X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/4b1fa532170fb94ea03a93102e346677e4dc819f..de9aa35ea67f3aab2c97b126adfdffabff754521:/export.go diff --git a/export.go b/export.go index 9546926c01..1ea08fe757 100644 --- a/export.go +++ b/export.go @@ -39,7 +39,7 @@ 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 @@ -47,7 +47,7 @@ type outputFormat interface { var outputFormats = map[string]func() outputFormat{ "hgvs-numpy": func() outputFormat { - return &formatHGVSNumpy{alleles: map[string][][]bool{}} + return &formatHGVSNumpy{alleles: map[string][][]int8{}} }, "hgvs-onehot": func() outputFormat { return formatHGVSOneHot{} }, "hgvs": func() outputFormat { return formatHGVS{} }, @@ -61,6 +61,8 @@ type exporter struct { 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 { @@ -79,6 +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`") @@ -129,7 +133,7 @@ func (cmd *exporter) RunCommand(prog string, args []string, stdin io.Reader, std Priority: *priority, APIAccess: true, } - err = runner.TranslatePaths(inputDir) + err = runner.TranslatePaths(inputDir, cases) if err != nil { return 1 } @@ -144,6 +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", @@ -169,7 +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 } @@ -214,6 +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 @@ -309,7 +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 } @@ -331,7 +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 { @@ -400,15 +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} @@ -481,9 +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 @@ -526,6 +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] @@ -544,7 +612,7 @@ 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 } @@ -577,7 +645,7 @@ 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 { @@ -628,17 +696,24 @@ func (formatPVCF) Print(out io.Writer, seqname string, varslice []tvVariant) err 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) 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{'.'}) @@ -664,11 +739,13 @@ func (formatHGVS) Print(out io.Writer, seqname string, varslice []tvVariant) err 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) 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 { @@ -685,6 +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 { @@ -704,13 +784,19 @@ func (formatHGVSOneHot) Print(out io.Writer, seqname string, varslice []tvVarian type formatHGVSNumpy struct { sync.Mutex writelock sync.Mutex - alleles map[string][][]bool // alleles[seqname][variantidx][genomeidx*2+phase] + 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 (*formatHGVSNumpy) Head(out io.Writer, cgs []CompactGenome) error { return nil } +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)) @@ -723,20 +809,34 @@ func (f *formatHGVSNumpy) Print(outw io.Writer, seqname string, varslice []tvVar 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) _, err := fmt.Fprintf(outw, "%d,%q\n", len(seqalleles)-1, seqname+"."+v.String()) if err != nil { @@ -752,8 +852,8 @@ func (f *formatHGVSNumpy) Print(outw io.Writer, seqname string, varslice []tvVar 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. - seqalleles := f.alleles[seqname] f.Lock() + seqalleles := f.alleles[seqname] delete(f.alleles, seqname) f.Unlock() if len(seqalleles) == 0 { @@ -767,10 +867,14 @@ func (f *formatHGVSNumpy) Finish(outdir string, _ io.Writer, seqname string) err 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 }