"bufio"
"bytes"
"encoding/gob"
+ "errors"
"flag"
"fmt"
"io"
"strconv"
"strings"
"sync/atomic"
+ "unsafe"
"git.arvados.org/arvados.git/sdk/go/arvados"
"github.com/arvados/lightning/hgvs"
"github.com/kshedden/gonpy"
+ "github.com/sirupsen/logrus"
log "github.com/sirupsen/logrus"
"golang.org/x/crypto/blake2b"
)
type sliceNumpy struct {
- filter filter
- threads int
- chi2CasesFile string
- chi2Cases []bool
- chi2PValue float64
- minCoverage int
- cgnames []string
+ filter filter
+ threads int
+ chi2CaseControlColumn string
+ chi2CaseControlFile string
+ chi2Cases []bool
+ chi2PValue float64
+ minCoverage int
+ cgnames []string
+ includeVariant1 bool
+ debugTag tagID
}
func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
mergeOutput := flags.Bool("merge-output", false, "merge output into one matrix.npy and one matrix.annotations.csv")
hgvsSingle := flags.Bool("single-hgvs-matrix", false, "also generate hgvs-based matrix")
hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
- onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix")
+ 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")
+ 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.chi2CasesFile, "chi2-cases-file", "", "text file indicating positive cases (for Χ² test)")
+ 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.StringVar(&cmd.chi2CaseControlColumn, "chi2-case-control-column", "", "name of case/control column in case-control files for Χ² test (value must be 0 for control, 1 for case)")
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)
if err == flag.ErrHelp {
}()
}
- if cmd.chi2CasesFile == "" && cmd.chi2PValue != 1 {
- log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-cases-file= value is empty", cmd.chi2PValue)
+ 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
}
+ cmd.debugTag = tagID(*debugTag)
+
if !*runlocal {
runner := arvadosContainerRunner{
Name: "lightning slice-numpy",
KeepCache: 2,
APIAccess: true,
}
- err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CasesFile)
+ err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CaseControlFile)
if err != nil {
return 1
}
"-merge-output=" + fmt.Sprintf("%v", *mergeOutput),
"-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
"-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
+ "-single-onehot=" + fmt.Sprintf("%v", *onehotSingle),
"-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
- "-chi2-cases-file=" + cmd.chi2CasesFile,
+ "-chi2-case-control-file=" + cmd.chi2CaseControlFile,
+ "-chi2-case-control-column=" + cmd.chi2CaseControlColumn,
"-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
+ "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
+ "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
}
runner.Args = append(runner.Args, cmd.filter.Args()...)
var output string
return 0
}
- infiles, err := allGobFiles(*inputDir)
+ infiles, err := allFiles(*inputDir, matchGobFile)
if err != nil {
return 1
}
}
cmd.cgnames = nil
- taglen := -1
- DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
+ var tagset [][]byte
+ err = DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
if len(ent.TagSet) > 0 {
- taglen = len(ent.TagSet[0])
+ tagset = ent.TagSet
}
for _, cseq := range ent.CompactSequences {
if cseq.Name == *ref || *ref == "" {
err = fmt.Errorf("%s: reference sequence not found", infiles[0])
return 1
}
- if taglen < 0 {
+ if len(tagset) == 0 {
err = fmt.Errorf("tagset not found")
return 1
}
+
+ taglib := &tagLibrary{}
+ err = taglib.setTags(tagset)
