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()
"-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.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
}
- annotations, err = ioutil.ReadFile(npydir + "/matrix.0002.annotations.csv")
+ 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{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})
+ }
+
+ annotations, err := ioutil.ReadFile(npydir + "/matrix.annotations.csv")
c.Assert(err, check.IsNil)
c.Logf("%s", annotations)
- c.Check(string(annotations), check.Equals, "")
+ for _, s := range []string{
+ "0,0,1,chr1:g.161A>T",
+ "0,0,1,chr1:g.178A>T",
+ "4,1,2,chr2:g.125_127delinsAAA",
+ } {
+ c.Check(string(annotations), check.Matches, "(?ms).*"+s+".*")
+ }
+ }
+
+ c.Log("=== slice-numpy + chunked hgvs matrix ===")
+ {
+ 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-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,
+ }, 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.470_472del
+1,chr2:g.471G>A
+2,chr2:g.472G>A
+`)
+ }
+
+ c.Log("=== slice-numpy + onehotChunked ===")
+ {
+ 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-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,
+ }, 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{4, 6})
+ 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
+ })
+ }
+ }
+
+ 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,
+ }, 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,
+ 1, 1, 2, 2, 5, 5, 7, 7, 9, 9, 11, 11, 13, 13, 15, 15,
+ })
+ }
}
}
projects / lightning.git / blobdiff