.LoadDir(context.Background(), *inputDir) if err != nil { return 1 } @@ -177,6 +191,9 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std 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]}) @@ -203,6 +220,44 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std } } + 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 + } + 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 + } + } + var bedout io.Writer var bedfile *os.File var bedbufw *bufio.Writer @@ -298,7 +353,7 @@ func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrar defer z.Close() outw[i] = z } - err = cmd.outputFormat.Head(outw[i], cgs) + err = cmd.outputFormat.Head(outw[i], cgs, cmd.cases, cmd.maxPValue) if err != nil { return err } @@ -320,7 +375,7 @@ func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrar defer z.Close() out = z } - cmd.outputFormat.Head(out, cgs) + cmd.outputFormat.Head(out, cgs, cmd.cases, cmd.maxPValue) merge(out, outw, "output") } if bedout != nil { @@ -328,6 +383,9 @@ func (cmd *exporter) export(outdir string, bedout io.Writer, tilelib *tileLibrar } 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 @@ -386,15 +444,14 @@ func eachVariant(bedw io.Writer, taglen int, seqname string, reftiles []tileLibR 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 + var variant tileVariantID + if i := int(libref.Tag)*2 + phase; len(cg.Variants) > i { + variant = cg.Variants[i] } - variant := cg.Variants[int(libref.Tag)*2+phase] - if variant == 0 { - continue + if variant > 0 { + tagcoverage++ } - tagcoverage++ - if variant == libref.Variant { + if variant == libref.Variant || variant == 0 { continue } glibref := tileLibRef{Tag: libref.Tag, Variant: variant} @@ -467,9 +524,29 @@ func eachVariant(bedw io.Writer, taglen int, seqname string, reftiles []tileLibR 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" } } flushvariants[i] = varslice @@ -512,6 +589,11 @@ 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 + } + if v.New == "-" { + // no-call continue } alts := byref[v.Ref] @@ -526,10 +608,11 @@ func bucketVarsliceByRef(varslice []tvVariant) map[string]map[string]int { 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) error { +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 } @@ -558,10 +641,11 @@ func (formatVCF) Print(out io.Writer, seqname string, varslice []tvVariant) erro 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) error { +func (formatPVCF) Head(out io.Writer, cgs []CompactGenome, cases []bool, p float64) error { fmt.Fprintln(out, `##FORMAT=`) fmt.Fprintf(out, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT") for _, cg := range cgs { @@ -612,16 +696,24 @@ func (formatPVCF) Print(out io.Writer, seqname string, varslice []tvVariant) err 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) 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.New == "-" || var2.New == "-" { + _, err := out.Write([]byte{'N'}) + if err != nil { + return err + } + continue + } if var1.Variant == var2.Variant { if var1.Ref == var1.New { _, err := out.Write([]byte{'.'}) @@ -647,10 +739,13 @@ func (formatHGVS) Print(out io.Writer, seqname string, varslice []tvVariant) err 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) 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 { @@ -667,6 +762,9 @@ func (formatHGVSOneHot) Print(out io.Writer, seqname string, varslice []tvVarian 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].Variant == v || varslice[i+1].Variant == v { @@ -685,14 +783,21 @@ func (formatHGVSOneHot) Print(out io.Writer, seqname string, varslice []tvVarian type formatHGVSNumpy struct { sync.Mutex - variants map[string][]hgvs.Variant // variants[seqname][variantidx] - alleles map[string][][]bool // alleles[seqname][variantidx][genomeidx*2+phase] + writelock sync.Mutex + alleles map[string][][]int8 // alleles[seqname][variantidx][genomeidx*2+phase] + cases []bool + maxPValue float64 } -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 { +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 { @@ -701,37 +806,56 @@ func (f *formatHGVSNumpy) Print(_ io.Writer, seqname string, varslice []tvVarian 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] + f.Unlock() - // append a row to seqvariants and seqalleles for each unique - // non-ref variant in varslice. + 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 { + if previous == v || v.Ref == v.New || v.New == "-" { continue } previous = v - newrow := make([]bool, len(varslice)) + chi2x, chi2y := chi2x, chi2y + newrow := make([]int8, len(varslice)) for i, allele := range varslice { if allele.Variant == v { - newrow[i] = true + 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) - seqvariants = append(seqvariants, v) + _, err := fmt.Fprintf(outw, "%d,%q\n", len(seqalleles)-1, seqname+"."+v.String()) + if err != nil { + return err + } } - f.variants[seqname] = seqvariants + + f.Lock() f.alleles[seqname] = seqalleles + f.Unlock() return nil } -func (f *formatHGVSNumpy) Finish(outdir string, outw io.Writer, seqname string) error { +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. - seqvariants := f.variants[seqname] + f.Lock() seqalleles := f.alleles[seqname] + delete(f.alleles, seqname) + f.Unlock() if len(seqalleles) == 0 { return nil } @@ -743,16 +867,25 @@ func (f *formatHGVSNumpy) Finish(outdir string, outw io.Writer, seqname string) 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 { + 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 || ab { + } else if aa > 0 || ab > 0 { // het out[g*cols+varidx*2+1] = 1 } } } - bufw := bufio.NewWriter(outw) + 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 @@ -763,25 +896,16 @@ func (f *formatHGVSNumpy) Finish(outdir string, outw io.Writer, seqname string) "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 } - - // Write annotations - csv, err := os.OpenFile(outdir+"/annotations."+seqname+".csv", os.O_CREATE|os.O_EXCL|os.O_WRONLY, 0777) + err = outf.Close() 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 }