+ if err != nil {
+ return 1
+ }
+ taglen := taglib.TagLen()
+
if len(cmd.cgnames) == 0 {
err = fmt.Errorf("no genomes found matching regexp %q", cmd.filter.MatchGenome)
return 1
}
sort.Strings(cmd.cgnames)
-
- cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
-
- if cmd.chi2CasesFile != "" {
- f, err2 := open(cmd.chi2CasesFile)
- if err2 != nil {
- err = err2
- return 1
- }
- buf, err2 := io.ReadAll(f)
- f.Close()
- if err2 != nil {
- err = err2
- return 1
- }
- cmd.chi2Cases = make([]bool, len(cmd.cgnames))
- ncases := 0
- for _, pattern := range bytes.Split(buf, []byte{'\n'}) {
- if len(pattern) == 0 {
- continue
- }
- pattern := string(pattern)
- idx := -1
- for i, name := range cmd.cgnames {
- if !strings.Contains(name, pattern) {
- continue
- }
- cmd.chi2Cases[i] = true
- ncases++
- if idx >= 0 {
- log.Warnf("pattern %q in cases file matches multiple genome IDs: %q, %q", pattern, cmd.cgnames[idx], name)
- } else {
- idx = i
- }
- }
- if idx < 0 {
- log.Warnf("pattern %q in cases file does not match any genome IDs", pattern)
- continue
- }
- }
- log.Printf("%d cases, %d controls", ncases, len(cmd.cgnames)-ncases)
+ err = cmd.useCaseControlFiles()
+ if err != nil {
+ return 1
}
+ cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
{
- labelsFilename := *outputDir + "/labels.csv"
+ labelsFilename := *outputDir + "/samples.csv"
log.Infof("writing labels to %s", labelsFilename)
var f *os.File
f, err = os.Create(labelsFilename)
}
defer f.Close()
for i, name := range cmd.cgnames {
- _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
+ cc := 0
+ if cmd.chi2Cases != nil && cmd.chi2Cases[i] {
+ cc = 1
+ }
+ _, 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
for seqname, cseq := range refseq {
pos := 0
for _, libref := range cseq {
+ if cmd.filter.MaxTag >= 0 && libref.Tag > tagID(cmd.filter.MaxTag) {
+ continue
+ }
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
}
+ foundthistag := false
+ taglib.FindAll(tiledata[:len(tiledata)-1], func(tagid tagID, offset, _ int) {
+ if !foundthistag && tagid == libref.Tag {
+ foundthistag = true
+ return
+ }
+ if dupref, ok := reftile[tagid]; ok {
+ log.Printf("dropping reference tile %+v from %s @ %d, tag not unique, also found inside %+v from %s @ %d", tileLibRef{Tag: tagid, Variant: dupref.variant}, dupref.seqname, dupref.pos, libref, seqname, pos+offset+1)
+ delete(reftile, tagid)
+ } else {
+ log.Printf("found tag %d at offset %d inside tile variant %+v on %s @ %d", tagid, offset, libref, seqname, pos+offset+1)
+ }
+ isdup[tagid] = true
+ })
if isdup[libref.Tag] {
log.Printf("dropping reference tile %+v from %s @ %d, tag not unique", libref, seqname, pos)
} else if reftile[libref.Tag] != nil {
if *mergeOutput || *hgvsSingle {
toMerge = make([][]int16, len(infiles))
}
+ var onehotIndirect [][2][]uint32 // [chunkIndex][axis][index]
+ var onehotChunkSize []uint32
+ var onehotXrefs [][]onehotXref
+ if *onehotSingle {
+ onehotIndirect = make([][2][]uint32, len(infiles))
+ onehotChunkSize = make([]uint32, len(infiles))
+ onehotXrefs = make([][]onehotXref, len(infiles))
+ }
+ chunkStartTag := make([]tagID, len(infiles))
throttleMem := throttle{Max: cmd.threads} // TODO: estimate using mem and data size
throttleNumpyMem := throttle{Max: cmd.threads/2 + 1}
log.Info("generating annotations and numpy matrix for each slice")
+ var errSkip = errors.New("skip infile")
var done int64
for infileIdx, infile := range infiles {
infileIdx, infile := infileIdx, infile
// masked-out tiles.
