import (
"bufio"
+ "bytes"
"flag"
"fmt"
"io"
"strings"
"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"
priority := flags.Int("priority", 500, "container request priority")
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)")
regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
cmd.filter.Flags(flags)
Name: "lightning slice-numpy",
Client: arvados.NewClientFromEnv(),
ProjectUUID: *projectUUID,
- RAM: 150000000000,
+ RAM: 250000000000,
VCPUs: 32,
Priority: *priority,
KeepCache: 1,
sort.Strings(infiles)
var cgnames []string
- refseqs := map[string]map[string][]tileLibRef{}
+ var refseq map[string][]tileLibRef
in0, err := open(infiles[0])
if err != nil {
return 1
}
+ taglen := -1
DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
+ if len(ent.TagSet) > 0 {
+ taglen = len(ent.TagSet[0])
+ }
for _, cseq := range ent.CompactSequences {
- refseqs[cseq.Name] = cseq.TileSequences
+ if cseq.Name == *ref || *ref == "" {
+ refseq = cseq.TileSequences
+ }
}
for _, cg := range ent.CompactGenomes {
cgnames = append(cgnames, cg.Name)
return 1
}
in0.Close()
+ if refseq == nil {
+ err = fmt.Errorf("%s: reference sequence not found", infiles[0])
+ return 1
+ }
+ if taglen < 0 {
+ err = fmt.Errorf("tagset not found")
+ return 1
+ }
sort.Strings(cgnames)
{
}
log.Info("building list of reference tiles to load") // TODO: more efficient if we had saved all ref tiles in slice0
- reftiledata := map[tileLibRef]*[]byte{}
- for _, ref := range refseqs {
- for _, cseq := range ref {
- for _, libref := range cseq {
- reftiledata[libref] = new([]byte)
- }
+ type reftileinfo struct {
+ seqname string // chr1
+ pos int // distance from start of chr1 to start of tile
+ tiledata []byte // acgtggcaa...
+ }
+ reftile := map[tagID]*reftileinfo{}
+ for seqname, cseq := range refseq {
+ for _, libref := range cseq {
+ reftile[libref.Tag] = &reftileinfo{seqname: seqname}
}
}
log.Info("loading reference tiles from all slices")
defer f.Close()
return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
for _, tv := range ent.TileVariants {
- libref := tileLibRef{tv.Tag, tv.Variant}
- if dst, ok := reftiledata[libref]; ok {
- *dst = tv.Sequence
+ if dst, ok := reftile[tv.Tag]; ok {
+ dst.tiledata = tv.Sequence
}
}
return nil
}
throttle.Wait()
+ log.Info("reconstructing reference sequences")
+ for seqname, cseq := range refseq {
+ seqname, cseq := seqname, cseq
+ throttle.Go(func() error {
+ defer log.Printf("... %s done", seqname)
+ pos := 0
+ for _, libref := range cseq {
+ rt := reftile[libref.Tag]
+ rt.pos = pos
+ pos += len(rt.tiledata) - taglen
+ }
+ return nil
+ })
+ }
+ throttle.Wait()
+
log.Info("TODO: determining which tiles intersect given regions")
log.Info("generating annotations and numpy matrix for each slice")
infileIdx, infile := infileIdx, infile
throttle.Go(func() error {
defer log.Infof("%s: done", infile)
- seq := map[tileLibRef][]byte{}
+ seq := map[tagID][][]byte{}
cgs := make(map[string]CompactGenome, len(cgnames))
f, err := open(infile)
if err != nil {
defer f.Close()
err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
for _, tv := range ent.TileVariants {
- seq[tileLibRef{tv.Tag, tv.Variant}] = tv.Sequence
+ variants := seq[tv.Tag]
+ for len(variants) <= int(tv.Variant) {
+ variants = append(variants, nil)
+ }
+ variants[int(tv.Variant)] = tv.Sequence
+ seq[tv.Tag] = variants
}
for _, cg := range ent.CompactGenomes {
cgs[cg.Name] = cg
if err != nil {
return err
}
+ tagstart := cgs[cgnames[0]].StartTag
+ tagend := cgs[cgnames[0]].EndTag
log.Infof("TODO: %s: filtering", infile)
log.Infof("TODO: %s: tidying", infile)
annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
log.Infof("%s: writing annotations to %s", infile, annotationsFilename)
- annow, err := os.Create(annotationsFilename)
+ annof, err := os.Create(annotationsFilename)
if err != nil {
return err
}
- // for libref, seq := range seq {
- // // TODO: diff from ref.
- // }
- err = annow.Close()
+ annow := bufio.NewWriterSize(annof, 1<<20)
+ for tag, variants := range seq {
+ rt, ok := reftile[tag]
+ if !ok {
+ // Reference does not use any
+ // variant of this tile.
+ // TODO: log this? mention it
+ // in annotations?
+ continue
+ }
+ outcol := tag - tagID(tagstart)
+ reftilestr := strings.ToUpper(string(rt.tiledata))
+ for v, seq := range variants {
+ if len(seq) == 0 || !bytes.HasSuffix(rt.tiledata, seq[len(seq)-taglen:]) {
+ continue
+ }
+ if lendiff := len(rt.tiledata) - len(seq); lendiff < -1000 || lendiff > 1000 {
+ continue
+ }
+ diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(seq)), 0)
+ for _, diff := range diffs {
+ diff.Position += rt.pos
+ fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, v, rt.seqname, diff.String())
+ }
+ }
+ }
+ err = annow.Flush()
+ if err != nil {
+ return err
+ }
+ err = annof.Close()
if err != nil {
return err
}
log.Infof("%s: preparing numpy", infile)
- tagstart := cgs[cgnames[0]].StartTag
- tagend := cgs[cgnames[0]].EndTag
rows := len(cgnames)
cols := 2 * int(tagend-tagstart)
out := make([]int16, rows*cols)
for row, name := range cgnames {
out := out[row*cols:]
for col, v := range cgs[name].Variants {
- if v == 0 {
- // out[col] = 0
- } else if _, ok := seq[tileLibRef{tagstart + tagID(col/2), v}]; ok {
+ if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v]) > 0 {
out[col] = int16(v)
} else {
out[col] = -1
projects / lightning.git / commitdiff