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=4,6,7",
+ "-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)
+ c.Check("\n"+string(dumped), check.Matches, `(?ms).*\n6,1,1,chr2,349,AAAACTG.*`)
+ }
+
c.Log("=== slice-numpy ===")
{
npydir := c.MkDir()
c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
variants, err := npy.GetInt16()
if c.Check(err, check.IsNil) {
- c.Check(variants, check.DeepEquals, []int16{2, 1, 3, 1, -1, -1, 4, 2, 2, 1, 3, 1, -1, -1, 4, 2})
+ c.Check(variants, check.DeepEquals, []int16{
+ 2, 1, 3, 1,
+ -1, -1, 4, 2,
+ 2, 1, 3, 1,
+ -1, -1, 4, 2,
+ })
}
annotations, err := ioutil.ReadFile(npydir + "/matrix.annotations.csv")
c.Log("=== slice-numpy + chunked hgvs matrix ===")
{
- err = ioutil.WriteFile(tmpdir+"/cases.txt", []byte("pipeline1/input1\npipeline1dup/input1\n"), 0600)
+ err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID CC
+pipeline1/input1 1
+pipeline1/input2 0
+pipeline1dup/input1 1
+pipeline1dup/input2 0
+`), 0600)
c.Assert(err, check.IsNil)
npydir := c.MkDir()
exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-hgvs-matrix=true",
- "-chi2-cases-file=" + tmpdir + "/cases.txt",
- "-chi2-p-value=0.05",
+ "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-chi2-case-control-column=CC",
+ "-chi2-p-value=0.5",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
"-output-dir=" + npydir,
`)
}
- c.Log("=== slice-numpy + onehot ===")
+ c.Log("=== slice-numpy + onehotChunked ===")
{
- err = ioutil.WriteFile(tmpdir+"/cases.txt", []byte("pipeline1/input1\npipeline1dup/input1\n"), 0600)
+ err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID CC
+pipeline1/input1 1
+pipeline1/input2 0
+pipeline1dup/input1 1
+pipeline1dup/input2 0
+`), 0600)
c.Assert(err, check.IsNil)
npydir := c.MkDir()
exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-onehot=true",
- "-chi2-cases-file=" + tmpdir + "/cases.txt",
- "-chi2-p-value=0.05",
+ "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-chi2-case-control-column=CC",
+ "-chi2-p-value=0.5",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
"-output-dir=" + npydir,
defer f.Close()
npy, err := gonpy.NewReader(f)
c.Assert(err, check.IsNil)
- c.Check(npy.Shape, check.DeepEquals, []int{4, 6})
+ c.Check(npy.Shape, check.DeepEquals, []int{4, 3})
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, 0, 0, 1, 0, 0, // input1
- 0, 1, 0, 0, 0, 1, // input2
- 0, 0, 0, 1, 0, 0, // dup/input1
- 0, 1, 0, 0, 0, 1, // dup/input2
+ 0, 1, 0, // input1
+ 1, 0, 1, // input2
+ 0, 1, 0, // dup/input1
+ 1, 0, 1, // dup/input2
})
}
}
+
+ c.Log("=== slice-numpy + onehotSingle ===")
+ {
+ err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID CC
+pipeline1/input1 1
+pipeline1/input2 0
+pipeline1dup/input1 1
+pipeline1dup/input2 0
+`), 0600)
+ c.Assert(err, check.IsNil)
+ npydir := c.MkDir()
+ exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
+ "-local=true",
+ "-single-onehot=true",
+ "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-chi2-case-control-column=CC",
+ "-chi2-p-value=0.5",
+ "-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, 16})
+ 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,
+ })
+ }
+
+ 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{8, 5})
+ 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{
+ 0, 0, 1, 4, 4, 4, 6, 6,
+ 2, 3, 2, 2, 3, 4, 2, 3,
+ 0, 1, 0, 0, 0, 0, 0, 0,
+ 157299, 157299, 157299, 157299, 157299, 157299, 157299, 157299,
+ 803273, 803273, 803273, 803273, 803273, 803273, 803273, 803273,
+ })
+ }
+ }
+}
+
+func (s *sliceSuite) Test_tv2homhet(c *check.C) {
+ cmd := &sliceNumpy{
+ cgnames: []string{"sample1", "sample2", "sample3", "sample4"},
+ chi2Cases: []bool{false, true, true, false},
+ chi2PValue: .5,
+ includeVariant1: true,
+ }
+ cgs := map[string]CompactGenome{
+ "sample1": CompactGenome{
+ Variants: []tileVariantID{0, 0, 1, 1}, // hom tv=1
+ },
+ "sample2": CompactGenome{
+ Variants: []tileVariantID{0, 0, 5, 5}, // hom tv=2
+ },
+ "sample3": CompactGenome{
+ Variants: []tileVariantID{0, 0, 5, 1}, // het tv=1, tv=2
+ },
+ "sample4": CompactGenome{
+ Variants: []tileVariantID{0, 0, 9, 9}, // hom tv=3
+ },
+ }
+ maxv := tileVariantID(3)
+ remap := []tileVariantID{0, 1, 0, 0, 0, 2, 0, 0, 0, 3}
+ chunkstarttag := tagID(10)
+ for tag := tagID(10); tag < 12; tag++ {
+ c.Logf("=== tag %d", tag)
+ chunk, xref := cmd.tv2homhet(cgs, maxv, remap, tag, chunkstarttag)
+ c.Logf("chunk len=%d", len(chunk))
+ for _, x := range chunk {
+ c.Logf("%+v", x)
+ }
+ c.Logf("xref len=%d", len(xref))
+ for _, x := range xref {
+ c.Logf("%+v", x)
+ }
+ out := onehotcols2int8(chunk)
+ c.Logf("onehotcols2int8(chunk) len=%d", len(out))
+ for i := 0; i < len(out); i += len(chunk) {
+ c.Logf("%+v", out[i:i+len(chunk)])
+ }
+ coords := onehotChunk2Indirect(chunk)
+ c.Logf("onehotChunk2Indirect(chunk) len=%d", len(coords))
+ for _, x := range coords {
+ c.Logf("%+v", x)
+ }
+ }
}
projects / lightning.git / blobdiff