continue
}
+ if tv.Tag == cmd.debugTag {
+ log.Printf("infile %d %s tag %d variant %d hash %x", infileIdx, infile, tv.Tag, tv.Variant, tv.Blake2b[:3])
+ }
variants := seq[tv.Tag]
if len(variants) == 0 {
variants = make([]TileVariant, 100)
seq[tv.Tag] = variants
}
for _, cg := range ent.CompactGenomes {
+ if cmd.filter.MaxTag >= 0 && cg.StartTag > tagID(cmd.filter.MaxTag) {
+ return errSkip
+ }
if !matchGenome.MatchString(cg.Name) {
continue
}
}
return nil
})
- if err != nil {
+ if err == errSkip {
+ return nil
+ } else if err != nil {
return err
}
tagstart := cgs[cmd.cgnames[0]].StartTag
tagend := cgs[cmd.cgnames[0]].EndTag
+ chunkStartTag[infileIdx] = tagstart
// TODO: filters
throttleCPU := throttle{Max: runtime.GOMAXPROCS(0)}
for tag, variants := range seq {
tag, variants := tag, variants
- throttleCPU.Acquire()
- go func() {
- defer throttleCPU.Release()
+ throttleCPU.Go(func() error {
count := make(map[[blake2b.Size256]byte]int, len(variants))
rt := reftile[tag]
count[blake2b.Sum256(rt.tiledata)] = 0
}
- for _, cg := range cgs {
+ for cgname, cg := range cgs {
idx := int(tag-tagstart) * 2
for allele := 0; allele < 2; allele++ {
v := cg.Variants[idx+allele]
if v > 0 && len(variants[v].Sequence) > 0 {
count[variants[v].Blake2b]++
}
+ if v > 0 && tag == cmd.debugTag {
+ log.Printf("tag %d cg %s allele %d tv %d hash %x count is now %d", tag, cgname, allele, v, variants[v].Blake2b[:3], count[variants[v].Blake2b])
+ }
}
}
// hash[i] will be the hash of
for i, h := range hash {
rank[h] = tileVariantID(i + 1)
}
+ if tag == cmd.debugTag {
+ for h, r := range rank {
+ log.Printf("tag %d rank(%x) = %v", tag, h[:3], r)
+ }
+ }
// remap[v] will be the new
// variant number for original
// variant number v.
for i, tv := range variants {
remap[i] = rank[tv.Blake2b]
}
+ if tag == cmd.debugTag {
+ for in, out := range remap {
+ if out > 0 {
+ log.Printf("tag %d remap %d => %d", tag, in, out)
+ }
+ }
+ }
variantRemap[tag-tagstart] = remap
if rt != nil {
- rt.variant = rank[blake2b.Sum256(rt.tiledata)]
+ refrank := rank[blake2b.Sum256(rt.tiledata)]
+ if tag == cmd.debugTag {
+ log.Printf("tag %d reftile variant %d => %d", tag, rt.variant, refrank)
+ }
+ rt.variant = refrank
}
- }()
+ return nil
+ })
}
throttleCPU.Wait()
var onehotChunk [][]int8
- var onehotXrefs []onehotXref
+ var onehotXref []onehotXref
annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
log.Infof("%04d: writing %s", infileIdx, annotationsFilename)
annow := bufio.NewWriterSize(annof, 1<<20)
outcol := 0
for tag := tagstart; tag < tagend; tag++ {
- rt, ok := reftile[tag]
- if !ok {
- if mask == nil {
- outcol++
- }
- // Excluded by specified
- // regions, or reference does
- // not use any variant of this
- // tile. (TODO: log this?
- // mention it in annotations?)
+ rt := reftile[tag]
+ if rt == nil && mask != nil {
+ // Excluded by specified regions
continue
}
+ if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
+ break
+ }
remap := variantRemap[tag-tagstart]
maxv := tileVariantID(0)
for _, v := range remap {
maxv = v
}
}
- if *onehotChunked {
+ if *onehotChunked || *onehotSingle {
onehot, xrefs := cmd.tv2homhet(cgs, maxv, remap, tag, tagstart)
+ if tag == cmd.debugTag {
+ log.WithFields(logrus.Fields{
+ "onehot": onehot,
+ "xrefs": xrefs,
+ }).Info("tv2homhet()")
+ }
onehotChunk = append(onehotChunk, onehot...)
