pipeline1dup/input2 0
`), 0600)
c.Assert(err, check.IsNil)
+
+ exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+ "-local=true",
+ "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-case-control-column=CC",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + tmpdir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+
npydir := c.MkDir()
- exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-hgvs-matrix=true",
- "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
- "-chi2-case-control-column=CC",
+ "-samples=" + tmpdir + "/samples.csv",
"-chi2-p-value=0.5",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
annotations, err := ioutil.ReadFile(npydir + "/hgvs.chr2.annotations.csv")
c.Assert(err, check.IsNil)
- c.Check(string(annotations), check.Equals, `0,chr2:g.470_472del
-1,chr2:g.471G>A
-2,chr2:g.472G>A
+ c.Check(string(annotations), check.Equals, `0,chr2:g.1_3delinsAAA
+1,chr2:g.125_127delinsAAA
+2,chr2:g.241_245delinsAAAAA
+3,chr2:g.291C>A
+4,chr2:g.470_472del
+5,chr2:g.471G>A
+6,chr2:g.472G>A
`)
}
pipeline1dup/input2 0
`), 0600)
c.Assert(err, check.IsNil)
+
+ exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+ "-local=true",
+ "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-case-control-column=CC",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + tmpdir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+
npydir := c.MkDir()
- exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-onehot=true",
- "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
- "-chi2-case-control-column=CC",
+ "-samples=" + tmpdir + "/samples.csv",
"-chi2-p-value=0.5",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
pipeline1dup/input2 0
`), 0600)
c.Assert(err, check.IsNil)
+
+ exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+ "-local=true",
+ "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-case-control-column=CC",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + tmpdir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+
npydir := c.MkDir()
- exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-single-onehot=true",
- "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
- "-chi2-case-control-column=CC",
+ "-samples=" + tmpdir + "/samples.csv",
"-chi2-p-value=0.5",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
defer f.Close()
npy, err := gonpy.NewReader(f)
c.Assert(err, check.IsNil)
- c.Check(npy.Shape, check.DeepEquals, []int{2, 16})
+ c.Check(npy.Shape, check.DeepEquals, []int{2, 12})
onehot, err := npy.GetUint32()
if c.Check(err, check.IsNil) {
for r := 0; r < npy.Shape[0]; r++ {
c.Logf("%v", onehot[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
}
c.Check(onehot, check.DeepEquals, []uint32{
- 0, 2, 1, 3, 0, 2, 1, 3, 0, 2, 1, 3, 0, 2, 0, 2,
- 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6, 7, 7,
+ 0, 2, 1, 3, 0, 2, 1, 3, 0, 2, 0, 2,
+ 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5,
+ })
+ }
+
+ f, err = os.Open(npydir + "/onehot-columns.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err = gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ c.Check(npy.Shape, check.DeepEquals, []int{5, 6})
+ onehotcols, err := npy.GetInt32()
+ if c.Check(err, check.IsNil) {
+ for r := 0; r < npy.Shape[0]; r++ {
+ c.Logf("%v", onehotcols[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
+ }
+ c.Check(onehotcols, check.DeepEquals, []int32{
+ 1, 4, 4, 4, 6, 6,
+ 2, 2, 3, 4, 2, 3,
+ 0, 0, 0, 0, 0, 0,
+ 157299, 157299, 157299, 157299, 157299, 157299,
+ 803273, 803273, 803273, 803273, 803273, 803273,
+ })
+ }
+ }
+}
+
+func (s *sliceSuite) TestSpanningTile(c *check.C) {
+ tmpdir := c.MkDir()
+ err := os.Mkdir(tmpdir+"/lib1", 0777)
+ c.Assert(err, check.IsNil)
+ err = os.Mkdir(tmpdir+"/lib2", 0777)
+ c.Assert(err, check.IsNil)
+ cwd, err := os.Getwd()
+ c.Assert(err, check.IsNil)
+ err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1")
+ c.Assert(err, check.IsNil)
+ err = os.Symlink(cwd+"/testdata/pipeline1", tmpdir+"/pipeline1dup")
+ c.Assert(err, check.IsNil)
+
+ err = ioutil.WriteFile(tmpdir+"/chr1-12-100.bed", []byte("chr1\t12\t100\ttest.1\n"), 0644)
+ c.Check(err, check.IsNil)
+
+ c.Log("=== import testdata/ref ===")
+ exited := (&importer{}).RunCommand("import", []string{
+ "-local=true",
+ "-tag-library", "testdata/tags",
+ "-output-tiles",
+ "-save-incomplete-tiles",
+ "-o", tmpdir + "/lib1/library1.gob",
+ "testdata/ref.fasta",
+ }, nil, os.Stderr, os.Stderr)
+ c.Assert(exited, check.Equals, 0)
+
+ c.Log("=== import testdata/spanningtile ===")
+ exited = (&importer{}).RunCommand("import", []string{
+ "-local=true",
+ "-tag-library", "testdata/tags",
+ "-output-tiles",
+ "-o", tmpdir + "/lib2/library2.gob",
