From 23c0b925eb9b65400868c3813ea798fdbdb9eed3 Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Tue, 31 Aug 2021 14:56:04 -0400 Subject: [PATCH] Add -p-value and -cases options for exporting hgvs numpy. refs #17562 Arvados-DCO-1.1-Signed-off-by: Tom Clegg --- export.go | 99 ++++++++++++++++++++++++++++++++++++++++---------- export_test.go | 17 +++++++++ 2 files changed, 97 insertions(+), 19 deletions(-) diff --git a/export.go b/export.go index f44f6a8724..b6b6263117 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 @@ -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`") @@ -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", @@ -214,6 +220,41 @@ 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) + f, err := open(*cases) + if err != nil { + return 1 + } + 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 +350,7 @@ 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 +372,7 @@ 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 { @@ -568,7 +609,7 @@ 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 } @@ -601,7 +642,7 @@ 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 { @@ -652,11 +693,11 @@ 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 { @@ -695,11 +736,13 @@ 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 { @@ -739,12 +782,18 @@ 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 (*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)) @@ -757,6 +806,9 @@ func (f *formatHGVSNumpy) Print(outw io.Writer, seqname string, varslice []tvVar 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 @@ -765,14 +817,23 @@ func (f *formatHGVSNumpy) Print(outw io.Writer, seqname string, varslice []tvVar 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 { diff --git a/export_test.go b/export_test.go index a2452c6ca3..ac7063d2fc 100644 --- a/export_test.go +++ b/export_test.go @@ -214,4 +214,21 @@ chr2 471 . GG AA . . AC=1 5,"chr2.470_472del" 6,"chr2.471_472delinsAA" `) + + c.Logf("export hgvs-numpy with p-value threshold") + outdir = c.MkDir() + err = ioutil.WriteFile(tmpdir+"/cases", []byte("input1\n"), 0777) + c.Assert(err, check.IsNil) + exited = (&exporter{}).RunCommand("export", []string{ + "-local=true", + "-input-dir=" + input, + "-p-value=0.05", + "-cases=" + tmpdir + "/cases", + "-output-dir=" + outdir, + "-output-format=hgvs-numpy", + "-ref=testdata/ref.fasta", + "-match-genome=input[12]", + }, nil, os.Stderr, os.Stderr) + c.Check(exited, check.Equals, 0) + } -- 2.30.2