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 variant tileVariantID
168 seqname string // chr1
169 pos int // distance from start of chr1 to start of tile
170 tiledata []byte // acgtggcaa...
172 reftile := map[tagID]*reftileinfo{}
173 for seqname, cseq := range refseq {
174 for _, libref := range cseq {
175 reftile[libref.Tag] = &reftileinfo{seqname: seqname, variant: libref.Variant}
178 log.Info("loading reference tiles from all slices")
179 throttle := throttle{Max: runtime.GOMAXPROCS(0)}
180 for _, infile := range infiles {
182 throttle.Go(func() error {
183 defer log.Infof("%s: done", infile)
184 f, err := open(infile)
189 return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
190 for _, tv := range ent.TileVariants {
191 if dst, ok := reftile[tv.Tag]; ok && dst.variant == tv.Variant {
192 dst.tiledata = tv.Sequence
201 log.Info("reconstructing reference sequences")
202 for seqname, cseq := range refseq {
203 seqname, cseq := seqname, cseq
204 throttle.Go(func() error {
205 defer log.Printf("... %s done", seqname)
207 for _, libref := range cseq {
208 rt := reftile[libref.Tag]
210 pos += len(rt.tiledata) - taglen
217 log.Info("TODO: determining which tiles intersect given regions")
219 log.Info("generating annotations and numpy matrix for each slice")
221 for infileIdx, infile := range infiles {
222 infileIdx, infile := infileIdx, infile
223 throttle.Go(func() error {
224 seq := map[tagID][][]byte{}
225 cgs := make(map[string]CompactGenome, len(cgnames))
226 f, err := open(infile)
231 log.Infof("reading %s", infile)
232 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
233 for _, tv := range ent.TileVariants {
234 variants := seq[tv.Tag]
235 for len(variants) <= int(tv.Variant) {
236 variants = append(variants, nil)
238 variants[int(tv.Variant)] = tv.Sequence
239 seq[tv.Tag] = variants
241 for _, cg := range ent.CompactGenomes {
249 tagstart := cgs[cgnames[0]].StartTag
250 tagend := cgs[cgnames[0]].EndTag
253 // TODO: tidy/renumber
255 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
256 log.Infof("writing %s", annotationsFilename)
257 annof, err := os.Create(annotationsFilename)
261 annow := bufio.NewWriterSize(annof, 1<<20)
262 for tag, variants := range seq {
263 rt, ok := reftile[tag]
265 // Reference does not use any
266 // variant of this tile.
267 // TODO: log this? mention it
271 outcol := tag - tagID(tagstart)
272 reftilestr := strings.ToUpper(string(rt.tiledata))
273 for v, seq := range variants {
274 if len(seq) == 0 || !bytes.HasSuffix(rt.tiledata, seq[len(seq)-taglen:]) {
277 if lendiff := len(rt.tiledata) - len(seq); lendiff < -1000 || lendiff > 1000 {
280 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(seq)), 0)
281 for _, diff := range diffs {
282 diff.Position += rt.pos
283 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, v, rt.seqname, diff.String())
296 log.Infof("%s: preparing numpy", infile)
298 cols := 2 * int(tagend-tagstart)
299 out := make([]int16, rows*cols)
300 for row, name := range cgnames {
301 out := out[row*cols:]
302 for col, v := range cgs[name].Variants {
303 if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v]) > 0 {
311 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
312 output, err := os.Create(fnm)
317 bufw := bufio.NewWriterSize(output, 1<<26)
318 npw, err := gonpy.NewWriter(nopCloser{bufw})
322 log.WithFields(logrus.Fields{
326 }).Info("writing numpy")
327 npw.Shape = []int{rows, cols}
337 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
341 if err = throttle.Wait(); err != nil {