"git.arvados.org/arvados.git/sdk/go/arvados"
"github.com/arvados/lightning/hgvs"
+ "github.com/james-bowman/nlp"
"github.com/kshedden/gonpy"
"github.com/sirupsen/logrus"
log "github.com/sirupsen/logrus"
"golang.org/x/crypto/blake2b"
+ "gonum.org/v1/gonum/mat"
)
const annotationMaxTileSpan = 100
}
func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
- var err error
- defer func() {
- if err != nil {
- fmt.Fprintf(stderr, "%s\n", err)
- }
- }()
+ err := cmd.run(prog, args, stdin, stdout, stderr)
+ if err != nil {
+ fmt.Fprintf(stderr, "%s\n", err)
+ return 1
+ }
+ return 0
+}
+func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) error {
flags := flag.NewFlagSet("", flag.ContinueOnError)
flags.SetOutput(stderr)
pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
onehotSingle := flags.Bool("single-onehot", false, "generate one-hot tile-based matrix")
onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix per input chunk")
onlyPCA := flags.Bool("pca", false, "generate pca matrix")
+ pcaComponents := flags.Int("pca-components", 4, "number of PCA components")
debugTag := flags.Int("debug-tag", -1, "log debugging details about specified tag")
flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
flags.StringVar(&cmd.chi2CaseControlFile, "chi2-case-control-file", "", "tsv file or directory indicating cases and controls for Χ² test (if directory, all .tsv files will be read)")
flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
cmd.filter.Flags(flags)
- err = flags.Parse(args)
+ err := flags.Parse(args)
if err == flag.ErrHelp {
- err = nil
- return 0
+ return nil
} else if err != nil {
- return 2
+ return err
}
if *pprof != "" {
}
if cmd.chi2PValue != 1 && (cmd.chi2CaseControlFile == "" || cmd.chi2CaseControlColumn == "") {
- log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-case-control-file= or -chi2-case-control-column= value is empty", cmd.chi2PValue)
- return 2
+ return fmt.Errorf("cannot use provided -chi2-p-value=%f because -chi2-case-control-file= or -chi2-case-control-column= value is empty", cmd.chi2PValue)
}
cmd.debugTag = tagID(*debugTag)
}
err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CaseControlFile)
if err != nil {
- return 1
+ return err
}
runner.Args = []string{"slice-numpy", "-local=true",
"-pprof=:6060",
var output string
output, err = runner.Run()
if err != nil {
- return 1
+ return err
}
fmt.Fprintln(stdout, output)
- return 0
+ return nil
}
infiles, err := allFiles(*inputDir, matchGobFile)
if err != nil {
- return 1
+ return err
}
if len(infiles) == 0 {
err = fmt.Errorf("no input files found in %s", *inputDir)
- return 1
+ return err
}
sort.Strings(infiles)
var reftiledata = make(map[tileLibRef][]byte, 11000000)
in0, err := open(infiles[0])
if err != nil {
- return 1
+ return err
}
matchGenome, err := regexp.Compile(cmd.filter.MatchGenome)
if err != nil {
err = fmt.Errorf("-match-genome: invalid regexp: %q", cmd.filter.MatchGenome)
- return 1
+ return err
}
cmd.cgnames = nil
return nil
})
if err != nil {
- return 1
+ return err
}
in0.Close()
if refseq == nil {
err = fmt.Errorf("%s: reference sequence not found", infiles[0])
- return 1
+ return err
}
if len(tagset) == 0 {
err = fmt.Errorf("tagset not found")
- return 1
+ return err
}
taglib := &tagLibrary{}
err = taglib.setTags(tagset)
if err != nil {
- return 1
+ return err
