"bufio"
"bytes"
"encoding/gob"
+ "encoding/json"
"errors"
"flag"
"fmt"
samples []sampleInfo
trainingSet []int // samples index => training set index, or -1 if not in training set
trainingSetSize int
+ pvalue func(onehot []bool) float64
+ pvalueCallCount int64
}
func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
arvadosVCPUs := flags.Int("arvados-vcpus", 96, "number of VCPUs to request for arvados container")
projectUUID := flags.String("project", "", "project `UUID` for output data")
priority := flags.Int("priority", 500, "container request priority")
+ preemptible := flags.Bool("preemptible", true, "request preemptible instance")
inputDir := flags.String("input-dir", "./in", "input `directory`")
outputDir := flags.String("output-dir", "./out", "output `directory`")
ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
Priority: *priority,
KeepCache: 2,
APIAccess: true,
+ Preemptible: *preemptible,
}
err = runner.TranslatePaths(inputDir, regionsFilename, samplesFilename)
if err != nil {
cmd.trainingSet[i] = -1
}
}
+ if cmd.pvalue == nil {
+ cmd.pvalue = func(onehot []bool) float64 {
+ return pvalue(onehot, cmd.chi2Cases)
+ }
+ }
}
if cmd.filter.MinCoverage == 1 {
// In the generic formula below, floating point
cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
}
- {
- samplesOutFilename := *outputDir + "/samples.csv"
- log.Infof("writing sample metadata to %s", samplesOutFilename)
- var f *os.File
- f, err = os.Create(samplesOutFilename)
- if err != nil {
- return err
- }
- defer f.Close()
- for i, si := range cmd.samples {
- var cc, tv string
- if si.isCase {
- cc = "1"
- } else if si.isControl {
- cc = "0"
- }
- if si.isTraining {
- tv = "1"
- } else {
- tv = "0"
- }
- _, err = fmt.Fprintf(f, "%d,%s,%s,%s\n", i, si.id, cc, tv)
- if err != nil {
- err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
- return err
- }
- }
- err = f.Close()
+ if len(cmd.samples[0].pcaComponents) > 0 {
+ cmd.pvalue = glmPvalueFunc(cmd.samples, cmd.pcaComponents)
+ // Unfortunately, statsmodel/glm lib logs stuff to
+ // os.Stdout when it panics on an unsolvable
+ // problem. We recover() from the panic in glm.go, but
+ // we also need to commandeer os.Stdout to avoid
+ // producing large quantities of logs.
+ stdoutWas := os.Stdout
+ defer func() { os.Stdout = stdoutWas }()
+ os.Stdout, err = os.Open(os.DevNull)
if err != nil {
- err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
return err
}
- log.Print("done")
+ }
+
+ // cgnamemap[name]==true for samples that we are including in
+ // output
+ cgnamemap := map[string]bool{}
+ for _, name := range cmd.cgnames {
+ cgnamemap[name] = true
+ }
+
+ err = writeSampleInfo(cmd.samples, *outputDir)
+ if err != nil {
+ return err
}
log.Info("indexing reference tiles")
if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
return errSkip
}
- if !matchGenome.MatchString(cg.Name) {
+ if !cgnamemap[cg.Name] {
continue
}
// pad to full slice size
if err != nil {
return err
}
+ fnm = fmt.Sprintf("%s/stats.json", *outputDir)
+ j, err := json.Marshal(map[string]interface{}{
+ "pvalueCallCount": cmd.pvalueCallCount,
+ })
+ if err != nil {
+ return err
+ }
+ err = os.WriteFile(fnm, j, 0777)
+ if err != nil {
+ return err
+ }
}
if *onlyPCA {
cols := 0
}
log.Print("done")
- samplesOutFilename := *outputDir + "/samples.csv"
- log.Infof("writing sample metadata to %s", samplesOutFilename)
- var f *os.File
- f, err = os.Create(samplesOutFilename)
- if err != nil {
- return err
- }
- defer f.Close()
- for i, si := range cmd.samples {
- var cc, tv string
- if si.isCase {
- cc = "1"
- } else if si.isControl {
- cc = "0"
- }
- if si.isTraining {
- tv = "1"
- } else {
- tv = "0"
- }
- var pcavals string
+ log.Print("copying pca components to sampleInfo")
+ for i := range cmd.samples {
+ cmd.samples[i].pcaComponents = make([]float64, outcols)
for c := 0; c < outcols; c++ {
- pcavals += fmt.Sprintf(",%f", pca.At(i, c))
- }
- _, err = fmt.Fprintf(f, "%d,%s,%s,%s%s\n", i, si.id, cc, tv, pcavals)
- if err != nil {
- err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
- return err
+ cmd.samples[i].pcaComponents[i] = pca.At(i, c)
}
}
- err = f.Close()
+ log.Print("done")
+
+ err = writeSampleInfo(cmd.samples, *outputDir)
if err != nil {
- err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
return err
}
- log.Print("done")
}
}
if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
isCase: split[2] == "1",
isControl: split[2] == "0",
isTraining: split[3] == "1",
- isValidation: split[3] == "0",
+ isValidation: split[3] == "0" && len(split[2]) > 0, // fix errant 0s in input
pcaComponents: pcaComponents,
})
}
return si, nil
}
+func writeSampleInfo(samples []sampleInfo, outputDir string) error {
+ fnm := outputDir + "/samples.csv"
+ log.Infof("writing sample metadata to %s", fnm)
+ f, err := os.Create(fnm)
+ if err != nil {
+ return err
+ }
+ defer f.Close()
+ pcaLabels := ""
+ if len(samples) > 0 {
+ for i := range samples[0].pcaComponents {
+ pcaLabels += fmt.Sprintf(",PCA%d", i)
+ }
+ }
+ _, err = fmt.Fprintf(f, "Index,SampleID,CaseControl,TrainingValidation%s\n", pcaLabels)
+ if err != nil {
+ return err
+ }
+ for i, si := range samples {
+ var cc, tv string
+ if si.isCase {
+ cc = "1"
+ } else if si.isControl {
+ cc = "0"
+ }
+ if si.isTraining {
+ tv = "1"
+ } else if si.isValidation {
+ tv = "0"
+ }
+ var pcavals string
+ for _, pcaval := range si.pcaComponents {
+ pcavals += fmt.Sprintf(",%f", pcaval)
+ }
+ _, err = fmt.Fprintf(f, "%d,%s,%s,%s%s\n", i, si.id, cc, tv, pcavals)
+ if err != nil {
+ return fmt.Errorf("write %s: %w", fnm, err)
+ }
+ }
+ err = f.Close()
+ if err != nil {
+ return fmt.Errorf("close %s: %w", fnm, err)
+ }
+ log.Print("done")
+ return nil
+}
+
func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
if cmd.chi2PValue >= 1 {
return true
if col < 4 && !cmd.includeVariant1 {
continue
}
- var p float64
- if len(cmd.samples[0].pcaComponents) > 0 {
- p = pvalueGLM(cmd.samples, obs[col], cmd.pcaComponents)
- } else {
- p = pvalue(obs[col], cmd.chi2Cases)
- }
+ atomic.AddInt64(&cmd.pvalueCallCount, 1)
+ p := cmd.pvalue(obs[col])
if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
continue
}
projects / lightning.git / blobdiff