1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
21 "git.arvados.org/arvados.git/sdk/go/arvados"
22 "github.com/arvados/lightning/hgvs"
23 "github.com/kshedden/gonpy"
24 "github.com/sirupsen/logrus"
25 log "github.com/sirupsen/logrus"
28 type sliceNumpy struct {
32 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
36 fmt.Fprintf(stderr, "%s\n", err)
39 flags := flag.NewFlagSet("", flag.ContinueOnError)
40 flags.SetOutput(stderr)
41 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
42 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
43 projectUUID := flags.String("project", "", "project `UUID` for output data")
44 priority := flags.Int("priority", 500, "container request priority")
45 inputDir := flags.String("input-dir", "./in", "input `directory`")
46 outputDir := flags.String("output-dir", "./out", "output `directory`")
47 ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
48 regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
49 expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
50 cmd.filter.Flags(flags)
51 err = flags.Parse(args)
52 if err == flag.ErrHelp {
55 } else if err != nil {
61 log.Println(http.ListenAndServe(*pprof, nil))
66 runner := arvadosContainerRunner{
67 Name: "lightning slice-numpy",
68 Client: arvados.NewClientFromEnv(),
69 ProjectUUID: *projectUUID,
76 err = runner.TranslatePaths(inputDir, regionsFilename)
80 runner.Args = []string{"slice-numpy", "-local=true",
82 "-input-dir", *inputDir,
83 "-output-dir", "/mnt/output",
84 "-regions", *regionsFilename,
85 "-expand-regions", fmt.Sprintf("%d", *expandRegions),
87 runner.Args = append(runner.Args, cmd.filter.Args()...)
89 output, err = runner.Run()
93 fmt.Fprintln(stdout, output)
97 infiles, err := allGobFiles(*inputDir)
101 if len(infiles) == 0 {
102 err = fmt.Errorf("no input files found in %s", *inputDir)
105 sort.Strings(infiles)
108 var refseq map[string][]tileLibRef
109 in0, err := open(infiles[0])
114 DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
115 if len(ent.TagSet) > 0 {
116 taglen = len(ent.TagSet[0])
118 for _, cseq := range ent.CompactSequences {
119 if cseq.Name == *ref || *ref == "" {
120 refseq = cseq.TileSequences
123 for _, cg := range ent.CompactGenomes {
124 cgnames = append(cgnames, cg.Name)
133 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
137 err = fmt.Errorf("tagset not found")
140 sort.Strings(cgnames)
143 labelsFilename := *outputDir + "/labels.csv"
144 log.Infof("writing labels to %s", labelsFilename)
146 f, err = os.Create(labelsFilename)
151 for i, name := range cgnames {
152 _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
154 err = fmt.Errorf("write %s: %w", labelsFilename, err)
160 err = fmt.Errorf("close %s: %w", labelsFilename, err)
165 log.Info("building list of reference tiles to load") // TODO: more efficient if we had saved all ref tiles in slice0
166 type reftileinfo struct {
167 seqname string // chr1
168 pos int // distance from start of chr1 to start of tile
169 tiledata []byte // acgtggcaa...
171 reftile := map[tagID]*reftileinfo{}
172 for seqname, cseq := range refseq {
173 for _, libref := range cseq {
174 reftile[libref.Tag] = &reftileinfo{seqname: seqname}
177 log.Info("loading reference tiles from all slices")
178 throttle := throttle{Max: runtime.GOMAXPROCS(0)}
179 for _, infile := range infiles {
181 throttle.Go(func() error {
182 defer log.Infof("%s: done", infile)
183 f, err := open(infile)
188 return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
189 for _, tv := range ent.TileVariants {
190 if dst, ok := reftile[tv.Tag]; ok {
191 dst.tiledata = tv.Sequence
200 log.Info("reconstructing reference sequences")
201 for seqname, cseq := range refseq {
202 seqname, cseq := seqname, cseq
203 throttle.Go(func() error {
204 defer log.Printf("... %s done", seqname)
206 for _, libref := range cseq {
207 rt := reftile[libref.Tag]
209 pos += len(rt.tiledata) - taglen
216 log.Info("TODO: determining which tiles intersect given regions")
218 log.Info("generating annotations and numpy matrix for each slice")
220 for infileIdx, infile := range infiles {
221 infileIdx, infile := infileIdx, infile
222 throttle.Go(func() error {
223 seq := map[tagID][][]byte{}
224 cgs := make(map[string]CompactGenome, len(cgnames))
225 f, err := open(infile)
230 log.Infof("reading %s", infile)
231 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
232 for _, tv := range ent.TileVariants {
233 variants := seq[tv.Tag]
234 for len(variants) <= int(tv.Variant) {
235 variants = append(variants, nil)
237 variants[int(tv.Variant)] = tv.Sequence
238 seq[tv.Tag] = variants
240 for _, cg := range ent.CompactGenomes {
248 tagstart := cgs[cgnames[0]].StartTag
249 tagend := cgs[cgnames[0]].EndTag
252 // TODO: tidy/renumber
254 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
255 log.Infof("writing %s", annotationsFilename)
256 annof, err := os.Create(annotationsFilename)
260 annow := bufio.NewWriterSize(annof, 1<<20)
261 for tag, variants := range seq {
262 rt, ok := reftile[tag]
264 // Reference does not use any
265 // variant of this tile.
266 // TODO: log this? mention it
270 outcol := tag - tagID(tagstart)
271 reftilestr := strings.ToUpper(string(rt.tiledata))
272 for v, seq := range variants {
273 if len(seq) == 0 || !bytes.HasSuffix(rt.tiledata, seq[len(seq)-taglen:]) {
276 if lendiff := len(rt.tiledata) - len(seq); lendiff < -1000 || lendiff > 1000 {
279 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(seq)), 0)
280 for _, diff := range diffs {
281 diff.Position += rt.pos
282 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, v, rt.seqname, diff.String())
295 log.Infof("%s: preparing numpy", infile)
297 cols := 2 * int(tagend-tagstart)
298 out := make([]int16, rows*cols)
299 for row, name := range cgnames {
300 out := out[row*cols:]
301 for col, v := range cgs[name].Variants {
302 if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v]) > 0 {
310 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
311 output, err := os.Create(fnm)
316 bufw := bufio.NewWriterSize(output, 1<<26)
317 npw, err := gonpy.NewWriter(nopCloser{bufw})
321 log.WithFields(logrus.Fields{
325 }).Info("writing numpy")
326 npw.Shape = []int{rows, cols}
336 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
340 if err = throttle.Wait(); err != nil {
346 func (*sliceNumpy) writeLibRefs(fnm string, tilelib *tileLibrary, librefs []tileLibRef) error {
347 f, err := os.OpenFile(fnm, os.O_CREATE|os.O_WRONLY, 0666)
352 for i, libref := range librefs {
353 _, err = fmt.Fprintf(f, "%d,%d,%d\n", i, libref.Tag, libref.Variant)