+ cwd + "/testdata/spanningtile",
+ }, nil, os.Stderr, os.Stderr)
+ c.Assert(exited, check.Equals, 0)
+
+ slicedir := c.MkDir()
+
+ c.Log("=== slice ===")
+ exited = (&slicecmd{}).RunCommand("slice", []string{
+ "-local=true",
+ "-output-dir=" + slicedir,
+ "-tags-per-file=2",
+ tmpdir + "/lib1",
+ tmpdir + "/lib2",
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ out, _ := exec.Command("find", slicedir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+
+ c.Log("=== dump ===")
+ {
+ dumpdir := c.MkDir()
+ exited = (&dump{}).RunCommand("dump", []string{
+ "-local=true",
+ "-tags=5,6",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + dumpdir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ out, _ := exec.Command("find", dumpdir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+ dumped, err := ioutil.ReadFile(dumpdir + "/variants.csv")
+ c.Assert(err, check.IsNil)
+ c.Logf("%s", dumped)
+ // spanning tile for tag 5 with A>G snp in tag 6
+ c.Check("\n"+string(dumped), check.Matches, `(?ms).*\n5,2,0,chr2,225,.*AAAACTGATCCGAAAAAAATACAA.*`)
+ c.Check("\n"+string(dumped), check.Matches, `(?ms).*\n6,1,1,chr2,349,AAAACTGATCCAAAAAAAATACAA.*`)
+ }
+
+ c.Log("=== slice-numpy ===")
+ {
+ npydir := c.MkDir()
+ exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ "-local=true",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + npydir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+
+ f, err := os.Open(npydir + "/matrix.0000.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err := gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
+ variants, err := npy.GetInt16()
+ c.Check(variants, check.DeepEquals, []int16{
+ -1, -1, 1, 1,
+ -1, -1, 1, 2,
+ })
+
+ annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
+ c.Assert(err, check.IsNil)
+ c.Logf("%s", annotations)
+
+ f, err = os.Open(npydir + "/matrix.0002.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err = gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
+ variants, err = npy.GetInt16()
+ c.Check(variants, check.DeepEquals, []int16{
+ 1, 1, 2, 1,
+ 1, 1, 1, 1,
+ })
+
+ annotations, err = ioutil.ReadFile(npydir + "/matrix.0002.annotations.csv")
+ c.Assert(err, check.IsNil)
+ c.Logf("%s", annotations)
+ for _, s := range []string{
+ "chr2:g\\.360A>G",
+ } {
+ c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
+ }
+ }
+
+ c.Log("=== slice-numpy + regions ===")
+ {
+ npydir := c.MkDir()
+ exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ "-local=true",
+ "-regions=" + tmpdir + "/chr1-12-100.bed",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + npydir,
+ "-chunked-hgvs-matrix=true",
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+
+ f, err := os.Open(npydir + "/matrix.0000.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err := gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ c.Check(npy.Shape, check.DeepEquals, []int{2, 2})
+ variants, err := npy.GetInt16()
+ c.Check(variants, check.DeepEquals, []int16{-1, -1, -1, -1})
+
+ annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
+ c.Assert(err, check.IsNil)
+ c.Check(string(annotations), check.Equals, "0,0,1,=,chr1,0,,,\n")
+
+ for _, fnm := range []string{
+ npydir + "/matrix.0001.annotations.csv",
+ npydir + "/matrix.0002.annotations.csv",
+ } {
+ annotations, err := ioutil.ReadFile(fnm)
+ c.Assert(err, check.IsNil)
+ c.Check(string(annotations), check.Equals, "", check.Commentf(fnm))
+ }
+ }
+
+ err = ioutil.WriteFile(tmpdir+"/chr1and2-100-200.bed", []byte("chr1\t100\t200\ttest.1\nchr2\t100\t200\ttest.2\n"), 0644)
+ c.Check(err, check.IsNil)
+
+ c.Log("=== slice-numpy + regions + merge ===")
+ {
+ npydir := c.MkDir()
+ exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ "-local=true",
+ "-regions=" + tmpdir + "/chr1and2-100-200.bed",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + npydir,
+ "-merge-output=true",
+ "-single-hgvs-matrix=true",
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+
+ f, err := os.Open(npydir + "/matrix.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err := gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ c.Check(npy.Shape, check.DeepEquals, []int{2, 4})
+ variants, err := npy.GetInt16()
+ if c.Check(err, check.IsNil) {
+ c.Check(variants, check.DeepEquals, []int16{
+ -1, -1, 1, 1,
+ -1, -1, 1, 1,
+ })
+ }
+
+ annotations, err := ioutil.ReadFile(npydir + "/matrix.annotations.csv")
+ c.Assert(err, check.IsNil)
+ c.Check(string(annotations), check.Equals, "")
+ }
+
+ c.Log("=== slice-numpy + chunked hgvs matrix ===")
+ {
+ err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID CC
+spanningtile/input1 1
+`), 0600)
+ c.Assert(err, check.IsNil)
+
+ exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+ "-local=true",
+ "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-case-control-column=CC",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + tmpdir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+
+ npydir := c.MkDir()
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ "-local=true",
+ "-chunked-hgvs-matrix=true",
+ "-samples=" + tmpdir + "/samples.csv",
+ "-chi2-p-value=1",
+ "-min-coverage=0.75",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + npydir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+
+ annotations, err := ioutil.ReadFile(npydir + "/hgvs.chr2.annotations.csv")
+ c.Assert(err, check.IsNil)
+ c.Check(string(annotations), check.Equals, `0,chr2:g.360A>G
+`)
+ }
+
+ c.Log("=== slice-numpy + onehotChunked ===")
+ {
+ err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID CC
+spanningtile/input1 1
+`), 0600)
+ c.Assert(err, check.IsNil)
+
+ exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+ "-local=true",
+ "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-case-control-column=CC",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + tmpdir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+
+ npydir := c.MkDir()
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ "-local=true",
+ "-chunked-onehot=true",
+ "-samples=" + tmpdir + "/samples.csv",
+ "-chi2-p-value=1",
+ "-min-coverage=0.75",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + npydir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+
+ f, err := os.Open(npydir + "/onehot.0002.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err := gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ c.Check(npy.Shape, check.DeepEquals, []int{1, 2})
+ onehot, err := npy.GetInt8()
+ if c.Check(err, check.IsNil) {
+ for r := 0; r < npy.Shape[0]; r++ {
+ c.Logf("%v", onehot[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
+ }
+ c.Check(onehot, check.DeepEquals, []int8{
+ 0, 1, // input1
+ })
+ }
+ }
+
+ c.Log("=== slice-numpy + onehotSingle ===")
+ {
+ err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID CC
+spanningtile/input1 1
+`), 0600)
+ c.Assert(err, check.IsNil)
+
+ exited := (&chooseSamples{}).RunCommand("choose-samples", []string{
+ "-local=true",
+ "-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-case-control-column=CC",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + tmpdir,
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+
+ npydir := c.MkDir()
+ exited = (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ "-local=true",
+ "-single-onehot=true",
+ "-samples=" + tmpdir + "/samples.csv",
+ "-chi2-p-value=1",
+ "-min-coverage=0.75",
+ "-input-dir=" + slicedir,
+ "-output-dir=" + npydir,
+ "-debug-tag=1",
+ }, nil, os.Stderr, os.Stderr)
+ c.Check(exited, check.Equals, 0)
+ out, _ := exec.Command("find", npydir, "-ls").CombinedOutput()
+ c.Logf("%s", out)
+
+ f, err := os.Open(npydir + "/onehot.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err := gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ c.Check(npy.Shape, check.DeepEquals, []int{2, 1})
+ onehot, err := npy.GetUint32()
+ if c.Check(err, check.IsNil) {
+ for r := 0; r < npy.Shape[0]; r++ {
+ c.Logf("%v", onehot[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
+ }
+ c.Check(onehot, check.DeepEquals, []uint32{0, 3})
+ }
+
+ f, err = os.Open(npydir + "/onehot-columns.npy")
+ c.Assert(err, check.IsNil)
+ defer f.Close()
+ npy, err = gonpy.NewReader(f)
+ c.Assert(err, check.IsNil)
+ c.Check(npy.Shape, check.DeepEquals, []int{5, 4})
+ onehotcols, err := npy.GetInt32()
+ if c.Check(err, check.IsNil) {
+ for r := 0; r < npy.Shape[0]; r++ {
+ c.Logf("%v", onehotcols[r*npy.Shape[1]:(r+1)*npy.Shape[1]])
+ }
+ c.Check(onehotcols, check.DeepEquals, []int32{
+ 1, 1, 5, 5,
+ 2, 2, 2, 2,
+ 1, 0, 1, 0,
+ 1000000, 1000000, 1000000, 1000000,
+ 0, 0, 0, 0,
})
}
}
chi2Cases: []bool{false, true, true, false},
chi2PValue: .5,
includeVariant1: true,
+ minCoverage: 3,
}
cgs := map[string]CompactGenome{
"sample1": CompactGenome{
maxv := tileVariantID(3)
remap := []tileVariantID{0, 1, 0, 0, 0, 2, 0, 0, 0, 3}
chunkstarttag := tagID(10)
+ fakevariant := TileVariant{Sequence: []byte("ACGT")}
+ seq := map[tagID][]TileVariant{}
for tag := tagID(10); tag < 12; tag++ {
+ seq[tag-chunkstarttag] = []TileVariant{TileVariant{}, fakevariant, TileVariant{}, TileVariant{}, TileVariant{}, fakevariant}
c.Logf("=== tag %d", tag)
- chunk, xref := cmd.tv2homhet(cgs, maxv, remap, tag, chunkstarttag)
+ chunk, xref := cmd.tv2homhet(cgs, maxv, remap, tag, chunkstarttag, seq)
c.Logf("chunk len=%d", len(chunk))
for _, x := range chunk {
c.Logf("%+v", x)
projects / lightning.git / blobdiff