- onehotXrefs = append(onehotXrefs, xrefs...)
+ onehotXref = append(onehotXref, xrefs...)
+ }
+ if rt == nil {
+ // Reference does not use any
+ // variant of this tile
+ outcol++
+ continue
}
fmt.Fprintf(annow, "%d,%d,%d,=,%s,%d,,,\n", tag, outcol, rt.variant, rt.seqname, rt.pos)
variants := seq[tag]
cols := len(onehotChunk)
log.Infof("%04d: preparing onehot numpy (rows=%d, cols=%d, mem=%d)", infileIdx, rows, cols, rows*cols)
throttleNumpyMem.Acquire()
- out := make([]int8, rows*cols)
- for row := range cmd.cgnames {
- out := out[row*cols:]
- for colnum, values := range onehotChunk {
- out[colnum] = values[row]
- }
- }
- seq = nil
- cgs = nil
- debug.FreeOSMemory()
- throttleNumpyMem.Release()
-
+ out := onehotcols2int8(onehotChunk)
fnm := fmt.Sprintf("%s/onehot.%04d.npy", *outputDir, infileIdx)
err = writeNumpyInt8(fnm, out, rows, cols)
if err != nil {
return err
}
-
fnm = fmt.Sprintf("%s/onehot-columns.%04d.npy", *outputDir, infileIdx)
- xcols := len(onehotXrefs)
- xdata := make([]int32, 4*xcols)
- for i, xref := range onehotXrefs {
- xdata[i] = int32(xref.tag)
- xdata[xcols+i] = int32(xref.variant)
- if xref.het {
- xdata[xcols*2+i] = 1
- }
- xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
- }
- err = writeNumpyInt32(fnm, xdata, 4, xcols)
+ err = writeNumpyInt32(fnm, onehotXref2int32(onehotXref), 4, len(onehotXref))
if err != nil {
return err
}
+ debug.FreeOSMemory()
+ throttleNumpyMem.Release()
+ }
+ if *onehotSingle {
+ onehotIndirect[infileIdx] = onehotChunk2Indirect(onehotChunk)
+ onehotChunkSize[infileIdx] = uint32(len(onehotChunk))
+ onehotXrefs[infileIdx] = onehotXref
+ n := len(onehotIndirect[infileIdx][0])
+ log.Infof("%04d: keeping onehot coordinates in memory (n=%d, mem=%d)", infileIdx, n, n*8*2)
}
- if !*onehotChunked || *mergeOutput || *hgvsSingle {
- log.Infof("%04d: preparing numpy", infileIdx)
+ if !(*onehotSingle || *onehotChunked) || *mergeOutput || *hgvsSingle {
+ log.Infof("%04d: preparing numpy (rows=%d, cols=%d)", infileIdx, len(cmd.cgnames), 2*outcol)
throttleNumpyMem.Acquire()
rows := len(cmd.cgnames)
cols := 2 * outcol
out := make([]int16, rows*cols)
for row, name := range cmd.cgnames {
- out := out[row*cols:]
- outcol := 0
+ outidx := row * cols
for col, v := range cgs[name].Variants {
tag := tagstart + tagID(col/2)
+ if cmd.filter.MaxTag >= 0 && tag > tagID(cmd.filter.MaxTag) {
+ break
+ }
if mask != nil && reftile[tag] == nil {
continue
}
- if variants, ok := seq[tag]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
- out[outcol] = int16(variantRemap[tag-tagstart][v])
+ if v == 0 {
+ out[outidx] = 0 // tag not found / spanning tile
+ } else if variants, ok := seq[tag]; ok && int(v) < len(variants) && len(variants[v].Sequence) > 0 {
+ out[outidx] = int16(variantRemap[tag-tagstart][v])
} else {
- out[outcol] = -1
+ out[outidx] = -1 // low quality tile variant
+ }
+ if tag == cmd.debugTag {
+ log.Printf("tag %d row %d col %d outidx %d v %d out %d", tag, row, col, outidx, v, out[outidx])
}
- outcol++
+ outidx++
}
}
seq = nil
log.Infof("%04d: matrix fragment %d rows x %d cols", infileIdx, rows, cols)
toMerge[infileIdx] = out
}
- if !*mergeOutput && !*onehotChunked {
+ if !*mergeOutput && !*onehotChunked && !*onehotSingle {
fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
err = writeNumpyInt16(fnm, out, rows, cols)
if err != nil {
}
}
}
+ if *onehotSingle {
+ nzCount := 0
+ for _, part := range onehotIndirect {
+ nzCount += len(part[0])
+ }
+ onehot := make([]uint32, nzCount*2) // [r,r,r,...,c,c,c,...]