}
taglen := taglib.TagLen()
if len(cmd.cgnames) == 0 {
err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
- return 1
+ return err
}
sort.Strings(cmd.cgnames)
err = cmd.useCaseControlFiles()
if err != nil {
- return 1
+ return err
}
if len(cmd.cgnames) == 0 {
err = fmt.Errorf("fatal: 0 cases, 0 controls, nothing to do")
- return 1
+ return err
}
if cmd.filter.MinCoverage == 1 {
// In the generic formula below, floating point
var f *os.File
f, err = os.Create(labelsFilename)
if err != nil {
- return 1
+ return err
}
defer f.Close()
for i, name := range cmd.cgnames {
_, err = fmt.Fprintf(f, "%d,%q,%d\n", i, trimFilenameForLabel(name), cc)
if err != nil {
err = fmt.Errorf("write %s: %w", labelsFilename, err)
- return 1
+ return err
}
}
err = f.Close()
if err != nil {
err = fmt.Errorf("close %s: %w", labelsFilename, err)
- return 1
+ return err
}
}
tiledata := reftiledata[libref]
if len(tiledata) == 0 {
err = fmt.Errorf("missing tiledata for tag %d variant %d in %s in ref", libref.Tag, libref.Variant, seqname)
- return 1
+ return err
}
foundthistag := false
taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
log.Printf("loading regions from %s", *regionsFilename)
mask, err = makeMask(*regionsFilename, *expandRegions)
if err != nil {
- return 1
+ return err
}
log.Printf("before applying mask, len(reftile) == %d", len(reftile))
log.Printf("deleting reftile entries for regions outside %d intervals", mask.Len())
var f *os.File
f, err = os.Create(*outputDir + "/tmp." + seqname + ".gob")
if err != nil {
- return 1
+ return err
}
defer os.Remove(f.Name())
bufw := bufio.NewWriterSize(f, 1<<24)
})
}
if err = throttleMem.Wait(); err != nil {
- return 1
+ return err
}
if *hgvsChunked {
}
err = encodeHGVS.Wait()
if err != nil {
- return 1
+ return err
}
for seqname := range refseq {
log.Infof("%s: reading hgvsCols from temp file", seqname)
f := tmpHGVSCols[seqname]
_, err = f.Seek(0, io.SeekStart)
if err != nil {
- return 1
+ return err
}
var hgvsCols hgvsColSet
dec := gob.NewDecoder(bufio.NewReaderSize(f, 1<<24))
err = dec.Decode(&hgvsCols)
}
if err != io.EOF {
- return 1
+ return err
}
log.Infof("%s: sorting %d hgvs variants", seqname, len(hgvsCols))
variants := make([]hgvs.Variant, 0, len(hgvsCols))
}
err = writeNumpyInt8(fmt.Sprintf("%s/hgvs.%s.npy", *outputDir, seqname), out, rows, cols)
if err != nil {
- return 1
+ return err
}
out = nil
}
err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0666)
if err != nil {
- return 1
+ return err
}
}
}
annoFilename := fmt.Sprintf("%s/matrix.annotations.csv", *outputDir)
annof, err = os.Create(annoFilename)
if err != nil {
- return 1
+ return err
}
annow = bufio.NewWriterSize(annof, 1<<20)
}
log.Infof("reading %s", annotationsFilename)
buf, err := os.ReadFile(annotationsFilename)
if err != nil {
- return 1
+ return err
}
if *mergeOutput {
err = os.Remove(annotationsFilename)
if err != nil {
- return 1
+ return err
}
}
for _, line := range bytes.Split(buf, []byte{'\n'}) {
rt, ok := reftile[tagID(tag)]
if !ok {
err = fmt.Errorf("bug: seeing annotations for tag %d, but it has no reftile entry", tag)
- return 1
+ return err
}
for ph := 0; ph < 2; ph++ {
for row := 0; row < rows; row++ {
if *mergeOutput {
err = annow.Flush()
if err != nil {
- return 1
+ return err
}
err = annof.Close()
if err != nil {
- return 1
+ return err
}
