1 // Copyright (C) The Lightning Authors. All rights reserved.
3 // SPDX-License-Identifier: AGPL-3.0
22 "git.arvados.org/arvados.git/sdk/go/arvados"
23 "github.com/arvados/lightning/hgvs"
24 "github.com/kshedden/gonpy"
25 "github.com/sirupsen/logrus"
26 log "github.com/sirupsen/logrus"
29 type sliceNumpy struct {
33 func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
37 fmt.Fprintf(stderr, "%s\n", err)
40 flags := flag.NewFlagSet("", flag.ContinueOnError)
41 flags.SetOutput(stderr)
42 pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
43 runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
44 projectUUID := flags.String("project", "", "project `UUID` for output data")
45 priority := flags.Int("priority", 500, "container request priority")
46 inputDir := flags.String("input-dir", "./in", "input `directory`")
47 outputDir := flags.String("output-dir", "./out", "output `directory`")
48 ref := flags.String("ref", "", "reference name (if blank, choose last one that appears in input)")
49 regionsFilename := flags.String("regions", "", "only output columns/annotations that intersect regions in specified bed `file`")
50 expandRegions := flags.Int("expand-regions", 0, "expand specified regions by `N` base pairs on each side`")
51 cmd.filter.Flags(flags)
52 err = flags.Parse(args)
53 if err == flag.ErrHelp {
56 } else if err != nil {
62 log.Println(http.ListenAndServe(*pprof, nil))
67 runner := arvadosContainerRunner{
68 Name: "lightning slice-numpy",
69 Client: arvados.NewClientFromEnv(),
70 ProjectUUID: *projectUUID,
77 err = runner.TranslatePaths(inputDir, regionsFilename)
81 runner.Args = []string{"slice-numpy", "-local=true",
83 "-input-dir", *inputDir,
84 "-output-dir", "/mnt/output",
85 "-regions", *regionsFilename,
86 "-expand-regions", fmt.Sprintf("%d", *expandRegions),
88 runner.Args = append(runner.Args, cmd.filter.Args()...)
90 output, err = runner.Run()
94 fmt.Fprintln(stdout, output)
98 infiles, err := allGobFiles(*inputDir)
102 if len(infiles) == 0 {
103 err = fmt.Errorf("no input files found in %s", *inputDir)
106 sort.Strings(infiles)
109 var refseq map[string][]tileLibRef
110 in0, err := open(infiles[0])
115 DecodeLibrary(in0, strings.HasSuffix(infiles[0], ".gz"), func(ent *LibraryEntry) error {
116 if len(ent.TagSet) > 0 {
117 taglen = len(ent.TagSet[0])
119 for _, cseq := range ent.CompactSequences {
120 if cseq.Name == *ref || *ref == "" {
121 refseq = cseq.TileSequences
124 for _, cg := range ent.CompactGenomes {
125 cgnames = append(cgnames, cg.Name)
134 err = fmt.Errorf("%s: reference sequence not found", infiles[0])
138 err = fmt.Errorf("tagset not found")
141 sort.Strings(cgnames)
144 labelsFilename := *outputDir + "/labels.csv"
145 log.Infof("writing labels to %s", labelsFilename)
147 f, err = os.Create(labelsFilename)
152 for i, name := range cgnames {
153 _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
155 err = fmt.Errorf("write %s: %w", labelsFilename, err)
161 err = fmt.Errorf("close %s: %w", labelsFilename, err)
166 log.Info("building list of reference tiles to load") // TODO: more efficient if we had saved all ref tiles in slice0
167 type reftileinfo struct {
168 variant tileVariantID
169 seqname string // chr1
170 pos int // distance from start of chr1 to start of tile
171 tiledata []byte // acgtggcaa...