+ var xrefs []onehotXref
+ chunkOffset := uint32(0)
+ outcol := 0
+ for i, part := range onehotIndirect {
+ for i := range part[1] {
+ part[1][i] += chunkOffset
+ }
+ copy(onehot[outcol:], part[0])
+ copy(onehot[outcol+nzCount:], part[1])
+ xrefs = append(xrefs, onehotXrefs[i]...)
+
+ outcol += len(part[0])
+ chunkOffset += onehotChunkSize[i]
+
+ part[0] = nil
+ part[1] = nil
+ onehotXrefs[i] = nil
+ debug.FreeOSMemory()
+ }
+ fnm := fmt.Sprintf("%s/onehot.npy", *outputDir)
+ err = writeNumpyUint32(fnm, onehot, 2, nzCount)
+ if err != nil {
+ return 1
+ }
+ fnm = fmt.Sprintf("%s/onehot-columns.npy", *outputDir)
+ err = writeNumpyInt32(fnm, onehotXref2int32(xrefs), 4, len(xrefs))
+ if err != nil {
+ return 1
+ }
+ }
+ if !*mergeOutput && !*onehotChunked && !*onehotSingle {
+ tagoffsetFilename := *outputDir + "/chunk-tag-offset.csv"
+ log.Infof("writing tag offsets to %s", tagoffsetFilename)
+ var f *os.File
+ f, err = os.Create(tagoffsetFilename)
+ if err != nil {
+ return 1
+ }
+ 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
+ }
+ }
+ err = f.Close()
+ if err != nil {
+ err = fmt.Errorf("close %s: %w", tagoffsetFilename, err)
+ return 1
+ }
+ }
return 0
}
+// Read case/control files, remove non-case/control entries from
+// cmd.cgnames, and build cmd.chi2Cases.
+func (cmd *sliceNumpy) useCaseControlFiles() error {
+ if cmd.chi2CaseControlFile == "" {
+ return nil
+ }
+ infiles, err := allFiles(cmd.chi2CaseControlFile, nil)
+ if err != nil {
+ return err
+ }
+ // index in cmd.cgnames => case(true) / control(false)
+ cc := map[int]bool{}
+ for _, infile := range infiles {
+ f, err := open(infile)
+ if err != nil {
+ return err
+ }
+ buf, err := io.ReadAll(f)
+ f.Close()
+ if err != nil {
+ return err
+ }
+ ccCol := -1
+ for _, tsv := range bytes.Split(buf, []byte{'\n'}) {
+ if len(tsv) == 0 {
+ continue
+ }
+ split := strings.Split(string(tsv), "\t")
+ if ccCol < 0 {
+ // header row
+ for col, name := range split {
+ if name == cmd.chi2CaseControlColumn {
+ ccCol = col
+ break
+ }
+ }
+ if ccCol < 0 {
+ return fmt.Errorf("%s: no column named %q in header row %q", infile, cmd.chi2CaseControlColumn, tsv)
+ }
+ continue
+ }
+ if len(split) <= ccCol {
+ continue
+ }
+ pattern := split[0]