err = writeNumpyInt16(fmt.Sprintf("%s/matrix.npy", *outputDir), out, rows, cols)
if err != nil {
- return 1
+ return err
}
}
out = nil
}
err = writeNumpyInt16(fmt.Sprintf("%s/hgvs.npy", *outputDir), out, rows, cols)
if err != nil {
- return 1
+ return err
}
fnm := fmt.Sprintf("%s/hgvs.annotations.csv", *outputDir)
log.Printf("writing hgvs labels: %s", fnm)
err = ioutil.WriteFile(fnm, hgvsLabels.Bytes(), 0777)
if err != nil {
- return 1
+ return err
}
}
}
- if *onehotSingle {
+ if *onehotSingle || *onlyPCA {
nzCount := 0
for _, part := range onehotIndirect {
nzCount += len(part[0])
onehotXrefs[i] = nil
debug.FreeOSMemory()
}
- fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
- err = writeNumpyUint32(fnm, onehot, 2, nzCount)
- if err != nil {
- return 1
+ if *onehotSingle {
+ fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
+ err = writeNumpyUint32(fnm, onehot, 2, nzCount)
+ if err != nil {
+ return err
+ }
+ fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
+ err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
+ if err != nil {
+ return err
+ }
}
- fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
- err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 5, len(xrefs))
- if err != nil {
- return 1
+ if *onlyPCA {
+ cols := 0
+ for _, c := range onehot[nzCount:] {
+ if int(c) >= cols {
+ cols = int(c) + 1
+ }
+ }
+ if cols == 0 {
+ return fmt.Errorf("cannot do PCA: one-hot matrix is empty")
+ }
+ log.Printf("creating matrix: %d rows, %d cols", len(cmd.cgnames), cols)
+ mtx := mat.NewDense(len(cmd.cgnames), cols, nil)
+ for i, c := range onehot[nzCount:] {
+ mtx.Set(int(onehot[i]), int(c), 1)
+ }
+ log.Print("fitting")
+ transformer := nlp.NewPCA(*pcaComponents)
+ transformer.Fit(mtx.T())
+ log.Printf("transforming")
+ pca, err := transformer.Transform(mtx.T())
+ if err != nil {
+ return err
+ }
+ pca = pca.T()
+ outrows, outcols := pca.Dims()
+ log.Printf("copying result to numpy output array: %d rows, %d cols", outrows, outcols)
+ out := make([]float64, outrows*outcols)
+ for i := 0; i < outrows; i++ {
+ for j := 0; j < outcols; j++ {
+ out[i*outcols+j] = pca.At(i, j)
+ }
+ }
+ fnm := fmt.Sprintf("%s/pca.npy", *outputDir)
+ log.Printf("writing numpy: %s", fnm)
+ output, err := os.OpenFile(fnm, os.O_CREATE|os.O_TRUNC|os.O_WRONLY, 0777)
+ if err != nil {
+ return err
+ }
+ npw, err := gonpy.NewWriter(nopCloser{output})
+ if err != nil {
+ return fmt.Errorf("gonpy.NewWriter: %w", err)
+ }
+ npw.Shape = []int{outrows, outcols}
+ err = npw.WriteFloat64(out)
+ if err != nil {
+ return fmt.Errorf("WriteFloat64: %w", err)
+ }
+ err = output.Close()
+ if err != nil {
+ return err
+ }
+ log.Print("done")
}
- }
- if *onlyPCA {
-
}
if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
var f *os.File
f, err = os.Create(tagoffsetFilename)
if err != nil {
- return 1
+ return err
}
defer f.Close()
for idx, offset := range chunkStartTag {
_, err = fmt.Fprintf(f, "%q,%d\n", fmt.Sprintf("matrix.%04d.npy", idx), offset)
if err != nil {
err = fmt.Errorf("write %s: %w", tagoffsetFilename, err)
- return 1
+ return err
}
}
err = f.Close()
if err != nil {
err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
- return 1
+ return err
}
}
- return 0
+ return nil
}
// Read case/control files, remove non-case/control entries from
projects / lightning.git / commitdiff