173 reftile := map[tagID]*reftileinfo{}
174 for seqname, cseq := range refseq {
175 for _, libref := range cseq {
176 reftile[libref.Tag] = &reftileinfo{seqname: seqname, variant: libref.Variant}
179 log.Info("loading reference tiles from all slices")
180 throttle := throttle{Max: runtime.GOMAXPROCS(0)}
181 for _, infile := range infiles {
183 throttle.Go(func() error {
184 defer log.Infof("%s: done", infile)
185 f, err := open(infile)
190 return DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
191 for _, tv := range ent.TileVariants {
192 if dst, ok := reftile[tv.Tag]; ok && dst.variant == tv.Variant {
193 dst.tiledata = tv.Sequence
202 log.Info("reconstructing reference sequences")
203 for seqname, cseq := range refseq {
204 seqname, cseq := seqname, cseq
205 throttle.Go(func() error {
206 defer log.Printf("... %s done", seqname)
208 for _, libref := range cseq {
209 rt := reftile[libref.Tag]
211 pos += len(rt.tiledata) - taglen
218 log.Info("TODO: determining which tiles intersect given regions")
220 log.Info("generating annotations and numpy matrix for each slice")
222 for infileIdx, infile := range infiles {
223 infileIdx, infile := infileIdx, infile
224 throttle.Go(func() error {
225 seq := make(map[tagID][]TileVariant, 50000)
226 cgs := make(map[string]CompactGenome, len(cgnames))
227 f, err := open(infile)
232 log.Infof("reading %s", infile)
233 err = DecodeLibrary(f, strings.HasSuffix(infile, ".gz"), func(ent *LibraryEntry) error {
234 for _, tv := range ent.TileVariants {
235 variants := seq[tv.Tag]
236 for len(variants) <= int(tv.Variant) {
237 variants = append(variants, TileVariant{})
239 variants[int(tv.Variant)] = tv
240 seq[tv.Tag] = variants
242 for _, cg := range ent.CompactGenomes {
250 tagstart := cgs[cgnames[0]].StartTag
251 tagend := cgs[cgnames[0]].EndTag
255 log.Infof("renumbering variants for tags %d-%d", tagstart, tagend)
256 variantRemap := make([][]tileVariantID, tagend-tagstart)
257 var wg sync.WaitGroup
258 for tag, variants := range seq {
259 tag, variants := tag, variants
263 count := make([]tileVariantID, len(variants))
264 for _, cg := range cgs {
265 idx := (tag - tagstart) * 2
266 count[cg.Variants[idx]]++
267 count[cg.Variants[idx+1]]++
269 ranked := make([]tileVariantID, len(variants))
270 for i := range ranked {
271 ranked[i] = tileVariantID(i)
273 sort.Slice(ranked, func(i, j int) bool {
275 return true // leave ranked[0] at position 0, unused
277 return false // ditto
279 if cri, crj := count[ranked[i]], count[ranked[j]]; cri != crj {
282 return bytes.Compare(variants[ranked[i]].Blake2b[:], variants[ranked[j]].Blake2b[:]) < 0
285 remap := make([]tileVariantID, len(ranked))
286 for i, r := range ranked {
287 remap[r] = tileVariantID(i)
289 variantRemap[tag-tagstart] = remap
294 annotationsFilename := fmt.Sprintf("%s/matrix.%04d.annotations.csv", *outputDir, infileIdx)
295 log.Infof("writing %s", annotationsFilename)
296 annof, err := os.Create(annotationsFilename)
300 annow := bufio.NewWriterSize(annof, 1<<20)
301 for tag, variants := range seq {
302 rt, ok := reftile[tag]
304 // Reference does not use any
305 // variant of this tile.
306 // TODO: log this? mention it
310 outcol := tag - tagID(tagstart)
311 reftilestr := strings.ToUpper(string(rt.tiledata))
312 remap := variantRemap[tag-tagstart]
313 for v, tv := range variants {
314 if len(tv.Sequence) < taglen || !bytes.HasSuffix(rt.tiledata, tv.Sequence[len(tv.Sequence)-taglen:]) {
317 if lendiff := len(rt.tiledata) - len(tv.Sequence); lendiff < -1000 || lendiff > 1000 {
320 diffs, _ := hgvs.Diff(reftilestr, strings.ToUpper(string(tv.Sequence)), 0)
321 for _, diff := range diffs {
322 diff.Position += rt.pos
323 fmt.Fprintf(annow, "%d,%d,%d,%s:g.%s\n", tag, outcol, remap[v], rt.seqname, diff.String())
336 log.Infof("%s: preparing numpy", infile)
338 cols := 2 * int(tagend-tagstart)
339 out := make([]int16, rows*cols)
340 for row, name := range cgnames {
341 out := out[row*cols:]
342 for col, v := range cgs[name].Variants {
343 if variants, ok := seq[tagstart+tagID(col/2)]; ok && len(variants) > int(v) && len(variants[v].Sequence) > 0 {
344 out[col] = int16(variantRemap[col/2][v])
351 fnm := fmt.Sprintf("%s/matrix.%04d.npy", *outputDir, infileIdx)
352 output, err := os.Create(fnm)
357 bufw := bufio.NewWriterSize(output, 1<<26)
358 npw, err := gonpy.NewWriter(nopCloser{bufw})
362 log.WithFields(logrus.Fields{
366 }).Info("writing numpy")
367 npw.Shape = []int{rows, cols}
377 log.Infof("%s: done (%d/%d)", infile, int(atomic.AddInt64(&done, 1)), len(infiles))
381 if err = throttle.Wait(); err != nil {