+ found := -1
+ for i, name := range cmd.cgnames {
+ if strings.Contains(name, pattern) {
+ if found >= 0 {
+ log.Warnf("pattern %q in %s matches multiple genome IDs (%qs, %q)", pattern, infile, cmd.cgnames[found], name)
+ }
+ found = i
+ }
+ }
+ if found < 0 {
+ log.Warnf("pattern %q in %s does not match any genome IDs", pattern, infile)
+ continue
+ }
+ if split[ccCol] == "0" {
+ cc[found] = false
+ }
+ if split[ccCol] == "1" {
+ cc[found] = true
+ }
+ }
+ }
+ allnames := cmd.cgnames
+ cmd.cgnames = nil
+ cmd.chi2Cases = nil
+ ncases := 0
+ for i, name := range allnames {
+ if cc, ok := cc[i]; ok {
+ cmd.cgnames = append(cmd.cgnames, name)
+ cmd.chi2Cases = append(cmd.chi2Cases, cc)
+ if cc {
+ ncases++
+ }
+ }
+ }
+ log.Printf("%d cases, %d controls, %d neither (dropped)", ncases, len(cmd.cgnames)-ncases, len(allnames)-len(cmd.cgnames))
+ return nil
+}
+
func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
if cmd.chi2PValue >= 1 {
return true
cases = append(cases, c)
}
return len(cases) >= cmd.minCoverage &&
- (pvalue(cases, col0) <= cmd.chi2PValue || pvalue(cases, col1) <= cmd.chi2PValue)
+ (pvalue(col0, cases) <= cmd.chi2PValue || pvalue(col1, cases) <= cmd.chi2PValue)
+}
+
+func writeNumpyUint32(fnm string, out []uint32, rows, cols int) error {
+ output, err := os.Create(fnm)
+ if err != nil {
+ return err
+ }
+ defer output.Close()
+ bufw := bufio.NewWriterSize(output, 1<<26)
+ npw, err := gonpy.NewWriter(nopCloser{bufw})
+ if err != nil {
+ return err
+ }
+ log.WithFields(log.Fields{
+ "filename": fnm,
+ "rows": rows,
+ "cols": cols,
+ "bytes": rows * cols * 4,
+ }).Infof("writing numpy: %s", fnm)
+ npw.Shape = []int{rows, cols}
+ npw.WriteUint32(out)
+ err = bufw.Flush()
+ if err != nil {
+ return err
+ }
+ return output.Close()
}
func writeNumpyInt32(fnm string, out []int32, rows, cols int) error {
type onehotXref struct {
tag tagID
variant tileVariantID
- het bool
+ hom bool
pvalue float64
}
-// Build onehot matrix (m[variant*2+isHet][genome] == 0 or 1) for all
+const onehotXrefSize = unsafe.Sizeof(onehotXref{})
+
+// Build onehot matrix (m[tileVariantIndex][genome] == 0 or 1) for all
// variants of a single tile/tag#.
//
// Return nil if no tile variant passes Χ² filter.
func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantID, remap []tileVariantID, tag, chunkstarttag tagID) ([][]int8, []onehotXref) {
- if maxv < 2 {
- // everyone has the most common variant
+ if tag == cmd.debugTag {
+ tv := make([]tileVariantID, len(cmd.cgnames)*2)
+ for i, name := range cmd.cgnames {
+ copy(tv[i*2:(i+1)*2], cgs[name].Variants[(tag-chunkstarttag)*2:])
+ }
+ log.WithFields(logrus.Fields{
+ "cgs[i].Variants[tag*2+j]": tv,
+ "maxv": maxv,
+ "remap": remap,
+ "tag": tag,
+ "chunkstarttag": chunkstarttag,
+ }).Info("tv2homhet()")
+ }
+ if maxv < 1 || (maxv < 2 && !cmd.includeVariant1) {
+ // everyone has the most common variant (of the variants we don't drop)
return nil, nil
}
tagoffset := tag - chunkstarttag
obs[i] = make([]bool, len(cmd.cgnames))
}
for cgid, name := range cmd.cgnames {
- cgvars := cgs[name].Variants
- for v := tileVariantID(2); v <= maxv; v++ {
- if remap[cgvars[tagoffset*2]] == v && remap[cgvars[tagoffset*2+1]] == v {
+ cgvars := cgs[name].Variants[tagoffset*2:]
+ tv0, tv1 := remap[cgvars[0]], remap[cgvars[1]]
+ for v := tileVariantID(1); v <= maxv; v++ {
+ if tv0 == v && tv1 == v {
obs[v*2][cgid] = true
- } else if remap[cgvars[tagoffset*2]] == v || remap[cgvars[tagoffset*2+1]] == v {
+ } else if tv0 == v || tv1 == v {
obs[v*2+1][cgid] = true
}
}
}
var onehot [][]int8
var xref []onehotXref
- for homcol := 4; homcol < len(obs); homcol += 2 {
- p := [2]float64{
- pvalue(cmd.chi2Cases, obs[homcol]),
- pvalue(cmd.chi2Cases, obs[homcol+1]),
- }
- if cmd.chi2PValue < 1 && !(p[0] < cmd.chi2PValue || p[1] < cmd.chi2PValue) {
+ for col := 2; col < len(obs); col++ {
+ // col 0,1 correspond to tile variant 0, i.e.,
+ // no-call; col 2,3 correspond to the most common
+ // variant; so we (normally) start at col 4.
+ if col < 4 && !cmd.includeVariant1 {
continue
}
- for het := 0; het < 2; het++ {
- onehot = append(onehot, bool2int8(obs[homcol+het]))
- xref = append(xref, onehotXref{
- tag: tag,
- variant: tileVariantID(homcol / 2),
- het: het == 1,
- pvalue: p[het],
- })
+ p := pvalue(obs[col], cmd.chi2Cases)
+ if cmd.chi2PValue < 1 && !(p < cmd.chi2PValue) {
+ continue
}
+ onehot = append(onehot, bool2int8(obs[col]))
+ xref = append(xref, onehotXref{
+ tag: tag,
+ variant: tileVariantID(col >> 1),
+ hom: col&1 == 0,
+ pvalue: p,
+ })
}
return onehot, xref
}
}
return out
}
+
+// convert a []onehotXref with length N to a numpy-style []int32
+// matrix with N columns, one row per field of onehotXref struct.
+//
+// Hom/het row contains hom=0, het=1.
+//
+// P-value row contains 1000000x actual p-value.
+func onehotXref2int32(xrefs []onehotXref) []int32 {
+ xcols := len(xrefs)
+ xdata := make([]int32, 4*xcols)
+ for i, xref := range xrefs {
+ xdata[i] = int32(xref.tag)
+ xdata[xcols+i] = int32(xref.variant)
+ if xref.hom {
+ xdata[xcols*2+i] = 1
+ }
+ xdata[xcols*3+i] = int32(xref.pvalue * 1000000)
+ }
+ return xdata
+}
+
+// transpose onehot data from in[col][row] to numpy-style
+// out[row*cols+col].
+func onehotcols2int8(in [][]int8) []int8 {
+ if len(in) == 0 {
+ return nil
+ }
+ cols := len(in)
+ rows := len(in[0])
+ out := make([]int8, rows*cols)
+ for row := 0; row < rows; row++ {
+ outrow := out[row*cols:]
+ for col, incol := range in {
+ outrow[col] = incol[row]
+ }
+ }
+ return out
+}
+
+// Return [2][]uint32{rowIndices, colIndices} indicating which
+// elements of matrixT[c][r] have non-zero values.
+func onehotChunk2Indirect(matrixT [][]int8) [2][]uint32 {
+ var nz [2][]uint32
+ for c, col := range matrixT {
+ for r, val := range col {
+ if val != 0 {
+ nz[0] = append(nz[0], uint32(r))
+ nz[1] = append(nz[1], uint32(c))
+ }
+ }
+ }
+ return nz
+}
projects / lightning.git / blobdiff